This application is a continuation of U.S. application Ser. No. 15/797,927, filed Oct. 30, 2017, now allowed, which is a continuation of U.S. application Ser. No. 13/571,661, filed Aug. 10, 2012, now U.S. Pat. No. 9,617,536, which is a continuation of U.S. application Ser. No. 13/250,520, filed Sep. 30, 2011, now U.S. Pat. No. 8,258,082, which is a continuation of U.S. application Ser. No. 12/762,051, filed Apr. 16, 2010, now U.S. Pat. No. 8,895,475, which is a continuation of U.S. application Ser. No. 11/416,460, filed on May 1, 2006, now abandoned, which is a continuation of U.S. application Ser. No. 10/026,925, filed on Dec. 18, 2001, now abandoned, which claims the benefit under 35 USC § 119 of U.S. provisional application 60/256,380, filed Dec. 18, 2000, the entire content of each of which is herein incorporated by reference.
The present invention relates to focused libraries of genetic packages that each display, display and express, or comprise a member of a diverse family of peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The focused diversity of the libraries of this invention comprises both sequence diversity and length diversity. In a preferred embodiment, the focused diversity of the libraries of this invention is biased toward the natural diversity of the selected family. In more preferred embodiment, the libraries are biased toward the natural diversity of human antibodies and are characterized by variegation in their heavy chain and light chain complementarity determining regions (“CDRs”).
The present invention further relates to vectors and genetic packages (e.g., cells, spores or viruses) for displaying, or displaying and expressing a focused diverse family of peptides, polypeptides or proteins. In a preferred embodiment the genetic packages are filamentous phage or phagemids or yeast. Again, the focused diversity of the family comprises diversity in sequence and diversity in length.
The present invention further relates to methods of screening the focused libraries of the invention and to the peptides, polypeptides and proteins identified by such screening.
BACKGROUND OF THE INVENTION It is now common practice in the art to prepare libraries of genetic packages that individually display, display and express, or comprise a member of a diverse family of peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the amino acid diversity of the family. In many common libraries, the peptides, polypeptides or proteins are related to antibodies (e.g., single chain Fv (scFv), Fv, Fab, whole antibodies or minibodies (i.e., dimers that consist of VH linked to VL)). Often, they comprise one or more of the CDRs and framework regions of the heavy and light chains of human antibodies.
Peptide, polypeptide or protein libraries have been produced in several ways in the prior art. See e.g., Knappik et al., J. Mol. Biol., 296, pp. 57-86 (20004, which is incorporated herein by references. One method is to capture the diversity of native donors, either naive or immunized. Another way is to generate libraries having synthetic diversity. A third method is combination of the first two. Typically, the diversity produced by these methods is limited to sequence diversity, i.e., each member of the library differs from the other members of the family by having different amino acids or variegation at a given position in the peptide, polypeptide or protein chain. Naturally diverse peptides, polypeptides or proteins, however, are not limited to diversity only in their amino acid sequences. For example, human antibodies are not limited to sequence diversity in their amino acids, they are also diverse in the lengths of their amino acid chains.
For antibodies, diversity in length occurs, for example, during variable region rearrangements. See e.g., Corbett et al., J. Mol. Biol., 270, pp. 587-97 (1997). The joining of V genes to J genes, for example, results in the inclusion of a recognizable D segment in CDR3 in about half of the heavy chain antibody sequences, thus creating regions encoding varying lengths of amino-acids. The following also may occur during joining of antibody gene segments: (i) the end of the V gene may have zero to several base deleted or changed; (ii) the end of the D segment may have zero to many bases removed or changed; (iii) a number of random bases may be inserted between V and D or between D and J; and (iv) the 5′ end of J may be edited to remove or to change several bases. These rearrangements result in antibodies that are diverse both in amino acid sequence and in length.
Libraries that contain only amino acid sequence diversity are, thus disadvantaged in that they do not reflect the natural diversity of the peptide, polypeptide or protein that the library is intended to mimic. Further, diversity in length may be important to the ultimate functioning of the protein, peptide or polypeptide. For example, with regard to a library comprising antibody regions, many of the peptides, polypeptides, proteins displayed, displayed and expressed, or comprised by the genetic packages of the library may not fold properly or their binding to an antigen may be disadvantaged, if diversity both in sequence and length are not represented in the library.
An additional disadvantage of prior art libraries of genetic packages that display, display and express, or comprise peptides, polypeptides and proteins is that they are not focused on those members that are based on natural occurring diversity and thus on members that are most likely to be functional. Rather, the prior art libraries, typically, attempt to include as much diversity or variegation at every amino acid residue as possible. This makes library construction time-consuming and less efficient than possible. The large number of members that are produced by trying to capture complete diversity also makes screening more cumbersome than it needs to be This is particularly true given that many members of the library will not be functional.
SUMMARY OF THE INVENTION One objective of this invention is focused libraries of vectors or genetic packages that encode members of a diverse family of peptides, polypeptides or proteins wherein the libraries encode populations that are diverse in both length and sequence. The diverse length comprising components that contain motifs that are likely to fold and function in the context of the parental peptide, polypeptide or protein.
Another object of this invention is focused libraries of genetic packages that display, display and express, or comprise a member of a diverse family of peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. These libraries are diverse not only in their amino acid sequences, but also in their lengths. And, their diversity is focused so as to more closely mimic or take into account the naturally-occurring diversity of the specific family that the library represents.
Another object of this invention is diverse, but focused, populations of DNA sequences encoding peptides, polypeptides or proteins suitable for display or display and expression using genetic packages(such as phage or phagemids) or other regimens that allow selection of specific binding components of a library.
A further object of this invention is focused libraries comprising the CDRs of human antibodies that are diverse in both their amino acid sequence and in their length (examples of such libraries include libraries of single chain Fv(scFv), Fv, Fab, whole antibodies or minibodies (i.e., dimers that consist of VH linked to VL). Such regions may be from the heavy or light chains or both and may include one or, more of the CDRs of those chains. More preferably, they diversity or variegation occurs in all of the heavy chain and light chain CDRs.
It is another object of this invention to provide methods of making and screening the above libraries and the peptides, polypeptides and proteins obtained in such screening.
Among the preferred embodiments of this invention are the following:
1. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a heavy chain CDR1 selected from the group consisting of:
-
- (1) <1>1Y2<1>3M4<1>5 (SEQ ID NO:100), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y;
- (2) (S/T)1(S/G/X)2(S/G/X)3Y4Y5W6(S/G/X)7 (SEQ ID NO:101) wherein (S/T) is a 1:1 mixture of S and T residues, (S/G/X) is a mixture of 0.2025 S, 0.2025 G and 0.035 of each of amino acid residues A, D, E, F, H, I, K, L, H, N, P, Q, R, T, V, W, and Y;
- (3) V1S2G3G4S5I6S7<1>8<l>9<l>10Y11Y12W13<1>14 (SEQ ID NO:1), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; and
- (4) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio: HC CDR1s (1):(2):(3)::0.80:0.17:0.02.
2. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express or comprise at least a portion of the diversity of the antibody facility, the vectors or genetic packages being characterized by variegated DNA sequences that encode a heavy chain CDR2 selected from the group consisting of:
-
- (1) <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), wherein <1> is an equimolar mixture of each of amino acid residues 211, 0, E, F, G, H, I, K, L, M, N, P, O, P, S, T, V, W, and Y; <2> is an equimolar mixture of each of amino acid residues Y, R, W, V, G, and S; and <3> is an equimolar mixture of each of amino acid residues P, S, and G or an equimolar mixture of P and S;
- (2) <1>I<4><1><1><G><5><1><1><1>YADSVKG (SEQ ID NO:3), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; <4> is an equimolar mixture of residues D, I, N, S, W, Y; and <5> is an equimolar mixture of residues S, G, D and N;
- (3)<1>I<4><1><1>G<5><1><1>YNPSLKG (SEQ ID NO:4), wherein <1> is an equimolar mixture of each of amino acid residues A, D, E, F, G, H, I, K, L, M, N; P, Q, R, S, T, V, W and Y, and <4> and <5> are as defined above;
- (4)<1>I<8>S<1><1><1>GGYY<1>YAASVKG (SEQ ID NO:5), wherein <1> is an equimolar mixture of each amino acid residues A, D, E, F, Gill, I, K, L, M, N, P, Q, R, S, T, V, and Y; <8> is 0.27 R and 0.027 of each of ADEFGHIKLMNPQSTVWY; and
- (5) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio: HC CDR2s: (1)/(2) (equimolar): (3):(4)::0.54:0.43:0.03.
3. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a heavy chain CDR3 was selected from the group consisting of:
-
- (1) YYCA21111YFDYWG (SEQ ID NO:6), Wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
- (2) YYCA2111111YFDYWG (SEQ ID NO:7), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
(SEQ ID NO: 8)
(3) YYCA211111111YFDAYTG,
wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, 1, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
(4)
(SEQ ID NO: 9)
YYCAR111S2S3111YFDYWG,
wherein 1 is an equimolar mixture of each amino acid residues A, D, E, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of S and G; and 3 is an equimolar mixture of Y and W;
(SEQ ID NO: 10)
(5) YYCA2111CSG11CY1YFDYWG,
wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R;
(SEQ ID NO: 11)
(6) YYCA211S1TIFG11111YFDYWG,
wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; and 2 is an equimolar mixture of K and R.
-
- (7) YYCAR111YY2S3344111YFDYWG (SEQ ID NO:12), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; 2 is an equimolar mixture of D and S; and 3 is an equimolar mixture of S and G;
- (8) YYCAR1111YC2231CY111YFDYWG (SEQ ID NO:13), wherein 1 is an equimolar mixture of each amino acid residues A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y; 2 is an equimolar mixture of S and G; and 3 is an equimolar mixture of T, D and G; and
- (9) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably the HC CDR3s (1) through (8) are in the following proportions in the mixture:
- (1) 0.10
- (2) 0.14
- (3) 0.25
- (4) 0.13
- (5) 0.13
- (6) 0.11
- (7) 0.04 and
- (8) 0.10; and more preferably the HC CDR3s
(1) through (8) are in the following proportions in the mixture: - (1) 0.02
- (2) 0.14
- (3) 0.25
- (4) 0.14
- (5) 0.14
- (6) 0.12
- (7) 0; 08 and
- (8) 0.11.
Preferably, 1 in one or all of HC CDR3s (1) through (8) is 0.095. of each of G and Y and 0.048 of each of A, D, E, F H, 1, K, L, M, N, P, Q, R, S, T, V, and W.
4. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encodes a kappa light chain CDR1 selected from the group consisting of:
(SEQ ID NO: 14)
(1) RASQ<1>V<2><2><3>LA
(SEQ ID NO: 15)
(2) RASQ<1>V<2><2><2><3>LA;
wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <2> is 0.2 S and .0.044 of each of ADEFGHIKLMNPQRTVWY; and <3> is 0.2Y and 0.044 each of ADEFGHIKLMNPQRTVW and Y; and
-
- (3) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio CDR1s (1):(2)::0.68:0.32.
5. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the-antibody family the vectors or genetic packages being characterized by variegated DNA sequences that encode a kappa light-chain CDR2 having the sequence:
(SEQ ID NO: 102)
<1>AS<2>R<4><1>,
wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <2> is 0.2 S and 0.044 of each of ADEFGHIKLMNPQRTVWY; and <4> is 0.2.A and 0.044 each of DEFGHIKLMNPQRSTVWY.
6. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a kappa light chain CDR3 selected from the groups consisting of:
(SEQ ID NO: 16)
(1) QQ<3><1><1><1>P<1>T,
wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <3> is 0.2 Y and 0.044 each of ADEFGHIKIMNPQRTVW;
-
- (2) QQ33111P (SEQ ID NO:103), wherein 1 and 3 are as defined in (1) above;
- (3) QQ3211PP1T(SEQ ID NO:17), wherein 1 and 3 are as defined in (1) above and 2 is 0.2 S and 0.044 each of ADEFGHIKLMNPQRTVWY; and
- (4) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio CDA3s (1):(2):(3)::0.65:0.1:0.25.
7. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a lambda light chain CDR1 selected from the group consisting of:
-
- (1) TG<1>SS<2>VG<1><3><2><3>VS(SEQ ID NO:18), wherein <1> is 0.27 T, 0.27 G and 0.027 each of ADEFRIKLMNPQRSVWY: <2> is 0.27 D, 0.27 N and 0.027 each of AEFGHIKLMPQRSTVWY, and <3> is 0.36 Y and 0.036 each of ADEFGHIKLMNPQRSTVW;
(SEQ ID NO: 104)
(2) G<2><4>L<4><4><4><3><4><4>,
wherein <2> is as defined in (1) above and <4> is an equimolar mixture of amino acid residues ADEFGHIKIMNPQRSTVWY; and
-
- (3) mixtures of vectors or genetic packages 5 characterized by any of the above DNA sequences, preferably in the ratio CDR1 (1):(2)::0.67:0.33;
8. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a lambda light chain CDR2 has the sequence:
(SEQ ID NO: 105)
<4><4><4><2>RPS
wherein <2> is 0.27 D, 0.27 N, and 0.027 each of AEFGHIKIMPQRSTVWY and <4> is an equimolar mixture of amino acid residues ADEFGHIKLONPQRSTVW.
9. A focused library of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of human antibody related peptides, polypeptides and proteins and collectively display, display and express, or comprise at least a portion of the diversity of the antibody family, the vectors or genetic packages being characterized by variegated DNA sequences that encode a lambda light chain CDR3 selected from the group consisting of:
-
- (1) <4><5><4><2><4>S<4><4><4><4>V (SEQ ID NO:106), wherein <2> is 0.27 D, 0.27 N, and 0.027 each of AEFGHIKIMPQRSTVWY; <4> is an equimolar mixture of amino acid residues ADEFGHIKLMVPQRSTVW; and <5> is 0.36 S and 0.6355 each of ADEFGHIKLMNPQRTVWY;
(SEQ ID NO: 19)
(2) <5>SY<1><5>S<5><1><4>V,
wherein <1> is an equimolar mixture of ADEFGHIKLMNPQRSTVWY; and <4> and 5<5> are as defined in (1) above; and
-
- (3) mixtures of vectors or genetic packages characterized by any of the above DNA sequences, preferably in the ratio CDR3s
10. A focused library comprising variegated-DNA sequences that encode a heavy chain CDR selected from the group consisting of:
-
- (1) one or more of the heavy chain CDR1s of 1 above;
- (2) one or more of the heavy chain CDR2s of 2 above;
- (3) one or more of the heavy chain CDR3s of 3 above; and
- (4) mixtures of vectors or genetic-packages characterized by (1), (2) and (3).
11. The focused library comprising one or more of the variegated DNA sequences that encodes a heavy chain CDR of 1, 2 and 3 and further comprising variegated DNA sequences that encodes a light chain CDR selected from the group consisting of
-
- (1) one or more the kappa light chain CDR1s of 4;
- (2) the kappa light chain CDR2 of 5;
- (3) one or more of the kappa light chain CDR3s of 6;
- (4) one or more of the kappa light chain CDR1s of 7;
- (5) the lambda light chain ‘CDR2’ of 8;
- (6) one or more of the lambda light chain CDR3s of 9; and
- (7) mixtures of vectors and genetic packages characterized by one or more of (1) through (6).
12. A population of variegated DNA sequences as described in 1-11 above.
13. A population of vectors comprising the variegated DNA sequences as described in 1-11 above.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS Antibodies (“Ab”) concentrate their diversity into those regions that are involved in determining affinity and specificity of the Ab for particular targets. These regions may be diverse in sequence or in length. Generally, they are diverse In both ways. However, within families of human antibodies the diversities, both in sequence and in length, are not truly random. Rather, some amino acid residues are preferred at certain positions of the CDRs and some CDR lengths are preferred. These preferred diversities account for the natural diversity of the antibody family.
According to this invention, and as more fully described below, libraries of vectors and genetic packages that more closely mirror the natural diversity, both in sequence and in length, of antibody families, or portions thereof are prepared and used.
Human Antibody Heavy Chain Sequence and Length Diversity (a) Framework
The heavy chain (“HC”) Germ-Line Gene (GLG) 3-23 (also known as 1/1)-47) accounts for about 12% of all human Abs and is preferred as the framework in the preferred embodiment of the invention. It should, however, be understood that other well-known frameworks, such as 4-34, 3-30, 3-30.3 and 4-30.1, may also be used without departing from the principles of the focused diversities of this invention.
In addition, JH4(YFDYWGQGTLVTVSS; SEQ ID NO:20) occurs more often than JH3 in native antibodies. Hence, it is preferred for the focused libraries of this invention. However, JH3 (AFDIWGQGTMVTVSS; SEQ ID NO:21) could as well be used.
(b) Focused Length Diversity: CDR1, 2 and 3 (i) CDR1
For CDR1, GLGs provide CDR1s only Of the lengths 5, 6, and 7. Mutations during the maturation of the v-domain gene, however, can lead to CDR1s having lengths as short as 2 and as long as 16. Nevertheless, length 5, predominates. Accordingly, in the preferred embodiment of this invention the preferred HC CDR1 is 5 amino acids, with less preferred CDR1s having lengths of 7 and 14. In the most preferred libraries of this invention, all three lengths are used in proportions similar to those found in natural antibodies.
(ii) CDR2
GLGs provide CDR2s only of the lengths 15:19, but mutations during maturation may result in CDR2s of lengths from 16 to 28 amino acids. The lengths 16 and 17 predominate in mature Ab genes. Accordingly, length 17 is the preferred length for HC CDR2 of the present invention. Less preferred HC CDR2s of this invention have lengths 16 and 19. In the most preferred focused libraries of this invention, all three lengths are included in proportions similar to those found in natural antibody families.
(iii) CDR3
HC CDR3s vary in length. About half of human HCs consist of the components: V::nz::D::ny::JHn where V is a V gene, nz is a series of bases (mean 12) that are essentially random, D is a D segment, often with heavy editing at both ends, ny is a series of bases (mean 6) that are essentially random, and JH is one of the six JH segments, often with heavy editing at the 5′ end. The D segments appear to provide spacer segments that allow folding of the IgG. The greatest diversity is at the junctions of y with D and of D with JH.
In the preferred-libraries of this invention both types of HC CDR3s are used. In HC CDR3s that have no identifiable D segment, the structure is V::nz::JHn where JH is usually edited at the 5′ end. In HC CDR3s that have an identifiable D segment, the structure is V::nz::D::ny::JHn.
(c) Focused Sequence Diversity: CDR1, 2 and 3 (i) CDR1
In 5 amino acid length CDR1, examination of a 3D model of a humanized Ab showed that the side groups of residues 1, 3, and 5 were directed toward the combining pocket. Consequently, in the focused libraries of this invention, each of these positions may be selected from any of the native amino acid residues, except cysteine (“C”). Cysteine can form disulfide bonds, which are an important component of the canonical Ig fold. Having free thiol groups Could, thus, interfere with proper folding of the HC and could lead to problems in production or manipulation of selected Abs. Thus, in the focused libraries of this invention cysteine is excluded from positions 1; 3 and 5 of the preferred 5 amino acid CDR1s. The other 19 natural amino acids residues may be used at positions 1, 3 and 5. Preferably, each is present in equimolar ratios in the variegated libraries of this invention.
3D modeling also suggests that the side groups of residue 2 in a 5 amino acid CDR1 are directed away from the combining pocket. Although this position shows substantial diversity, both in GLG and mature genes, in the focused libraries of this invention this residue is preferably Tyr (Y) because it occurs in 681/820 mature antibody genes. However, any of the other native amino acid residues, except Cys (C), could also be used at this position.
For position 4, there is also some diversity in GLG and mature antibody genes. However, almost all mature genes have uncharged hydrophobic amino acid residues: A, G, L, P, F, M, W, I, V, at this position. Inspection of a 3D model also shows that the side group of residue 4 is packed into the innards of the HC. Thus, in the preferred embodiment of this invention which uses framework 3-23, residue 4 is preferably Met because it Is likely to fit very well into the framework of 3-23. With other frameworks, a similar fit consideration is used to assign residue 4.
Thus, the most preferred HC CDR1 of this invention consists of the amino acid sequence <1>Y<I>M<1> where <1> can be any one of amino acid residues: A, D, E, G, H, I, K, L, M, N, R, Q, S, T, V, W, Y. (not C), preferably present at each position in an equimolar amount. This diversity is shown in the context of a framework 3-23:JH4 in Table 1. It has a diversity of 6859-fold.
The two less preferred HC CDR1s of this invention have length 7 and length 14. For length 7, a preferred variegation is (S/T)1(S/G/<1>)2(S/G/<1>)3Y4Y5W6(S/G/<1>)7 (SEQ ID NO:107); where (S/T) indicates an equimolar mixture of Ser and Thr codons; (S/G/<1>) indicates a mixture Of 0.2025 S, 0.2025 G, and 0.035 for each of A, D, E, F, H, I, K, L, M, N, P, Q, R, T, V, W, Y. This design gives a predominance of Ser and Gly at positions 2, 3, and 7, as occurs in mature HC genes. For length 14, a preferred variegation is VSGGSIS<1><1><1>YYW<l>(SEQ ID NO:108),where <1> is an equimolar mixture of the 19 native amino acid residues, except Cys (C).
The DNA that encodes these preferred HC CDR1s is preferably synthesized using trinucleotide building blocks so that each amino acid residue ii present in essentially equimolar or other described amounts. The preferred codons for the <1> amino acid residues are gct, gat, gag, ttt, ggt, cat, att, aag, ctt, atg, aat, cct, cag, cgt, tct, act, gtt, tgg, and tat. Of course, other codons for the chosen amino acid residue could also be used.
The diversity oligonucleotide (ON). is preferably synthesized from BspEI to BstXI (as shown in Table 1) and can, therefore, be incorporated either by PCR synthesis using overlapping ONs or introduced by ligation of BspEI/BstXI-cut fragments. Table 2 shows the oligonucleotides that embody the specified variegations of the preferred length 5 HC CDR1s of this invention. PCR using ON-R1V1vg, ON-R1top, and ON-R1bot gives a dsDNA product of 73 base-pairs, cleavage with 14spEI and BstXI trims 11 and 13 bases from the ends and provides cohesive ends that can be ligated to similarly cut vector having the 3-23 domain shown in Table 1. Replacement of ON-R1V1vg with either ONR1V2vg or ONR1V3vg (see Table 2) allows synthesis of the two alternative diversity patterns—the 7 residue length and the 14 residue length HC CDR1.
The more preferred libraries of this invention comprise the 3 preferred HC CDR1 length diversities. Most preferably, the 3 lengths should be incorporated in approximately the ratios in which they are observed in antibodies selected without reference to the length of the CDRs. For example, one sample of 1095 HC genes have the three lengths present in the ratio: L=5:L=7:L=14::820:175:23::0.80:0.17:0.02. This is the preferred ratio in accordance with this invention.
(ii) CDR2
Diversity in HC CDR2 was designed with the same considerations as for HC CORI: GLG sequences, mature sequences and 3D structure. A preferred length for CDR2 is 17, as shown in Table 1. For this preferred 17 length CDR2, the preferred variegation in accordance with the invention is: <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), where <2> indicates any amino acid residue selected from the group of Y, R, W, V, G and S (equimolar mixture), <3> is P, S and G or P and S only (equimolar mixture), and <1> is any native amino acid residue except C (equimolar mixture).
ON-R2V1vg shown in Table 3 embodies this diversity pattern. It is preferably synthesized so that fragments of dsDNA containing the BstXI and XbaI site can be generated by PCR. PCR with ON-R2V1vg, ON-R2top, and ONR2bot gives a dsDNA product of 122 base pairs. Cleavage with BstXI and XbaI removes about 10 bases from each end and produces cohesive ends that can be ligated to similarly cut vector that contains the 3-23 gene-shown in Table 1.
In an alternative embodiment for a 17 length HC CDR2, the following variegation may be used; <1>I<4><1><1>G<5><1><1><1>YADSVKG(SEQ ID NO:3), where <1> is as described above for the more preferred alternative of HC CDR2; <4> indicates an equimolar mixture of DINSWY, and <5> indicates an equimolar mixture of SGDN. This diversity pattern is embodied in ON-R2V2vg shown in Table 3. Preferably, the two embodiments are used in equimolar mixtures in the libraries of this invention.
Other preferred HC CDR2s have lengths 16 and 19.
Length 16:
(SEQ ID NO: 4)
<1>I<4><1><1>G<5<1><1>YNPSLKG;
(SEQ ID NO: 5)
Length: 19:
<1>I<8>S<1><1><1>GGYY<1>YAASVKG,
wherein <1> is an equimolar mixture of all native amino acid residues except C; <4> is a equimolar mixture of DINSWY; <5> is an equimolar mixture of SGDN; and <8> is 0.27 R and 0:0 7 of each of residues ADEFGHIKLMNPQSTVWY. Table 3 shows ON-R2V3vg which embodies a preferred aDR2 variegation of length 16 and ON7R2V4vg which embodies a preferred CDR2 variegation of length 19. To prepare these variegations ON-R2V3vg may be PCR amplified with ON-A2top and ON-R2bo3 and ON-R2V4vg may be PCR amplified with ON-R2top and ON-R2-bo4. See Table 3. In the most preferred embodiment of this invention, all three HC CDR2 lengths are used. Preferably, they are present in a ratio 17:16:19::579:464:31::0.54:0.43:0.03.
(iii) CDR3
The preferred libraries of this invention comprise several BC CDR3 components. Some of these will have only sequence diversity. Others will have sequence diversity with embedded D segments to extend the length, while also incorporating sequences known to allow Igs to fold. The HC CDR3 components of the preferred libraries of this invention and their diversities are depicted in Table 4: Components 1-8.
This set of components was chosen after studying the sequences of 1383 human BC sequences. The proposed components are meant to fulfill the following goals:
1) approximately the same distribution of lengths as seen in native Ab genes;
2) high level of sequence diversity at places having high diversity in native Ab genes; and
3) incorporation of constant sequences often seen in native Ab genes.
Component 1 represents all the genes having lengths 0 to 8 (counting from the YYCAR motif at the end of FR3 to the WG dipeptide motif near the start of the J region, i.e., FR4). Component 2 corresponds the all the genes having lengths 9 or 10. Component 3. corresponds to the genes having lengths 11 or 12 plus half the genes having length 13. Component 4 corresponds to those having length 14 plus half those having length 13. Component 5 corresponds to the genes having length 15 and half of those having length 16. Component. 6 corresponds to genes of length 17 plus half of those with length 16. Component 7 corresponds to those with length 18. Component 8 corresponds to those having length 19 and greater. See Table 4.
For each HC CDR3 residue having the diversity <1>, equimolar ratios are preferably not used. Rather, the following ratios are used 0.095 [G and Y] and 0.048 [A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, and W]. Thus, there is a double dose of G and Y with the other residues being in equimolar ratios. For the other diversities, e.g., KR or SG, the residues are present in equimolar mixtures.
In the preferred libraries of this invention the eight components are present in the following fractions: 1 (0.10), 2 (0.14), 3 (0.25), 4 (0.13), 5 (0.13), 6 (0.11), 7 (0.04) and 8 (0.10). See Table 4.
In the more preferred embodiment of this invention, the amounts of the eight components is adjusted because the first component is not complex enough to justify including it as 10% of the library. For example, if the final library were to have 1×109 members, then 1×108 sequences would come from component 1, but it has only 2.6×105 CDR3 sequences so that each one would occur in ˜385 CDR1/2 contexts. Therefore, the more preferred amounts of the eight components are 1(0.02), 2(0.14), 3(0.25), 4(0.14), 510.14), 6(0.12), 7(0.68), 8(0.11). In accordance with the more preferred embodiment component 1 occurs in ˜77 CDR1/2 contexts and the other, longer CDR3s occur more often.
Table 5 shows vgDNA that embodies each of the eight HC CDR3 components shown in Table 4. In Table 5, the oligonucleotides (ON) Ctop25, CtprmA, C8prmB, and CBot25 allow PCR amplification of each of the variegated ONs (vgDNA): C1t08, C2t10, C3t12, C4t14, C5t15, C6t17, C7t18, and C8t19. After amplification, the dsDNA can be cleaved with AfiII and BstEII (or KpnI) and ligated to similarly cleaved vector that contains the remainder of the 3-23 domain. Preferably, this vector already contains diversity in one, or both, of CDR1 and CDR2 as disclosed herein. Most preferably, it contains diversity in both the CDR1 and CDR2 regions. It is, of course, to be understood that the various diversities can be incorporated into the vector in any order.
Preferably, the recipient vector originally contains a stuffer in place of CDR1, CDR2 and CDR3 so that there will be no parental sequence that would then occur in the resulting library. Table 6 shows a version of the V3-23 gene segment with each CDR replaced by a short segment that contains both stop codons and restriction sites that will allow specific cleavage of any vector that does not have the stuffer removed. The stuffer can either be short and contain a restriction enzyme site that will not occur in the finished library, allowing removal of vectors that are not cleaved by both AfiII and BstEII (or AionI) and religated. Alternatively, the stuffer could be 200-400 bases long so that uncleaved or once-cleaved vector can be readily separated from doubly cleaved vector.
Human Antibody Light Chain: Sequence and Length Diversity (i) Kappa Chain
(a) Framework
In the preferred embodiment of this invention, the kappa light chain is built in an A27 framework with a JK1 region. These are the most common V and J regions in the native genes. Other frameworks, such as 012, L2, and All, and other J regions, such as JK4, however, may be used without departing from the scope of this invention.
(b) CDR1
In native human kappa chains, CDR1s with lengths of 11, 12, 13, 16, and 17 were observed with length 11 being predominant and length 12 being well represented. Thus, in the preferred embodiments of this invention LC CDR1s of length 11 and 12 are used in an and mixture similar to that observed in native antibodies), length 11 being most preferred. Length 11 has the following sequence: RASQ<1>V<2><2><3>LA (SEQ ID NO:14) and Length 12 hag the following sequence: RASQ<1>V<25<2><2><3>LA (SEQ ID NO:15), wherein <1> is an equimolar mixture of ill of the native.-amino acid residues, except C, <2> is 0.2 S and 0.044 of each of ADEFGHIKLMNPQRTVWY, and <3> is 0.2.Y and 0.044 each of A. D, E, F, G, H, 1, K, L, M, N, Q, R, T, V, W and Y. In the most preferred embodiment of this invention, both CDR1. lengths are used. Preferably, they are present in a ratio of 11:12::154:73:0.68:0.32.
(c) CDR2
In native kappa, CDR2 exhibits only length 7. This length is used in the preferred embodiments of-this invention. It has the sequence <1>AS<2>R<4><1>, wherein <1> is an-equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY; <2> is 0.2 S and 0.004 of each of ADEFGHIKLMNPQRTVWY; and <4> is 0.2 A and 0.044 of each of DEFGHIKLMNPQRSTUWY.
(d) CDR3
In native kappa, CDR3 exhibits lengths of 4, 6, 7; 8, 9, 10, 11, 12, 13, 0.0 . . . and 19. While any of these lengths and mixtures of them can be employed in this invention, we prefer lengths 8, 9 and 10, length 9 being more preferred. For the preferred Length 9, the sequence is, QQ<3><1><1><1>P<1>T, wherein <1> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY and <3> is 0.2? and 0.044 each of ADEFGHIKLWQRSVW. Length 8 is preferably QQ33111P and Length 10 is Preferably QQ3211PP1T, wherein 1 and 3 are as defined for Length 9 and 2 is S (0.2) and 0.044 each of ADEFGHIKLMNPQRTVWY. A mixture of all 3 lengths being most preferred (ratios as in native antibodies), i.e., 8:9:10i28:166:63::0.1:0.65:0.25.
Table 7 shows a kappa chain gene of this invention, including a PlacZ promoter a ribosome-binding site, and signal sequence (MI3 III signal). The DNA sequence encodes the GLG amino acid sequence but does not comprise the GLG DNA sequence. Restriction sites are designed to fall within each framework region so that diversity can be cloned into the CDRs. XmaI and EspI are in FR1, SexAI is in FR2, RsrII is in FR3, and KpnI (or Acc65I), are in FR4. Additional sites are provided in the constant kappa chain to facilitate construction of the gene.
Table 7 also shows a suitable scheme of variegation for kappa. In .CDR1, the most preferred length 11 is depicted. However, most preferably both lengths 11 and 12 are used. Length 12 in CDR1 can be construed by introducing codon 51 as <2> (i.e. a Ser-biased mixture). CDR2 of kappa is always 7 codons. Table 7 shows a preferred variegation scheme for CDR2. Table 7 Shows a variegation scheme for the most preferred CDR3 (length 9). Similar variegations can be lied for CDRs of length 8 and 10. In the preferred embodiment of this invention, those three lengths (8, 9 and 10) are included in the libraries of this invention in the native ratios, as described above.
Table 9 shows series of diversity oligonucleotides and primers that may be used to construct the kappa chain diversities depicted in Table 7.
(ii) Lambda Chain
(a) Framework
The lambda chain is preferably built in a 2a2 framework with an L2J region. These are the most common V and J regions in the native genes. Other frameworks, such as 31, 4b, la and 6a, and other J regions, such as L1J, L3J and L7J, however, may be used without departing from the scope of this invention.
(b) CDR1
In native human lambda chains, CDR1s with length 14. predominate, lengths 11, 12 and 13 also occur. While any of these can be used in this invention, lengths 11 and 14 are preferred. For length 11 the sequence is: TG<2><4>L<4><4><4><3><4><4>(SEQ ID NO:22) and for Length 14 the sequence is: TG<1>SS<2>VG<1><3><2><3>VS (SEQ ID NO:18), wherein <1> is 0.27 T, 0.21 G and 0.027 each of ADEFHIKLMNPQRSVWY; <2> is 0.27 D, 0.27 N and 0.027 each of AEFGHIKLMPQRSTVWY; <3> is 0.36 Y and 0.0355 each of ADEFGHIKLMNPQRSTVW; and <4> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVWY. Most preferably, Mixtures (similar to those occurring in native antibodies) preferably, the ratio is 11:14::23:46::0.33:0.67 of the three lengths are used.
(c) CDR2
In native human lambda chains4.CDR2s with length 7 are by far the most common. This length is preferred in this invention. The sequence of this Length 7 CDR2 is <4><4><4><2>RPS, wherein <2> is 0.27 D, 0.27 N, and 0.027 each of AEFGHIKLMPQRTVWY and <4> is an equimolar mixture of amino acid residues ADEFGHIKLMNPQRSTVW.
(d) CDR3
In native human lambda chains, CDR3s of length 10 and 11 predominate, while length 9 is also common. Any of these three lengths can be used in the invention. Length 11 is preferred and mixtures of 10 and 11 more preferred. The sequence of Length 11 is <4><5><4><2><4>S<4><4><4><4>V, where <2> and <4> are as defined for the lambda CORI and <5> is 0.36 S and 0.0355 each of ADFFGHIKLMNFORTVWY. The sequence of Length 10 is <5>SY<1><5>S<5><1><4>V (SEQ ID NO:19), wherein <1> is an equimolar mixture of ADEFGHIKLMNPQRSTVWY; and <4> and <5> are as defined for Length 11. The preferred mixtures of this invention comprise an equimolar mixture of Length 10 and Length 11. Table 8 shows a preferred focused lambda light chain diversity in accordance with this invention.
Table 9 shows a series of diversity oligonucleotides and primers that may be used to construct 10 the lambda chain diversities depicted in Table 7.
Method of Construction of the Genetic Package The diversities of heavy chain and the kappa and lambda light chains are best constructed in separate vector's. First a synthetic gene is designed to embody each of the synthetic variable domains. The light chains are bounded by restriction sites for ApaLI (positioned at the very end of the signal sequence) and AscI (positioned after the stop codon). The heavy chain is bounded by SfiI (positioned within the PelB signal sequence) and NotI (positioned in the linker between CH1 and the anchor protein). Signal sequences other than PelB may also need, e.g., a M13 pIII signal sequence.
The initial genes are made with “stuffer” sequences in place of the desired CDRs. A “stuffer” is a sequence that is to be cut away and replaced by diverse DNA but which does not allow expression ‘of a functional antibody gene. For example, the stuffer may contain several stop codons and restriction sites that will not occur in the correct finished library vector. For example, in Table 10, the stuffer for CDR1 of kappa A27 contains a StuI site. The vgDNA for CDR1 is introduced as a cassette from EspI, XmaI, or Af1II to dither SexAI or KasI. After the ligation, the DNA is cleaved with Still; there should be no StuI sites in the desired vectors.
The sequences of the heavy chain gene with stuffers is depicted in Table 6. The sequences of the kappa light chain gene with stuffers is depicted in Table 10. The sequence of the lambda light chain gene with stuffers is depicted in Table 11.
In another embodiment of the present invention the diversities of heavy chain and the kappa or lambda light chains are constructed in .a single vector or genetic packages (e.g., for display or display and expression) having appropriate restriction sites that allow cloning of these chains. The processes to construct such vectors are well known and widely used in the art. Preferably, a heavy chain and Kappa light Chain library and a heavy chain and lambda light chain library would be prepared separately. The two libraries, most preferably, will then be mixed in equimolar amounts to attain maximum diversity.
Most preferably, the display is had on the surface of a derivative of M13 phage. The most preferred vector contains all the genes of M13, an antibiotic resistance-gene, and the display cassette. The preferred vector is provided with restriction sites that allow introduction and excision of members of the diverse family of genes, as cassettes. The preferred vector is stable against rearrangement under the growth conditions used to amplify phage.
In another embodiment of this invention, the diversity captured by the methods of the present invention may be displayed and/or expressed in a phagemid vector (e.g., pCES1) that displays and/or expresses the peptide, polypeptide or protein. Such vectors may also be used to store the diversity for subsequent display and/or expression using other vectors or phage.
In another embodiment of this invention, the diversity captured by the methods of the present invention may be displayed and/or expressed in a yeast vector.
TABLE 1
3-23:JH4 CDR1/2 diversity = 1.78 × 108
FR1(VP47/V3-23)---------------
20 21 22 23 24 25 26 27 28 29 30
(SEQ ID NO: 99) A M A E V Q L L E S G
ctgtctgaac cc atg gcc gaa/gtt/caa/ttg/tta/gag/tct/ggt/
Scab ..... NcoI.... MfeI
----------FR1---------------------------------
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
G G L V Q P G G S L R L S C A
/ggc/ggt/ctt/gtt/cag/cct/ggt/ggt/tct/tta/cgt/ctt/tct/tgc/gct/
Sites of variegation <1><1> <1> <1> 6859-fold diversity
----FR1 ------------- >/ .. CDR1........... ./---FR2-----
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
A S G F T F S - Y - M - W V R
/gct/tcc/gga/ttc/act/ttc/tct/ - /tac/ - /atg/ - /tgg/gtt/cgc/
BspEI BsiWI BstXI.
Sites of variegation-><2> <2> <3>
-----FR2-------------------- >/ ..CDR2
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
Q A P G K G L E W V S - I - -
/caa/gct/cct/gtt/aaa/ggt/ttg/gag/tgg/gtt/tct/ - /atc/ - / - /
...BstXI
<1> <1> 25992-fold diversity in CDR2
...CDR2 ..................................... /---FR3-----
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
S G G - T - Y A D S V K G R F
/tct/ggt/ggc/ - /act/ - /tat/gct/gac/tcc/gtt/aaa/ggt/cgc/ttc/
-- - - FR3-------------------------------------------------
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
T I S R D N S K N T L Y L Q M
/act/atc/tct/aga/gac/aac/tct/aag/aat/act/ctc/tac/ttg/cag/atg/
XbaI
---FR3------------------------------------------------------
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
N S L R A E D T A V Y Y C A K
/aac/agc/tta/agg/gct/gag/gac/acc/gct/gtc/tac/tac/tgc/gcc/aaa/
Af1II
.....CDR3................../ Replaced by the various components!
121 122 123 124 125 126 127
D Y E G T G Y (SEQ ID NO: 24)
/gac/tat/gaa/ggt/act/ggt/tat/ (SEQ ID NO: 23)
/---------- FR4 ---(JH4)--------------------------------------------------
Y F D Y W G Q G T L V T V S S (SEQ ID NO: 26)
/tat/ttc/gat/tat/tgg/ggt/caa/ggt/acc/ctg/gtc/acc/gtc/tct/agt/. (SEQ ID NO: 25)
KpnI BstEII
<1> = Codons for ADEFGHIKLMNPQRSTVWY (equimolar mixture)
<2> = Codons for YRWVGS (equimolar mixture)
<3> = Codons for PS or PS and G (equimolar mixture)
TABLE 2
Oligonucleotides used to variegate CDR1 of human HC
CDR1 - 5 residues
(ON-R1V1vg): 5′-ct/tcc/gga/ttc/act/ttc/tct/<1>/tac/<1>/atg/<1>/tgg/gtt/cgc/caa/gct/cct/gg-3′
(SEQ ID NO: 27)
<1> = Codons of ADEFGHIKLMNPQRSTVWY 1:1
(ON-Rltop): 5′-cctactgtct/tcc/gga/ttc/act/ttc/tct-3′ (SEQ ID NO: 28)
(ON-Rlbot)[RC]: 5′-′tgg/gtt/cgc/caa/gct/cct/ggttgctcactc-3′ (SEQ ID NO: 29)
CDR1 - 7 residues
(ON-R1V2vg): 5′-ct/tcc/gga/ttc/act/ttc/tct/<6>/<7>/<7>/tac/tac/tgg/<7>/tgg/gtt/cgc/caa/gct/
cct/gg-3′ (SEQ ID NO: 30)
<6> = Codons for ST, 1:1
<7> 0.2025(Codons for SG) + 0.035(Codons for ADEFHIKLMNPQRTVWY)
CDR1 - 14 residues
(ON-R1V3vg): 5′- ct/tcc/gga/ttc/act/ttc/tct/atc/agc/ggt/ggt/tct/atc/tcc/<1>/<1>/<1>/-
tac/tac/tgg/<1>/tgg/gtt/cgc/caa/gct/cct/gg-3′(SEQ ID NO: 31)
<1> = Codons for ADEFGHIKLMNPQRSTVWY 1:1
TABLE 3
Oligonucleotides used to variegate CDR2 of human HC
CDR2 - 17 residues
(ON-R2V1vg): 5′-ggt/ttg/gag/tgg/gtt/tct/<2>/atc/<2>/<3>/tct/ggt/ggc/<1>/act/<1>/tat/gct/-
gac/tcc/gtt/aaa/gg-3′ (SEQ ID NO: 32)
(ON-R2top): 5′-ct/tgg/gtt/cgc/caa/gct/cct/ggt/aaa/ggt/ttg/gag/tgg/gtt/tct-3′ (SEQ ID NO: 33)
(ON-R2bot)[RC]: 5′-tat/gct/gac/tcc/gtt/aaa/ggt/cgc/ttc/act/atc/tct/aga/ttcctgtcac-3′
(SEQ ID NO: 34)
<I> = Codons for A, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W and Y
(equimolar mixture)
<2> = Codons for Y, R, W, V, G and S (equimolar mixiure)
<a> = Codons for P and S (equimolar mixture) or P, S and G (equimolar mixture)
(ON-R2V2vg): 5′-ggt/ttg/gag/tgg/gtt/tct/<1>/atc/<4>/<1>/<1>/ggt/<5>/<1>/<1>/<1>/tat/gct/-
gac/tcc/gtt/aaa/gg-3′ (SEQ ID NO: 35)
<4> = Codons for DINSWY (equimolar mixture)
<5> = Codons for SGDN, (equimolar mixture)
CDR2 -16 residues
(ON-R2V3vg): 5′-ggt/ttg/gag/tgg/gtt/tct/<1>/att/<4>/<1>/<1>/ggt/
<5>/<1>/<1>/tat/aac/cct/tcc/ctt/aag/gg-3′ (SEQ ID NO: 36)
(ON-R2bo3)[RC]: 5′-tat/aac/cct/tcc/ctt/aag/ggt/cgc/ttc/act/atc/tct/aga/ttcctgtcac-3′
(SEQ ID NO: 37)
CDR2 19 residues
(ON-R2V4vg): 5′-ggt/ttg/gag/tgg/gtt/tct/<1>/atc/<8>/agt/<1>/<1>/
<1>/ggt/ggt/act/act/<1>/tat/gcc/gct/tcc/gtt/aag/gg-3′ (SEQ ID NO: 38)
(ON-R2bo4)[RC]: 5′-tat/gcc/gct/tcc/gtt/aag/ggt/cgc/ttc/act/atc/tct/aga/ttcctgtcac′-3′
(SEQ ID NO: 39)
<1>, <2>, <3>, <4> and <5> are as defined above
<8> is 0.27 R and 0.027 each of ADEFGHIKLMNPQSTVWY
TABLE 4
Preferred Components
Preferred
Fraction of Adjusted
Component Length Complexity Library Fraction
1 YYCA21111YFDYWG. 8 2.6 × 105 .10 .02
(SEQ ID NO: 6)
(1 = any amino acid residue, except C; 2 = K and R)
2 YYCA2111111YFDYWG. 10 9.4 × 107 .14 .14
(SEQ ID NO: 7)
(1 = any amino acid residue, except C; 2 = K and R)
3 YYCA211111111YFDYTG. 12 3.4 × 1010 .25 .25
(SEQ ID NO: 8)
(1 = any amino acid residue, except C; 2 = K and R)
4 YYCAR111S2S3111YFDYWG. 14 1.9 × 108 .13 .14
(SEQ ID NO: 9)
(1 = any amino acid residue, except C; 2 = S and G 3 = Y and W)
5 YYCA2111CSG11CY1YFDYWG. 15 9.4 × 107 .13 .14
(SEQ ID NO: 10)
(1 = any amino acid residue except C; 2 = K and R)
6 YYCA211S1TIFG11111YFDYWG. 17 1.7 × 1010 .11 .12
(SEQ ID NO: 11)
(1 = any amino acid residue, except C; 2 = K and R)
7 YYCAR111YY2S33YY111YFDYMG. 18 3.8 × 108 .04 .08
(SEQ ID NO: 12)
(1 = any amino acid residue, except C; 2 = D or G; 3 = S and G)
8 YYCAR1111YC2231CY111YFDYWG. 19 2.0 × 1011 .10 .11
(SEQ ID NO: 13)
(1 = any amino acid residue, except C; 2 = S and G; 3 = T, D and G)
TABLE 5
Oligonucleotides used to variegate the eight components of HC CDR3
(Ctop25): 5′-gctctggtcaac/tta/agg/gct/gag/g-3′ (SEQ ID NO: 40)
(CtprmA): 5′-gctctggtcaac/tta/agg/gct/gag/gac/acc/gct/gtc/tac/tac/tgc/gcc-3′
AflLL. . . (SEQ ID NO: 41)
(CBprmB)[RC]: 5′-/tac/ttc/gat/tac/tgg/ggc/caa/ggt/acc/ctg/gtc/acc/tcgctccacc-3′
(SEQ ID NO: 42) BstEII...
(CBot25)[RC]: 5′-/ggt/acc/ctg/gtc/acc/tcgctccacc-3′ (SEQ ID NO: 43)
The 20 bases at 3′ end of CtprmA are identical to the most 5′ 20 bases
of each of the vgDNA molecules.
Ctop25 is identical to the most 5′ 25 bases of CtprmA.
The 23 most 3′ bases of CBprmB are the reverse complement of the
most 3′ 23 bases of each of the vgDNA molecules.
CBot25 is identical to the 25 bases at the 5′ end of CBprmB.
Component 1
(C1t08):
5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′
(SEQ ID NO: 44)
<1> = 0.095 Y + 0.095 G + 0.048 each of the residues ADEFHIKLMNPQRSTVW, no C; <2> = K and R
(equimolar mixture)
component 2
(C2t10):
5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′
(SEQ ID NO: 45)
<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = K and R (equimolar
mixture)
Component 3
(C3t12):
5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/<1>/<1>/<1>/<1>/<1>/tac/ttc/gat/tac/-
tgg/ggc/caa/gg-3′ (SEQ ID NO: 46)
<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = K and R (equimolar
mixture)
Component 4
(C4t140):
5′-cc/gct/gtc/tac/tac/tgc/gcc/cgt/<1>/<1>1<1>/tct/<2>/tct/<3>/<1>/<1>/<1>/tac/ttc/gat/-
tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 47)
<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = S and G (equimolar
mixture); <3> = Y and W (equimolar mixture)
Component 5
(C5t15):
5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/<1>/tgc/tct/ggt/<1>/<1>/tgc/tat/<1>/tac/-
ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 48)
<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = K and R (equimolar
mixture)
Component 6
(C6t17):
5′-cc/gct/gtc/tac/tac/tgc/gcc/<2>/<1>/<1>/tct/<1>/act/atc/ttc/ggt/<1>/<1>/<1>/<1>/-
<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 49)
<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = K and R (equimolar
mixture)
Component 7
(C7t18):
5′-cc/gct/gtc/tac/tac/tgc/gcc/cgt/<1>/<1>/<1>/tat/tac/<2>/tct/<3>/<3>/tac/tat/-
<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 50)
<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = D and G (equimolar
mixture); <3> = S and G (equimolar mixture)
Component 8
(c8t19):
5′-cc/gct/gtc/tac/tac/tgc/gcc/cgt/<1>/<1>/<1>/<1>/tat/tgc/<2>/<2>/<3>/<1>/tgc/tat/-
<1>/<1>/<1>/tac/ttc/gat/tac/tgg/ggc/caa/gg-3′ (SEQ ID NO: 51)
<1> = 0.095 Y + 0.095 G + 0.048 each of ADEFHIKLMNPQRSTVW, no C; <2> = S and G (equimolar
mixture); <3> = TDG (equimolar mixture);
TABLE 6
3-23:: JH4 Stuffers in place of CDRs
FR1(DP47/V3-23)------------------------
20 21 22 23 24 25 26 27 28 29 30
A M A E V Q L L E S G
ctgtctgaac cc atg gcc gaa/gtt/caa/ttg/tta/gag/tct/ggt/
(SEQ ID NO: 99)
Scab .......NcoI.... MfeI
---------------------------- FR1----------------------------
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
G G L V Q P G G S L R L S C A
/ggc/ggt/ctt/gtt/cag/cct/ggt/ggt/tct/tta/cgt/ctt/tct/tgc/gct/
---FR1--------------------->/...CDR1 stuffer..../---FR2------
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
A S G F T F S S Y A / / W V R
/gct/tcc/gga/ttc/act/ttc/tct/tcg/tac/gct/tag/taa/tgg/gtt/cgc/
BspEI BsiWI BstXI.
-------FR2-------------------------------->/...CDR2 stuffer.
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
Q A P G K G L E W V S / P R /
/caa/gct/cct/ggt/aaa/ggt/ttg/gag/tgg/gtt/tct/taa/cct/agg/tag/
...BstXI AvrII..
....CDR2 stuffer..................................../---FR3---
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
T I S R D N S K N T L Y L Q M
/act/atc/tct/aga/gac/aac/tct/aag/aat/act/ctc/tac/ttg/cag/atg/
XbaI
--FR3------------..> CDR3 Stuffer ------------>/
106 107 108 109 110
N S L R A (SEQ ID NO: 53)
/aac/agc/tta/agg/gct/tag taa agg cct taa (SEQ ID NO: 52)
AflII StuI...
/-----FR4 --- (JH4) -------------------------------------------
Y F D Y W G Q G T L V T V S S (SEQ ID NO: 26)
/tat/ttc/gat/tat/tgg/ggt/caa/ggt/acc/ctg/gtc/acc/gtc/tct/agt/... (SEQ ID NO: 25)
KpnI BstEII
TABLE 7
A27:JH1 Human Kappa light chain gene
gaggacc attgggcccc ctccgagact ctcgagcgca
Scab ......Eco0109I XhoI
ApaI
acgcaattaa tgtgagttag ctcactcatt aggcacccca ggctttacac tttatgcttc
..−35.. Plac ..−10.
cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacacagga
aacagctatg accatgatta
cgccaagctt tggagccttt tttttggaga ttttcaac (SEQ ID NO: 54)
pflMI.......
Hind III
M13 III signal sequence (AA seg) ------------------------------
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
M K K L L F A I P L V V P F Y
gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac
--Signal-->FR1--------------------------------------------->
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
S H S A Q S V L T Q S P G T L
/agc/cat/agt/gca/caa/tcc/gtc/ctt/act/caa/tct/cct/ggc/act/ctt/
ApaLI...
---- FR1 -------------------------------------->/ CDR1---->
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
S L S P G E R A T L S C R A S
(SEQ ID NO: 55)
/tcg/cta/agc/ccg/ggt/gaa/cgt/gct/acc/tta/agt/tgc/cgt/gct/tcc/
(SEQ ID NO: 54; Cont'd)
EspI..... AflII ...
XmaI...
For CDR1:
<1> ADEFGHIKLMNPQRSTVWY 1:1
<2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)
<3> Y(0.2) ADEFGHIKLMNPQRSTVW (0.044 each)
(CDR1 installed as AflII-(SexAI or KasI) cassette.) For the most
preferred 11 length codon 51 (XXX) is omitted; for the preferred
12 length this codon is <2>
------ CDR1--------------------- --->/ --- FR2------------->
<1> <2> <2> xxx <3>
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
Q - V - - - - L A W Y Q Q K P
(SEQ ID NO: 55; Cont'd)
/cag/ - /gtt/ - / - / - / - /ctt/gct/tgg/tat/caa/cag/aaa/cct/
(SEQ ID NO: 54; Cont'd)
SexAI....
For CDR2:
<1> ADEFGHIKLMNPQRSTVWY 1:1
<2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)
<4> A(0.2) DEFGHIKLMNPQRSTVWY (0.044 each)
CDR2 installed as (SexAI or KasI) to (BamHI or RsrII) cassette.)
----- FR2 ------------------------->/------CDR2----------->
<1> <2> <4>
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
G Q A P R L L I Y - A S - R -
(SEQ ID NO: 55; Cont'd)
/ggt/cag/gcg/ccg/cgt/tta/ctt/att/tat/ - /gct/tct/ - /cgc/ -
(SEQ ID NO: 54; Cont'd)
SexAI.... KasI....
CDR2-->/--- FR3 ------------------------------------------>
<1>
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
- G I P D R F S G S G S G T D
/ - /ggg/atc/ccg/gac/cgt/ttc/tct/ggc/tct/ggt/tca/ggt/act/gac/
BamHI
RsrII .....
--------FR3------------------------------------------------>
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
F T L T I S R L E P E D F A V
(SEQ ID NO: 55′ Cont'd)
/ttt/acc/ctt/act/att/tct/aga/ttg/gaa/cct/gaa/gac/ttc/gct/gtt/
(SEQ ID NO: 54; Cont'd) XbaI
For CDR3 (Length 9):
<1> ADEFGHIKLMNPQRSTVWY 1:1
<3> Y(0.2) ADEFGHIKLMNPQRTVW (0.044 each)
For CDR3 (Length 8): QQ33111P
1 and 3 as defined for Length 9
For CDR3 (Length 10): QQ3211PP1T
1 and 3 as defined for Length 9
2 S(0.2) and 0.044 each of ADEFGHIKLMNPQRTVWY
CDR3 installed as XbaI to (StyI Or BsiWI)cassette.
------------->/----CDR3-------------------------->/----FR4--->
<3> <1> <1> <1> <1>
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
Y Y C Q Q - - - - P - T F G Q
(SEQ ID NO: 55; Cont'd)
/tat/tat/tgc/caa/cag/ - / - / - / - /cct/ - /act/ttc/ggt/caa/
(SEQ ID NO: 54; Cont'd)
BstXI.........
----FR4-------------------->/ <-------Ckappa --------------
121 122 123 124 125 126 127 128 129 130 131 132 133 134
G T K V E I K R T V A A P S
/ggt/acc/aag/gtt/gaa/atc/aag/ /cgt/acg/gtt/gcc/gct/cct/agt/
StyI.... BsiWI..
135 136 137 138 139 140 141 142 143 144 145 146 147 148 149
V F I F P P S D E Q L K S G T
/gtg/ttt/atc/ttt/cct/cct/tct/gac/gaa/caa/ttg/aag/tca/ggt/act/
MfeI...
150 151 152 153 154 155 156 157 158 159 160 161 162 163 164
A S V V C L L N N F Y P R E A
(SEQ ID NO: 55; Cont'd)
/gct/tct/gtc/gta/tgt/ttg/ctc/aac/aat/ttc/tac/cct/cgt/gaa/gct/
(SEQ ID NO: 54; Cont'd)
BssSI..
165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
K V Q W K V D N A L Q S G N S
/aaa/gtt/cag/tgg/aaa/gtc/gat/aac/gcg/ttg/cag/tcg/ggt/aac/agt/
MluI....
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194
Q E S V T E Q D S K D S T Y S
/caa/gaa/tcc/gtc/act/gaa/cag/gat/agt/aag/gac/tct/acc/tac/tct/
195 196 197 198 199 200 201 202 203 204 205 206 207 208 209
L S S T L T L S K A D Y E K H
/ttg/tcc/tct/act/ctt/act/tta/tca/aag/gct/gat/tat/gag/aag/cat/
210 211 212 213 214 215 216 217 218 219 220 221 222 223 224
K V Y A C E V T H Q G L S S P
(SEQ ID NO: 55; Cont'd)
/aag/gtc/tat/GCt/TGC/gaa/gtt/acc/cac/cag/ggt/ctg/agc/ttc/cct/
(SEQ ID NO: 54; Cont'd)
SacI....
225 226 227 228 229 230 231 232 233 234
V T K S F N R G E C
(SEQ ID NO: 55; Cont'd)
/gtt/acc/aaa/agt/ttc/aac/cgt/ggt/gaa/tgc/taa/tag ggcgcgcc
DsaI.... AscI....
BssHII
acgcatctctaa gcggccgc aacaggaggag
(SEQ ID NO: 54; Cont'd)
NotI....
TABLE 8
2a2:JH2 Human lambda-chain gene
gaggaccatt gggcccc ttactccgtgac
Scab...... Eco0109I
---------FR1-------------------------------------------->
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
S A Q S A L T Q P A S V S G S P G
(SEQ ID NO: 57)
agt/gca/caa/tcc/gct/ctc/act/cag/cct/gct/agc/gtt/tcc/ggg/tca/cct/ggt/
(SEQ ID NO: 56)
ApaLI... NheI... BstEII...
SexAI....
For CDR1 (length 14):
<1> = 0.27 T, 0.27 G, 0.027 each of ADEFHIKLMNPQRSVWY, no C
<2> = 0.27 D, 0.27 N, .0.027 each of AEFGHIKLMPQRSTVWY, no C
<3> = 0.36 Y, 0.0355 each of ADEFGHIKLMNPQRSTVW, no C
T G <1> S S <2> V G
-----FR1 ----------------> /----CDR1-----------------------
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
Q S I T I S C T G - S S - V G
/caa/agt/atc/act/att/tct/tgt/aca/ggt/ - /tct/tct/ - /gtt/ggc/
BsrGI..
<1> <3> <2> <3> V S = vg Scheme #1, length = 14
-----CDR1 -------------> /------------- FR2-----------------
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
- - - - V S W Y Q Q H P G K A
(SEQ ID NO: 57; Cont'd)
/ - / - / - / - /gtt/tct/tgg/tat/caa/caa/cac/ccg/ggc/aag/gcg/
(SEQ ID NO: 56; Cont'd)
XmaI.... KasI.....
AvaI....
A second Vg scheme for CDR1 gives segments of length 11:
T22G<2><4>L<4><4><4><3><4><4> where
<4> = equimolar mixture of each of ADEFGHIKLMNPQRSTVWY, no C
<3> = as defined above for the alternative CDR1
For CDR2:
<2> and <4> are the same variegation as for CDR1
<4> <4> <4> <2> R P S
--FR2---------------> /-------CDR2--------- ----->/------FR3-
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
P K L M I Y - - - - R P S G V
/ccg/aag/ttg/atg/atc/tac/ - / - / - / - /cgt/cct/tct/ggt/gtt/
KasI....
--------FR3-------------------------------------------------
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
S N R F S G S K S G N T A S L
(SEQ ID NO: 57; Cont'd)
/agc/aat/cgt/ttc/tcc/gga/tct/aaa/tcc/ggt/aat/acc/gca/agc/tta/
(SEQ ID NO: 56; Cont'd)
BspEI.. HindIII.
BsaBI..............(blunt)
------FR3------------------------------------------------->
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
T I S G L Q A E D E A D Y Y C
(SEQ ID NO: 57; Cont'd)
/act/atc/tct/ggt/ctg/cag/gct/gaa/gac/gag/gct/gac/tac/tat/tgt/
(SEQ ID NO: 56; Cont'd)
PstI...
CDR3 (Length 11):
<2> and <4> are the same variegation as for CDR1
<5> = 0.36 S, 0.0355 each of ADEFGHIKLMNPQRTVWY no C
CDR3 (Length 10): <5> SY <1> <5> S <5> <1> <4> V
<1> is an equimolar mixture of ADEFGHIKLMNPQRSTVWY, no C
<4> and <5> are as defined for Length 11
<4> <5> <4> <2> <4> S <4> <4> <4> <4> V
------CDR3--------------------------------->/----FR4-------
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
- - - - - S - - - - V F G G G
/ - / - / - / - / - /tct/ - / - / - / - /gtc/ttc/ggc/ggt/ggt/
KpnI..
-------FR4------------->
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
T K L T V L G Q P K A A P S V
/acc/aaa/ctt/act/gtc/ctc/ggt/caa/cct/aag/gct/gct/cct/tcc/gtt/
KpnI... HincII..
Bsu36I...
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
T L F P P S S E E L Q A N K A
(SEQ ID NO: 57; Cont'd)
/act/ctc/ttc/cct/cct/agt/tct/gaa/gag/ctt/caa/gct/aac/aag/gct/
(SEQ ID NO: 56; Cont'd)
SapI.....
136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
T L V C L I S D F Y P G A V T
/act/ctt/gtt/tgc/ttg/atc/agt/gac/ttt/tat/cct/ggt/gct/gtt/act/
BclI....
151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
V A W K A D S S P V K A G V E
/gtc/gct/tgg/aaa/gcc/gat/tct/tct/cct/gtt/aaa/gct/ggt/gtt/gag/
BsmBI...
166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
T T T P S K Q S N N K Y A A S
/acg/acc/act/cct/tct/aaa/caa/tct/aac/aat/aag/tac/gct/gcg/agc/
BsmBI... SacI....
181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
S Y L S L T P E Q W K S H K S
(SEQ ID NO: 57; Cont'd)
/tct/tat/ctt/tct/ctc/acc/cct/gaa/caa/tgg/aag/tct/cat/aaa/tcc/
(SEQ ID NO: 56; Cont'd)
SacI...
196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
Y S C Q V T H E G S T V E K T
/tat/tcc/tgt/caa/gtt/act/cat/gaa/ggt/tct/acc/gtt/gaa/aag/act/
BspHI...
211 212 213 214 215 216 217 218 219
V A P T E C S
(SEQ ID NO: 57; Cont'd)
/gtt/gcc/cct/act/gag/tgt/tct/tag/tga/ggcgcgcc
AscI....
BssHII
aacgatgttc aag gcggccgc aacaggaggag
(SEQ ID NO: 56; Cont'd)
NotI.... Scab.......
TABLE 9
Oligonucleotides For Kappa and Lambda Light Chain Variegation
(Ctop25):
5′-gctctggtcaac/tta/agg/gct/gag/g-3′ (SEQ ID NO: 58)
(CtprmA):
5′-gctctggtcaac/tta/agg/gct/gag/gac/acc/gct/gtc/tac/tac/tgc/gcc-3′
(SEQ ID NO: 59) AflII...
(CBprmB)[RC]:
5′-/tac/ttc/gat/tac/ttg/ggc/caa/ggt/acc/ctg/gtc/acc/tcgctccacc-3′
(SEQ ID NO: 60) BstEII...
(CBot25)[RC]:
5′-/ggt/acc/ctg/gtc/acc/tcgaccacc-3′ (SEQ ID NO: 61)
Kappa chains: CDR1 (“1”), CDR2 (“2”), CDR1 (“3”)
CDR1
(Ka1Top610):
5′-ggtctcagttg/cta/agc/ccg/ggt/gaa/cgt/gct/acc/tta/agt/tgc/cgt/
gct/tcc/cag-3′ (SEQ ID NO: 62)
(Ka1STp615):
5′-ggtctcagttg/cta/agc/ccg/ggt/g-3′ (SEQ ID NO: 63)
(Ka1Bot620)[RC]:
′5′-ctt/gct/tgg/tat/caa/cag/aaa/cct/ggt/cag/gcg/ccaagtcgtgtc-3′
(SEQ ID NO: 64)
(Ka1SB625)[RC]:
5′-cct/ggt/cag/gcg/ccaagtcgtgtc-3′ (SEQ ID NO: 65)
(Ka1vg600):
5′-gct/acc/tta/agt/tgc/cgt/gct/tcc/cag-
/<1>/gtt/<2>/<2>/<3>/ctt/gct/tgg/tat/caa/cag/aaa/cc-3′
(SEQ ID NO: 66)
(Ka1vg600-12):
5′-gct/acc/tta/agt/tgc/cgt/gct/tcc/cag-
/<1>/gtt/<2>/<2>/<2>/<3>/ctt/gct/tgg/tat/caa/cag/aaa/cc-3′
(SEQ ID NO: 67)
CDR2
(Ka2Tshort657):
5′-cacgagtccta/cct/ggt/cag/gc-3′ (SEQ ID NO: 68)
(Ka2Tlong655):
5′-cacgagtccta/cct/ggt/cag/gcg/ccg/cgt/tta/ctt/att/tat-3′
(SEQ ID NO: 69)
(Ka2Bshort660):[RC]:
5′-/gac/cgt/ttc/tct/ggt/tctcacc-3′ (SEQ ID NO: 70)
(Ka2vg650):
5′-cag/gcg/ccg/cgt/tta/ctt/att/tat/<1>/gct/tct/<2>/-
/cgc/<4>/<1>/ggg/atc/ccg/gac/cgt/ttc/tct/ggt/tctcacc-3′
(SEQ ID NO: 71)
CDR3
(Ka3Tlon672):
5′-gacgagtccttct/aga/ttg/gaa/cct/gaa/gac/ttc/gct/gtt/tat/
tat/tgc/caa/c-3′ (SEQ ID NO: 72)
(Ka3BotL682)[RC]:
5′-act/ttc/ggt/caa/ggt/acc/aag/gtt/gaa/atc/aag/cgt/acg/
tcacaggtgag-3′ (SEQ ID NO: 73)
(Ka3Bsho694)[RC]:
5′-gaa/atc/aag/cgt/acg/tcacaggtgag-3′ (SEQ ID NO: 74)
(Ka3vg670):
5′-gac/ttc/gct/gtt/ -
/tat/tat/tgc/caa/cag/<3>/<1>/<1>/<1>/cct/<1>/act/ttc/ggt/caa/-
/ggt/acc/aag/gtt/g-3′ (SEQ ID NO: 75)
(Ka3v670-8):
5′-gac/ttc/gct/gtt/-
/tat/tat/tgc/caa/cag/<3>/<3>/<1>/<1>/<1>/cct/ttc/ggt/caa/-
/ggt/acc/aag/gtt/g-3′ (SEQ ID NO: 76)
(Ka3vg670-10):
5′-gac/ttc/gct/gtt/tat/-
/tat/tgc/caa/cag/<3>/<2>/<1>/<1>/cct/cct/<1>/act/ttc/ggt/caa/-
/ggt/acc/aag/gtt/g-3′ (SEQ ID NO: 77)
Lambda Chains: CDR1(“1”), CDR2(“2”), CDR3(“3”)
CDR1
(Lm1TPri75):
5′-gacgagtcctgg/tca/cct/ggt/-3′ (SEQ ID NO: 78)
(Lm1t1o715):
5′-gacgagtcctgg/tca/cct/ggt/caa/agt/atc/act/att/tct/tgt/aca/ggt-3′
(SEQ ID NO: 79)
(Lm1b1o724)[rc]:
5′-/gtt/tct/tgg/tat/caa/caa/cac/ccg/ggc/aag/gcg/agatcttcacaggtgag-3′
(SEQ ID NO: 80)
(Lm1bsh737)[rc]:
5′-gc/aag/gcg/agatcttcacaggtgag-3′ (SEQ ID NO: 81)
(Lm1vg710b):
5′-gt/atc/act/att/tct/tgt/aca/ggt/<2>/<4>/ctc/<4>/<4>/<4>/-
/<3>/<4>/<4>/tgg/tat/caa/caa/cac/cc-3′ (SEQ ID NO: 82)
(Lm1vg710):
5′-gt/atc/act/att/tct/tgt/aca/ggt/<1>/tct/tct/<2>/gtt/ggc/-
/<1>/<3>/<2>/<3>/gtt/tct/tgg/tat/caa/caa/cac/cc-3′ (SEQ ID NO: 83)
CDR2
(Lm2TSh757):
5′-gagcagaggac/ccg/ggc/aag/gc-3′ (SEQ ID NO: 84)
(Lm2TLo753):
5′-gagcagaggac/ccg/ggc/aag/gcg/ccg/aag/ttg/atg/atc/tac/-3′
(SEQ ID NO: 85)
(Lm2BLo762)[RC]:
5′-cgt/cct/tct/ggt/gtc/agc/aat/cgt/ttc/tcc/gga/tcacaggtgag-3′
(SEQ ID NO: 86)
(Lm2Bsh765)[RC]:
5′-cgt/ttc/tcc/gga/tcacaggtgag-3′ (SEQ ID NO: 87)
(Lm2vg750):
5′-g/ccg/aag/ttg/atg/atc/tac/-
<4>/<4>/<4>/<2>/cgt/cct/tct/ggt/gtc/agc/aat/c-3′ (SEQ ID NO: 88)
CDR3
(Lm3TSh822):
5′-ctg/cag/gct/gaa/gac/gag/gct/gac-3′ (SEQ ID NO: 89)
(Lm3TLo819):
5′-ctg/cag/gct/gaa/gac/gag/gct/gac/tac/tat/tgt/-3′ (SEQ ID NO: 90)
(Lm3BLo825)[RC]:
5′-gtc/ttc/ggc/ggt/ggt/acc/aaa/ctt/act/gtc/ctc/ggt/caa/cct/aag/g-
acacaggtgag-3′ (SEQ ID NO: 91)
(Lm3BSh832)[RC]:
5′ c/ggt/caa/cct/aag/gacacaggtgag (SEQ ID NO: 92)
(Lm3vg17):
5′-gac/gag/gct/gac/tac/tat/tgt/-
/<4>/<5>/<4>/<2>/<4>/tct/<4>/<4>/<4>/<4>/-
Gtc/ttc/ggc/ggt/ggt/acc/aaa/ctt/ac-3′ (SEQ ID NO: 93)
(Lm3vg817-10):
5′-gac/gag/gct/gac/tac/tat/tgt/-
/<5>/agc/tat/<1>/<5>/tct/<5>/<1>/<4>/gtc/ttc/ggc/ggt/ggt/-
/acc/aaa/ctt/ac-3′ (SEQ ID NO: 94)
TABLE 10
A27:JH1 Kappa light chain gene with stuffers in place of CDRs
Each stuffer contains at least one stop codon and a
restriction site that will be unique within the diversity vector.
gaggacc attgggcccc ctccgagact ctcgagcgca
Scab..... EcoO109I
ApaI. XhoI..
acgcaattaa tgtgagttag ctcactcatt aggcacccca ggctttacac tttatgcttc
..−35.. Plac ..−10.
cggctcgtat gttgtgtgga attgtgagcg gataacaatt tcacacagga aacagctatgac
catgatta cgccaagctt tggagccttt tttttggaga ttttcaac (SEQ ID NO: 95)
PflMI .............
Hind3.
M13 III signal sequence (AA seq)-------------------------->
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
M K K L L F A I P L V V P F Y
gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac
--Signal--> FR1--------------------------------------------
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
S H S A Q S V L T Q S P G T L
/agc/cat/agt/gca/caa/tcc/gtc/ctt/act/caa/tct/cct/ggc/act/ctt/
ApaLI...
----- FR1------------------- -------------->/---------Stuffer->
31 32 33 34 35 36 37 38 39 40 41 42 43
S L S P G E R A T L S / / (SEQ ID NO: 96)
/tcg/cta/agc/ccg/ggt/gga/cgt/gct/acc/tta/agt/tag/taa/gct/ccc/
(SEQ ID NO: 95; Cont'd)
EspI..... AflII...
XmaI....
- Stuffer for CDR1--> FR2 --------------- FR2--- >/ Stuffer for CDR2
59 60 61 62 63 64 65 66
K P G Q A P R
/agg/cct/ctt/tga/tct/g/aaa/cct/ggt/cag/gcg/ccg/cgt/taa/tga/aagcgctaatggccaacagtg
StuI... SexAI... KasI.... AfeI.. MscI..
Stuffer-->/--- FR3 ------------------------------------------>
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
T G I P D R F S G S G S G T D
(SEQ ID NO: 96; Cont'd)
/act/ggg/atc/ccg/gac/cgt/ttc/tct/ggc/tct/ggt/tca/ggt/act/gac/
(SEQ ID NO: 95; Cont'd)
BamHI...
RsrII............
--------FR3------>----------------STUFFER for CDR3------------------->
91 92 93 94 95 96 97
F T L T I S R / /
/ttt/acc/ctt/act/att/tct/aga/taa/tga/ gttaac tag acc tacgta acc tag
XbaI... HpaI.. SnaBI.
----------------------CDR3 stuffer---------------->/------FR4------->
118 119 120
F G Q
/ttc/ggt/caa/
-----FR4--------------------> <--------Ckappa -----------
121 122 123 124 125 126 127 128 129 130 131 132 133 134
G T K V E I K R T V A A P S
(SEQ ID NO: 96; Cont'd)
/ggt/acc/aag/gtt/gaa/atc/aag/ /cgt/acg/gtt/gcc/gct/cct/agt/
StyI.... BsiWI..
(SEQ ID NO: 95; Cont'd)
135 136 137 138 139 140 141 142 143 144 145 146 147 148 149
V F I F P P S D E Q L K S G T
(SEQ ID NO: 96; Cont'd)
/gtg/ttt/atc/ttt/cct/cct/tct/gac/gaa/caa/ttg/aag/tca/ggt/act/
MfeI...
acgcatctctaa gcggccgc aacaggaggag (SEQ ID NO: 95; Cont'd)
NotI....
EagI..
TABLE 11
2a2:JH2 Human lambda-chain gene with stuffers in place of CDR3
gaggaccatt gggcccc ttactccgtgac
Scab . . . EcoO109I
ApaI
----------FR1-------------- ------------------------------ >
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
S A Q S A L T Q P A S V S G S P G
agt/gca/caa/tcc/gct/ctc/act/cag/cct/gct/agc/gtt/tcc/ggg/tca/cct/ggt/
ApaLI . . . NheI . . . BstEll . . .
SexAI . . .
-------FR1----------------> /---------stuffer for CDR1 ---------
16 17 18 19 20 21 22 23
Q S I T I S C T (SEQ ID NO: 98)
/caa/agt/atc/act/att/tct/tgt/aca/tct tag tga ctc (SEQ ID NO: 97)
BsrGI..
----Stuffer----------------------------->--------FR2------->
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
R S / / P / H P G K A
aga tct taa tga ccg tag cac/ccg/ggc/aag/gcg/
BglII XmaI . . . KasI . . .
AvaI . . .
--/-------------Stuffer for CDR2--------------------------------->
P
/ccg/taa/tga/atc/tcg tac g ct/ggt/gtt/
KasI . . . BsiWI . . .
-------FR3------------------------------------------------
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
S N R F S G S K S G N T A S L (SEQ ID NO: 98; Cont'd)
/agc/aat/cgt/ttc/tcc/gga/tct/aaa/tcc/ggt/aat/acc/gca/agc/tta/ (SEQ ID NO: 97; Cont'd)
BseEI . . . HindIII . . .
BsaBI . . . (blunt)
------FR3------------->/--Stuffer for ORD3------------------>/
76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
T I S G L Q
/act/atc/tct/ggt/ctg/cag/gtt ctg tag ttc caattg ctt tag tga ccc
PstI . . . MfeI . . .
-----Stuffer------------------------------->/---FR4---------
103 104 105
G G G
/ggc/ggt/ggt/
KpnI . . .
--------FR4-------------->
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
T K L T V L G Q P K A A P S (SEQ ID NO: 98; Cont'd)
V/acc/aaa/ctt/act/gtc/ctc/ggt/caa/cct/aag/gct/gct/cct/tcc/gtt/ (SEQ ID NO: 97; Cont'd)
KpnI . . . HincII . . .
Bsu36I . . .
121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
T L F P P S S E E L Q A N K A
/act/ctc/ttc/cat/cct/agt/tct/gaa/gag/ctt/caa/gct/aac/aag/gct/
SapI . . .
136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
T L V C L I S D F Y P G A V T (SEQ ID NO: 98; Cont'd)
/act/cct/gtt/tgc/ttg/atc/agt/gac/ttt/tat/cct/ggt/gct/gtt/act/ (SEQ ID NO: 97; Con'td)
BclI . . .
The invention relates to generation of useful diversity in synthetic antibody (Ab) gene, especially to Ab genes having frameworks derived from human Abs.
BACKGROUND OF THE INVENTION Antibodies are highly useful molecules because of their ability to bind almost any substance with high specificity and affinity and their ability to remain in circulation in blood for prolonged periods as therapeutic or diagnostic agents. For treatment of humans, Abs derived from human Abs are much preferred to avoid immune response to the Ab. For example, murine Abs very often cause Human Anti Mouse Antibodies (HAMA) which at a minimum prevent the therapeutic effects of the murine Ab. For many medical applications, monoclonal Abs are preferred. Nowadays the preferred method of obtaining a human Ab having a particular binding specificity is to select the Ab from a library of human-derived Abs displayed on a genetic package, such as filamentous phage.
Libraries of phage-displayed Fabs and scFvs have been produced in several ways. One method is to capture the diversity of donors, either naive or immunized. Another way is to generate libraries having synthetic diversity. The present invention relates to methods of generating useful diversity in human Ab scaffolds.
As is well known, typical Abs consist of two heavy chains (HC) and two light chains (LC). There are several types of HCs: gamma, mu, epsilon, delta, etc. Each type has an N-terminal V domain followed by three or more constant domains. The LCs comprise an N-terminal V domain followed by a constant domain. LCs come in two types: kappa and lambda.
Within each V domain (LC or HC) there are seven canonical regions, named FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4, where “FR” stands for “Framework Region” and “CDR” stands for “Complementarity Determining Region”. For LC and HC, the FR and CDR GLGs have been selected over time to be secretable, stable, non-antigenic and these properties should be preserved as much as possible. Actual Ab genes contain mutations in the FR regions and some of these mutations contribute to binding, but such useful FR mutations are rare and are not necessary to obtain high-affinity binding. Thus, the present invention will concentrate diversity in the CDR regions.
In LC, FR1 up to FR3 and part of CDR3 comes from a genomic collection of genes called “V-genes”. The remainder of CDR3 and FR4 comes from a genomic collection of genes called “J-genes”. The joining may involve a certain degree of mutation, allowing diversity in CDR3 that is not present in the genomic sequences. After the LC gene is formed, somatic mutations can give rise to mature, rearranged LC genes that have higher affinity for an antigen (Ag) than does any LC encoded by genomic sequences. A large fraction of somatic mutations occur in CDRs.
The HC V region is more complicated. A V gene is joined to a J gene with the possible inclusion of a D segment. About half of HC Abs sequences contain a recognizable D segment in CDR3. The joining is achieved with an amazing degree of molecular sloppiness. Roughly, the end of the V gene may have zero to several bases deleted or changed, the D segment may have zero to many bases removed or changed at either end, a number of random bases may be inserted between V and D or between D and J, and the 5′ end of J may be edited to remove or change several bases. Withal, it is amazing that human heavy chains work, but they do. The upshot is that the CDR3 is highly diverse both in encoded amino-acid sequences and in length. In designing synthetic libraries, there is the temptation to just throw in a high degree of synthetic diversity and let the phage sort it out. Nevertheless, D regions serve a function. They cause the Ab repertoire to be rich in sequences that a) allow Abs to fold correctly, and b) are conducive to binding to biological molecules, i.e. antigens.
One purpose of the present invention is to show how a manageable collection of diversified sequences can confer these advantages on synthetic Ab libraries. Another purpose of the present invention is to disclose analysis of known mature Ab sequences that lead to improved designs for diversity in the CDR1 and CDR2 of HC and the three CDRs of lambda and kappa chains.
BRIEF STATEMENT OF THE INVENTION The invention is directed to methods of preparing synthetically diverse populations of Ab genes suitable for display on genetic packages (such as phage or phagemids) or for other regimens that allow selection of specific binding. Said populations concentrate the diversity into regions of the Ab that are likely to be involved in determining affinity and specificity of the Ab for particular targets. In particular, a collection of actual Ab genes has been analyzed and the sites of actual diversity have been identified. In addition, structural considerations were used to determine whether the diversity is likely to greatly influence the binding activity of the Ab. Schemes of variegation are presented that encode populations in which the majority of members will fold correctly and in which there is likely to be a plurality of members that will bind to any given Ag. Specifically, a plan of variegation is presented for each CDR of the human heavy chain, kappa light chain, and lambda light chain. The variegated CDRs are presented in synthetic HC and LC frameworks.
In one embodiment, the invention involves variegation of human HC variable domains based on a synthetic 3-23 domain joined to a JH4 segment in which the variability in CDR1 and CDR2 comprises sequence variation of segments of fixed length while in CDR3 there are several components such that the population has lengths roughly corresponding to lengths seen in human Abs and having embedded D segments in a portion of the longer segments. In the light chains, the kappa chain is built in an A27 framework and a JK1 while lambda is built in a 2a2 framework with an L2 J region.
EXAMPLES Choice of a Heavy-Chain V Domain The HC Germ-Line Gene (GLG) 3-23 (also known as VP-47) accounts for about 12% of all human Abs and it suitable for the framework of the library. Certain types of Ags elicit Abs having particular types of VH genes; in some cases, the types elicited are otherwise rarely found. This apparent Ag/Ab type specificity has been ascribed to possible structural differences between the various families of V genes. It is also possible that the selection has to do with the availability of particular AA types in the GLG CDRs. Suppose, for example, that the sequence YR at positions 4 and 5 of CDR2 is particularly effective in binding a particular type of Ag. Only the V gene 6-1 provides this combination. Most Abs specific for the Ag will come from GLG 6-1. If Y4-R5 were provided in other frameworks, then other frameworks are likely to be as effective in binding the Ag.
Analysis of HC CDR1 and CDR2: In CDR1 and CDR2 of HCs, the GLGs provide limited length diversity as shown in Table 15P. Note that GLGs provide CDR's only of the lengths 5, 6, and 7. Mutations during the maturation of the V-domain gene leads to CDR's having lengths as short as 2 and as long as 16. Nevertheless, length 5 predominates. The preferred length for the present invention is 5 AAs in CDR1 with a possible supplemental components having lengths of 7 and 14.
GLGs provide CDR2s only of the lengths 15-19, but mutations during maturation result in CDR2s of length from 16 to 28 AAs. The lengths 16 and 17 predominate in mature Ab genes and length 17 is the most preferred length for the present invention. Possible supplementary components of length 16 and 19 may also be incorporated.
Table 20P shows the AA sequences of human GLG CDR1s and CDR2. Table 21P shows the frequency of each amino-acid type at each position in the GLGs. The GLGs as shown in Table 20P have been aligned by inserting gaps near the middle of the segment so that the ends align.
The 1398 mature V-domain genes used in studying D segments (vide infra) were scanned for examples in which CDR1 and CDR2 could be readily identified. Of this sample 1095 had identifiable CDR1, 2, and 3. The CDRs were identified by finding subsequences of the GLGs in an open reading frame. There are 51 human HC V genes. At the end of FR1, there are 20 different 9-mers. At the start of FR2, there are 11 different 9-mers. At the end of FR2 there are 14 different 9-mers. At the start of FR3, there are 14 different 9-mers. At the end of FR3, there are 13 different 9-mers. At the start of JH, there are three different 9-mers. These motifs were compared to the reported gene in frame and a match, at the site of maximum similarity, of seven out of nine was deemed acceptable. Only when all three CDRs were identified were any of the CDRs included in the analysis. In addition, the type of the gene was determined by comparing the framework regions to the GLG frameworks; the results are shown in Table 22P.
Design of HC CDR1 and CDR2 Diversity. Diversity in CDR1 and CDR2 was designed from: a) the diversity of the GLGs, b) observed diversity in mature HC genes, and c) structural considerations. In CDR1, examination of a 3D model of a humanized Ab showed that the side groups of residues 1, 3, and 5 were directed toward the combining pocket. Consequently, we allow each of these positions to be any amino-acid type except cysteine. Cysteine can form disulfide bonds. Disulfide bonds are an important component of the canonical Ig fold. Having free thiol groups could interfere with proper folding of the HC and could lead to problems in production or manipulation of selected Abs. Thus, I exclude cysteine from the menu. The side groups of residue 2 is directed away from the combining pocket. Although this position shows substantial diversity, both in GLG and mature genes, I fixed this residue as Tyr because it occurs in 681/820 mature genes (Table 21P). Position 4 is fixed as Met. There is some diversity here, but almost all mature genes have uncharged hydrophobic AA types: M, W, I, V, etc. (Table 21P). Inspection of a 3D model shows that the side group of residue 4 is packed into the innards of the HC. Since we are using a single framework (3-23), we retain the Met that 3-23 has because it is likely to fit very well into the framework of 3-23. Thus, the most preferred CDR1 library consists of XYXMX (SEQ ID NO:109) where X can be any one of [A,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y] (no C). The DNA that encodes this is preferably synthesized using trinucleotide building blocks so that each AA type is present in essentially equimolar amounts. Specifically, the X codons are synthesized using a mixture of the codons [gct, gat, gag, ttt, ggt, cat, att, aag, atg, aat, cct, cag, cgt, tct, act, gtt, tgg, tat]. This diversity is shown in the context of a synthetic 3-23 gene in Table 18P. The diversity oligonucleotide (ON) is synthesized from BspEI to BstXI and can be incorporated either by PCR synthesis using overlapping ONs or introduced by ligation of BspEI/BstXI-cut fragments. Table 22P shows ONs that embody the specified variegation. PCR using ON-R1V1vg, ON-R1top, and ON-R1bot gives a dsDNA product of 73 base pairs, cleavage with BspEI and BstXI trims 11 and 13 bases from the ends and provides cohesive ends that can be ligated to similarly cut vector having the synthetic 3-23 domain shown in Table 18P. Replacement of ON-R1V1vg with either ONR1V2vg or ONR1V3vg allows synthesis of the two alternative diversity patterns given below.
Alternatively, one can include CDR's of length 7 and/or 14. For length 7, a preferred diversity is (S/T)1(S/G/x)2(S/G/x)3Y4Y5W6(S/G/x)7 (SEQ ID NO:107); where (S/T) indicates an equimolar mixture of Ser and Thr codons; (S/G/x) indicates a mixture of 0.2025 S, 0.2025 G, and 0.035 for each of A, D, E, F, H, I, K, L, M, N, P, Q, R, T, V, W, Y. Other proportions could be used. The design gives a predominance of Ser and Gly at positions 2, 3, and 7, as occurs in mature HC genes. For length 14, a preferred pattern of diversity is VSGGSISXXXYYWX (SEQ ID NO:1) where X can be any AA type except Cys. This pattern appears to arise by insertions into the GLG sequences (SGGYYWS; SEQ ID NO:110, (4-30.1 and 4-31) and similar sequences. There is a preference for a hydrophobic residue at position 1 (V or C) with a second insertion of SISXXX (SEQ ID NO:111) between GG and YY. Diversity ONs having CDR1s of length 7 or 14 are synthesized from BspEI to BstXI and introduced into the library in appropriate proportions to the CDR1 of length 5. The components should be incorporated in approximately the ratios in which they are observed in antibodies selected without reference to the length of the CDRs. For example, the sample of 1095 HC genes examined here have them in the ratios (L=5:L=7:L=14::820:175:23::0.80:0.17:0.02).
CDR2 Diversity at CDR2 was designed with the same considerations: GLG sequences, mature sequences and 3D structure. A preferred length for CDR2 is 17, as shown in Table 18P. Examination of a 3D model suggests that the residues shown as varied in Table 18P are the most likely to interact directly with Ag. Thus a preferred pattern of variegation is: <2>I<2><3>SGG<1>T<1>YADSVKG (SEQ ID NO:2), where <2> indicates a mixture of YRWVGS, <3> is a mixture of P and S, and <1> is a mixture of ADEFGHIKLMNPQRSTVWY (no C). ON-R2V1vg shown in Table 22P embodies this diversity pattern. PCR with ON-R2V1vg, ON-R2top, and ONR2bot gives a dsDNA product of 122 base pairs. Cleavage with BstXI and XbaI removes about 10 bases from each end and produces cohesive ends that can be ligated to similarly cut vector that contains the 3-23 gene shown in Table 18P.
An alternative pattern would include the variability seen in mature CDR2s as shown in Table 21P: <1>I<4><1><1>G<5><1><1><1>YADSVKG (SEQ ID NO:3), where <4> indicates a mixture of DINSWY, and <5> indicates a mixture of SGDN. This diversity pattern is embodied in ON-R2V2vg shown in Table 22P. For either case, the variegated ONs would be synthesized so that fragments of dsDNA containing the BstXI and XbaI site can be generated by PCR. ON-R2V2vg embodies this diversity pattern.
Alternatively, one can allow shorter or longer CDR2s. Table 22P shows ON-R2V3vg which embodies a CDR2 of length 16 and ON-R2V4vg which embodies a CDR2 of length 19. Table 22P shows ON-R2V3vg is PCR amplified with ON-R2top and ON-R2bo3 while ON-R2V4vg is amplified with ON-R2top and ONR2-bo4.
Analysis of HC CDR3: CDR3s of HC vary in length and in sequence. About half of human HCs consist of the components: V::nz::D::ny::JHn where V is a V gene, nz is a series of bases (mean 12) that are essentially random, D is a D segment, often with heavy editing at both ends, ny is a series of bases (mean 6) that are essentially random, and JH is one of the six JH segments, often with heavy editing at the 5′ end. In HCs that have no identifiable D segment, the structure is V::nz::JHn where JH is usually edited at the 5′ end. Our goal is to mimic the diversity of CDR3, but not to duplicate it (which would be impossible). The D segments appear to provide spacer segments that allow folding of the IgG. The greatest diversity is at the junctions of V with D and of D with JH. The planned CDR3 library will consist of several components. Some of these will have only sequence diversity. Others will have sequence diversity with embedded D segments to extend the length while incorporating sequences known to allow Igs to fold.
There are many papers on D segments. Corbett et al. (1997) show which D segments are used in which reading frames. My analysis basically confirms their findings. They did not report, however, the level of editing of each D segment and this information is needed for design of an effective library.
The following diversified sequences would be incorporated in the indicated proportions: “1” stands for 0.095 [G, Y] and 0.048 [A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W]; double dose of Gly and Tyr plus all other AAs except Cys at equal level.
The amount of each component is assigned from the tabulation of lengths of the collection of natural VH genes. Component 1 represents all the genes having length 0 to 8 (counting from the YYCAR (SEQ ID NO:112) motif to the WG dipeptide motif). Component 2 corresponds the all the chains having length 9 or 10. Component 3 corresponds to the genes having length 11 or 12 plus half the genes having length 13. Component 4 corresponds to those having length 14 plus half those having length 13. Component 5 corresponds to the genes having length 15 and half of those having length 16. Component 6 corresponds to genes of length 17 plus half of those with length 16. Component 7 corresponds to those with length 18. Component 8 corresponds to those having length 19 and greater.
The composition has been adjusted because the first component is not complex enough to justify including it as 10% of the library. If the final library were to be 1. E 9, then 1. E 8 sequences would come from component 1, but it has only 2.6 E 5 CDR3 sequences so that each one would occur in ˜385 CDR1/2 contexts. I think it better to have this short CDR3 diversity occur in ˜77 CDR1/2 contexts and have the other, longer CDR3s occur more often.
The ONs would be PCR amplified with the primers CtprmA and CBprmB, cut with AflII and BstEII, and ligated to similarly cut V3-23.
This set of components was designed after studying the sequences of 1383 human HC sequences as described below. The proposed components are meant to fulfill the goals:
1) approximately the same distribution of lengths as seen in real Ab genes,
2) high level of sequence diversity at places having high diversity in real Ab genes, and
3) incorporation of constant sequences often seen in real Ab genes.
Note that the design uses JH4 (YFDYWGQGTLVTVSS; SEQ ID NO:20), which is found more often, instead of JH3 (AFDIWGQGTMVTVSS; SEQ ID NO:21). This involves three changes in AA sequence, shown as double underscored bold. An alternative JH segment is shown.
How the Library Components were Designed:
The processing of sequence data was accomplished by a series of custom-written FORTRAN programs, each of which carries out a fairly simple transformation on the data and writes its results as one or more ASCII files. The next program then uses these files as input.
A set of 2049 human heavy-chain genes was selected from the version of GenBank that was available at Dyax on the Sun server on 26 Jun. 2000. A program named “Reformat” changed the format of the files to that of GenBank from the GCG format, creating one file per sequence. A second program named “IDENT_CDR3” processed each of these files as follows. Files were tested for duplication by previous entries, duplicates were discarded. Each reading frame was tested. Most entries had a single open reading frame (ORF), none had two, and some had none. Entries with multiple stops in every reading frame were discarded because this indicates poor quality of sequencing. The sequence was written in triplets in the ORF or in all three reading frames if no ORF was found. The sequence was examined for three motifs: a) AA sequence=“YYCxx”, b) DNA sequence=“tgg ggc (=WG)”, and DNA sequence=“g gtc acc (=BstEII)”. FR3 ends with a conserved motif YYCAR or a close approximation. When writing the DNA sequence, IDENT_CDR3 prints the DNA mostly in lower case. Cysteine codons (TGT or TGC) are printed in uppercase. When the motif “tay tay tgy” is found, IDENT_CDR3 starts a new line that contains “< > xxx xxx xxx xxx xxx” where the xxx's stand for the actual five codons that encode YYC and the next two codons (most often AR or AK). The following DNA is printed in triplets on new lines. A typical processed entry appears as in Table 1P.
Following the YYC motif, IDENT_CDR3 seeks the sequence “TGG GGC” (the “WG” motif) in the correct reading frame, 5/6 bases is counted as a hit. If found, the DNA is made uppercase. Following the WG motif (if found) or the YYC motif (if no WG found), IDENT_CDR3 seeks the sequence “G GTC ACC” (the BstEII site) in the correct reading frame, 6/7 bases is counted as a hit. If found, the bases are made upper case. If either the WG or BstEII motif are not found, a note is inserted saying that the feature was not identified. The output of IDENT_CDR3 was processed by hand. In many cases, the lacking YYC motif could be seen as a closely related sequence, such as YFC, FYC, or HYC. When this was supported by an appropriately positioned WG and/or BstEII site, the effective YYC site was marked and the sequence retained for further analysis. If the YYC motif could not be identified or if the WG or BstEII sites could not be found, the entry was discarded. For example, the entry in Table 2P had no YYC motif.
The double underscored sequence encodes YHCAS and is taken as the end of FR3. Note that there is a WG motif at bases 403-408 (bold upper case) and a BstEII site at bases 420-426 (bold upper case). Using WordPerfect, I first made all occurrences of TGC and TGT bold. I then searched for “YYC not found”. If I could see the “YYC”-related sequence quickly, I edited the entry so that a YYC was shown. The entry above would be converted to that shown in Table 3P. This processing reduced the list of entries to 1669.
A third program named “New_DJ” processed the output of IDENT_CDR3. The end of the YYC motif (including the two codon following TGy=Cys) was taken as the end of FR3. The WG motif was taken as the end of the region that might contain a D segment. If WG was not observed and BstEII was, the WG site was assumed to be 17 bases upstream of BstEII. Using the WG motif for alignment, the sequence was compared to each human GLG JH segment (1-6) and the best one identified (New_DJ always assigned a JH segment). Starting from the WG motif of JH and moving toward the 5′ end, the program looked for the first codon having more than one mismatch. The region from YYCxx (SEQ ID NO:113) to this codon was taken as the region that might contain a D segment.
The region that might contain a D segment was tested against all the germ-line genes (GLGs) of human D segments and the best D segment was identified. The scoring involved matching the observed sequence to the GLG sequence in all possible ways. Starting at each base, multiply by 4 for a match and divide by 4 for a mismatch. Record the maximum value obtained for this function. The match was deemed significant if 7/7, 8/9, 9/11, etc. or more bases matched. Of the 1383 sequences examined for D segments,
“Assign_D” processes the output of New_DJ. For each sequence that had a significant match with a GLG D segment, a file was written containing the putative D segment, the DJ segment, the identified GLG D segment, the identified JH segment, the phase of the match between observed and GLG gene. For example, “D1_1-01_Phz0_hsa239356.txt” is a file recording the match of entry hsa239356 with D1-01 in phase 0. The file contains the information shown in Table 4P. The final DV of the second sequence immediately precedes the WG in JH and is ascribed to JH3. Other files that begin D1_1-01_Phz0 match the same GLG D segment and these can be aligned by sliding amino-acid sequences across each other.
Table 5P shows how sequence hs6d4xb7 is first assigned to JH4 and then to D3-22. Note that the DNA sequence TGGGGG is aligned to the TGG GGC of the GLG and that the sequence is truncated on the left to fit. The program finds that JH4 has the best fit (5 misses and 18 correct out of 23). From the right, the program sees that DYWGQ (underscored) come from JH, but then the match drops off and the rest of the sequence on the left comes either from added bases or a D segment.
The lower part of Table 5P shows that the possible D segment matches D #13 (3-23) is a very good match.
Of 1383 files accepted by Assign_D, 757 had identifiable D segments. The tally of His in Table 6P shows that JH4 is by far the most common.
JH4 is most common, JH6 next, followed by JH3 and JH5. JH1 and JH2 are seldom used. Table 7P shows the length distributions of each JH class; they do not differ significantly class to class. These lengths count only amino-acids that are not accounted for by JH and so are shorter that the lengths given in Table 8P which cover from YYCAR (SEQ ID NO:112) to WG.
Table 8P contains the distribution of lengths for a) all the CDR3 segments, b) the CDR3 segments with identified D segments, and c) the CDR3 segments having no identifiable D segment. The CDR3s with identifiable D segments (13.9) are systematically longer than are those that lack D segments (11.2).
The identified CDR3 segments can be collated in two ways: aligned to the left (looking for a pattern following YYCAR; SEQ ID NO:112) or aligned to the right (looking for a pattern preceding WG). Table 9P shows the collation of left-aligned sequences while Table 10P shows the right-aligned sequences. For each position, I have tabulated the frequency of each AA type (A-M in the first block and N-Y in the second). The column headed “#” shows how many sequences have some AA at that position. The final column shows all of the AA types seen at that position with the most frequent first and the least frequent last. In the left-aligned sequences, we see that Gly is highly over-represented in the first seven positions while Tyr is over-represented at positions 8-16.
In Table 11P, I have tabulated the AA frequencies for the sequences having between 7 and 15 AAs between YYCAR (SEQ ID NO:112)_and WG. The last four positions can be viewed as coming from JH and so would be given lower levels of diversity than would earlier positions. From these tabulations, I conclude that most AA types are allowed at all the positions, but there is a fairly strong tendency to have Gly at the early positions and to end in Asp-Tyr (DY). We could use these tendencies in designing a pattern of variegation. I would not exclude any AA except Cys, but I might increase the frequency of Gly in the first several positions and Tyr in the last few.
There are 80 sequences (5.8%) having a pair of cysteines in CDR3. It is more surprising that 53 (3.8%) have a single Cys in CDR3.
MS-DOS was used to make a list of the files written by Assign_D. “Filter” converts the output of MS-DOS Dir into a form that can be read into WordPerfect and sorted to bring a files belonging to the same D region together.
“Filter2” collects the sequences and produces a draft table of sequences, grouped by the D-segment used, and written so that the sequences can be aligned. The output of Filter2 were edited by hand. For each group, the translation of the GLG was inserted and the collection of observed sequences was aligned to the conserved part of the GLG. “Filter3” collated the aligned sequences. Table 12P shows an example of an alignment and the tabulation of AA types. The entries are as follows: “Entry” is the name used in the data base, “Seq1” is the sequence from the YYCAR (SEQ ID NO:112) motif to the first amino acid not assigned to JH and “L1” is the length of the segment. The segments are shown aligned to the identified D segment. Seq2 is the sequence from the YYCAR (SEQ ID NO:112) motif to the WG motif (i.e. including part of JH) and “L2” is the length of that sequence. JH is the identified JH segment for this sequence. “P” is the phase of the match. For positive values of P, P bases are found in the observed sequence that do not correspond to any from the GLG, i.e. the observed sequence has had that many bases inserted. For negative values of P, there are |P| bases in the GLG sequence for which there are no corresponding bases in the observed sequence. “Score” is approximately 1/(probability of accidental match). This is calculated by looking at all possible alignments. For each alignment, the score is first set to 1.0. Base by base, the score is multiplied by 4. if the bases match and divided by 4. if they do not. This is done for all starting points and ending points and the maximum value is recorded.
Table 13P is a summary of how often each D segment was identified and in which reading frame. I have not been consistent with Corbett et al. in assigning the phases of the GLG D segments. The MRC Web page that I took the GLGs from did not have D segments D1-14, D4-11, D5-18, or D6-25. None of these contribute to any great extent and this omission is unlikely to have any serious effect on the conclusions. The column headed “%” contains the percentage of the sequences examined here. The column headed “C %” contains the percentage reported by Corbett et al. I assume that the data used in Corbett et al. is mostly included in my collection. Nevertheless, the observed frequencies differ in detail. For example, my compilation shows that 10.7% of the collection contains a D segment encoding two cysteines while they have only 4.16% in this category. In D3 phase “0”, I see 19.4% of the collection while they report 11.8%.
The most common actual D segments were further analyzed. The GLGs are heavily edited at either end. The aligned sequences were aligned. For each D-segment having more than seven examples, Filter3 produced a table of the frequency of each amino-acid type at each position. From these tabulations, library components shown in Table 17P were designed. At each position where at least half the examples have an amino acid, I entered either the dominant AA type or “x”. An AA type was “dominant” if it occurred more than 50% of the time. L is the length and f is the number of sequences observed that have related sequences.
Table 14P shows possible library components for a library of CDR3's. “L” is the length of the insert and “f” is the frequency of the motif in the assayed collection. Table 17P shows vgDNA that embodies each of the components shown in Table 14P. In Table 17P, the oligonucleotides (ON) Ctop25, CtprmA, CBprmB, and CBot25 allow PCR amplification of each of the variegated ONs (vgDNA): C1t08, C2t10, C3t12, C4t14, C5t15, C6t17, C7t18, and c8t19. After amplification, the dsDNA can be cleaved with AflII and BstEII (or KpnI) and ligated to similarly cleaved vector that contains the remainder of the 3-23 synthetic domain. Preferably, this vector already contains diversity in CDR1 and CDR2 as disclosed herein. Preferably, the recipient vector contains a stuffer in place of CDR3 so that there will be no parental sequence that would then occur in the resulting library. Table 50P shows a version of the V3-23 gene segment with each CDR replaced by a short segment that contains both stop codons and restriction sites that will allow specific cleavage of any vector that does not have the stuffer removed. The stuffer can either be short and contain a restriction enzyme site that will not occur in the finish library, allowing removal of vectors that are not cleaved by both AflII and BstEII (or KpnI) and religated. Alternatively, the stuffer could be 200-400 bases long so that uncleaved or once cleaved vector can be readily separated from doubly cleaved vector.
In the vgDNA for HC CDR3, <1> means a mixture comprising 0.27 Y, 0.27 G, and 0.027 of each of the amino-acid codons {A, D, E, F, H, I, K, L, M, N, P, Q, R, S, T, V, W}; <2> means an equimolar mixture of K and R; and <3> means an equimolar mixture of S and G.
Analysis of Human Kappa Light Chains and Preferred Variegation Scheme: A collection of 285 human kappa chains was assembled from the public data base. Table 27 shows the names of the entries used. The GLG sequences of nine bases at each end of the framework regions were used to find the FR/CDR junctions. Only in cases where all six junctions could be found was the sequences included. Table 25P shows the distribution of lengths in CDRs in human kappas. CDR1s with lengths of 11, 12, 13, 16, and 17 were observed with 11 being predominant and 12 well represented. CDR2 exhibits only length 7. CDR3 exhibits lengths of 1, 4, 6, 7, 8, 9, 10, 11, 12, 13, and 19. Essentially all examples are in the 8, 9, or 10 length groups. Table 26P shows the distribution of V and J genes seen in the sample. A27 is the most common V and JK1 is the most common J. Thus, a suitable synthetic kappa gene comprises A27 joined to JK1. Table 30P shows a suitable synthetic kappa chain gene, including a PlacZ promoter, ribosome-binding site, and signal sequence (M13 III signal). The DNA sequence encodes the GLG amino-acid sequence, but does not comprise the GLG DNA sequence. Restriction sites are designed to fall within each framework region so that diversity can be cloned into the CDRs. XmaI and EspI are in FR1, SexAI is in FR2, RsrII is in FR3, and KpnI (or Acc65I) are in FR4. Additional sites are provided in the constant kappa chain to facilitate construction of the gene.
Table 30P also shows a suitable scheme of variegation for kappa. In CDR1, a preferred length is 11 codons. The A27 GLG has a CDR1 of 12 codons, but the sample of mature kappa chains has length 11 predominating. One could also introduce a component of kappas having length 12 in CDR1 by introducing codon 52 as <2> (i.e. a Ser-biased mixture). CDR2 of kappa is always 7 codons. Table 31P shows a tally of 285 CDR2s and a preferred variegation scheme for CDR2. The predominant length of CDR3 in kappa chains is 9 codons. Table 32P shows a tally of 166 CDR3s from human kappas and a preferred variegation scheme (which is also shown in Table 30P).
Analysis of Lambda Chains and Preferred Variegation Scheme: A collection of 158 lambda sequences was obtained from the public data base. Of these 93 contained sequences in which the FR/CDR boundaries could be identified automatically. Table 33P shows the distribution of lengths of CDRs.
Method of Construction: The diversity of HC, kappa, and lambda are best constructed in separate vectors. First a synthetic gene is designed to embody each of the synthetic variable domains. The light chains are bounded by restriction sites for ApaLI (positioned at the very end of the signal sequence) and AscI (positioned afer the stop codon). The heavy chain is bounded by SfiI (positioned within the PelB signal sequence) and NotI (positioned in the linker between CH1 and the anchor protein. The initial genes are made with “stuffer” sequences in place of the desired CDRs. A “Stuffer” is a sequence the is to be cut away and replaced by diverse DNA but which does not allow expression of a functional antibody gene. For example, the stuffer may contain several stop codons and restriction sites that will not occur in the correct finished library vector. In Table 40P, the stuffer for CDR1 of kappa A27 contains a StuI site. The vgDNA for CDR1 is introduced as a cassette from EspI, XmaI, or AflII to either SexAI or KasI. After the ligation, the DNA is cleaved with StuI; there should be no StuI sites in the desired vectors.
REFERENCES
- Corbett, S J, Tomlinson, I M, Sonnhammer, E L L, Buck, D, Winter, G. “Sequences of the Human Immunoglobulin Diversity (D) Segment Locus: A Systematic Analysis Provides No Evidence for the Use of DIR Segments, Inverted D Segments, ‘Minor’ D Segments or D-D Recombination”. J Molec Biol (1997) 270:587-597.
TABLES TABLE 1P
Typical entry in which YYC motif is found.
++++C: \tmp\haj10335.txt
LOCUS HAJ10335 306 bp mRNA PRI 18-AUG-1998
DEFINITION Homo sapiens mRNA for immunoglobulin heavy chain variable region,
clone ELD16/6.
ACCESSION AJ010335
VERSION AJ010335.1 GI: 3445266
Ngene = 306
Stop codons in reading frame 1
49 115 124 253 277
No stops in reading frame 2
Stop codons in reading frame 3
12 60 81 147 204 213
1 t ttg ggg tcc ctg aga ctc tcc TGT gca gcc tct gga ttc acc
44 gtc agt agc aac tac atg acc tgg gtc cgc cag gct cta ggg aag
89 ggg ctg gag tgg gtc tca gtt att tat agc ggt ggt agc aca tac
134 tac gca gac tcc gtg aag ggc gga ttc acc atc tcc aga gac aat
179 tcc aag aac aca ctg tat ctt caa atg aac agc ctg aga ccc gag
224 gac acg gct gtg
< > TAT TAC TGT gcg aca
251 ggt aat cgc ctg gaa atg gct gca att aac TGG GGC caa gga acc
263 ctG GTC ACC aa (SEQ ID NO: 113)
-----------------------------------------------------------------------------
TABLE 2P
entry in which YYC motif was not automatically identified
++C: \tmp\hs202g3.txt
!!NA_SEQUENCE 1.0
LOCUS HS202G3 522 bp mRNA PRI 03-AUG-1995
DEFINITION H. sapiens mRNA for immunoglobulin variable region (clone 202-G3).
ACCESSION Z47259
VERSION Z47259.1 GI: 619470
Ngene = 522
No stops in reading frame 1
Stop codons in reading frame 2
89 110 305 314
Stop codons in reading frame 3
84 192 321 351 369
1 atg gac tgg acc tgg agg ttc ctc ttt gtg gtg gca gca gct aca
46 ggt gtc cag tcc cag gtg cag ctg gtg cag tct ggg gct gag gtg
91 aag aag cct ggg tcc tcg gtg aag gtc tcc TGC aag gct tct gga
136 ggc acc ttc agc agc tat gct atc agc tgg gtg cga cag gcc cct
181 gga caa ggg ctt gag tgg atg gga ggg atc atc cct atc ttt ggt
226 aca gca aac tac gca cag aag ttc cag ggc aga gtc acg att acc
271 gcg gac gaa tcc acg agc aca gcc tac atg gag ctg agc agc ctg
316 aga tct gag gac acg gcc gtg tat cac TGT gcg agt gag gga tgg
361 gag agt TGT agt ggt ggt ggc TGC tac gac ggt atg gac gtc TGG
406 GGC caa ggg acc acG GTC ACC gtc tcc tca gct tcc acc aag ggc
451 cca tcg gtc ttc ccc ctg gcg ccc TGC tcc agg agc acc tct ggg
496 ggc aca gcg gcc ctg ggc TGC ctg (SEQ ID NO: 114)
YYC not found !!!
-----------------------------------------------------------------------------
TABLE 3P
Entry of Table 2P after editting.
++C: \tmp\hs202g3.txt
!!NA_SEQUENCE 1.0
LOCUS HS202G3 522 bp mRNA PRI 03-AUG-1995
DEFINITION H. sapiens mRNA for immunoglobulin variable region (clone 202-G3).
ACCESSION Z47259
VERSION Z47259.1 GI: 619470
Ngene = 522
No stops in reading frame 1
Stop codons in reading frame 2
89 110 305 314
Stop codons in reading frame 3
84 192 321 351 369
1 atg gac tgg acc tgg agg ttc ctc ttt gtg gtg gca gca gct aca
46 ggt gtc cag tcc cag gtg cag ctg gtg cag tct ggg gct gag gtg
91 aag aag cct ggg tcc tcg gtg aag gtc tcc TGC aag gct tct gga
136 ggc acc ttc agc agc tat gct atc agc tgg gtg cga cag gcc cct
181 gga caa ggg ctt gag tgg atg gga ggg atc atc cct atc ttt ggt
226 aca gca aac tac gca cag aag ttc cag ggc aga gtc acg att acc
271 gcg gac gaa tcc acg agc aca gcc tac atg gag ctg agc agc ctg
316 aga tct gag gac acg gcc gtg
<YHCAS> tat cac TGT gcg agt
(SEQ ID NO: 116)
gag gga tgg
361 gag agt TGT agt ggt ggt ggc TGC tac gac ggt atg gac gtc TGG
406 GGC caa ggg acc acG GTC ACC gtc tcc tca gct tcc acc aag ggc
451 cca tcg gtc ttc ccc ctg gcg ccc TGC tcc agg agc acc tct ggg
496 ggc aca gcg gcc ctg ggc TGC ctg (SEQ ID NO: 115)
YYC not found !!!
-----------------------------------------------------------------------------
TABLE 4P
contents of file D1_1-01_Phz0_hsa239356.txt
SRGGKYQLAPKGGM (SEQ ID NO: 117)
DRGGKYQLAPKGGMDV (SEQ ID NO: 118)
JH3 D# 1 Phase 15 Score 6.55D + 04
-----------------------------------------------------------------------------
TABLE 5P
alignment of a CDR3::JH segment to GLG JHs and D-segments.
+c:\tmp\hs6d4xb7.text
1 1 2 2 3 3 3
1234567890 5 0 5 0 5 9
Observed tatgatagtagtgggtcatactccgactacTGGGGGcag (SEQ ID NO: 119)
JH1 ------------gctgaatacttccagcactggggccagggcaccctggtcaccgtctcctcag--(SEQ ID NO: 120)
Miss = 9 Nt = 27
JH2 -----------ctactggtacttcgatctctggggccgtggcaccctggtcactgtctcctcag--(SEQ ID NO: 121)
Miss = 13 Nt = 28
JH3 --------------tgatgcttttgatatctggggccaagggacaatggtcaccgtctcttcag--(SEQ ID NO: 122)
Miss = 14 Nt = 25
JH4 ----------------actactttgactactggggccagggaaccctggtcaccgtctcctcag--(SEQ ID NO: 123)
Miss = 5 Nt = 23
JH5 -------------acaactggttcgacccctggggccagggaaccctggtcaccgtctcctcag--(SEQ ID NO: 124)
Miss = 11 Nt = 26
JH6 -attactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcag--(SEQ ID NO: 125)
Miss = 23 Nt = 38
4 tat gat agt agt ggg tca TAC Tcc GAC TAC TGG GGg CAG (SEQ ID NO: 126)
Y D S S G S Y S D Y W G Q (SEQ ID NO: 127)
JH4 --- --- --- --- --- -ac tac ttt gac tac tgg ggc cag gga acc ctg gtc acc gtc tcc tca g--
(SEQ ID NO: 128)
- - - - - - Y F D Y W G Q G T L V T V S S -(SEQ ID
NO: 129)
Fract = 0.783 = 18 / 23
Matching the rest to D segments:
D#13 --------gtattactatgatagtagtggttattactac GLG (SEQ ID NO: 130)
gatcgccacaattactatgatagtagtgggtcatactcc Observed (SEQ ID NO: 131)
--------gt...................t.at....a. . = match
D#13 Phase = 9 Score = 4.3980E+12
TABLE 6P
Number of sequences identified as having JH derived
from GLG JHn
JH 1 2 3 4 5 6
# sequences 17 40 198 707 160 261
TABLE 7P
Distribution of CDR3 fragments that might contain D segments.
For JH1
0 1 2 3 4 5 6 7 8 9 10 11 12 13
0 0 1 1 3 1 1 2 0 3 1 1 1 2
Total = 17 Median = 8.0
For JH2
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
0 0 0 0 0 2 4 6 2 6 3 4 5 2 3
15 16 17 18
2 0 0 1
Total = 40 Median = 9.0
For JH3
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
0 0 2 6 16 12 17 17 15 22 20 20 18 13 4
15 16 17 18 19
8 3 2 1 2
Total = 198 Median = 8.6
For JH4
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
0 0 7 15 19 40 63 82 81 77 81 53 57 44 30
15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
15 23 8 3 5 2 0 1 0 0 0 0 0 0 0
30 31 32 33 34 35
0 0 0 0 0 1
Total = 707 Median = 8.6
For JH5
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
0 0 0 3 4 6 13 19 12 14 22 18 10 18 10
15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
5 1 1 0 0 1 1 0 0 0 0 0 0 0 0
30 31 32 33 34 35 36 37 38 39 40 41 42 43 44
0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
45 46
0 1
Total = 160 Median = 9.4
For JH6
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
2 0 1 2 5 15 20 18 22 29 29 28 23 16 10
15 16 17 18 19 20
14 9 9 4 2 3
Total = 261 Median = 9.6
TABLE 8P
Lengths of CDR3 segments from YYCAR to WG.
Distribution of lengths from end of FR3 to WG motif all sequences.
L 0 1 2 3 4 5 6 7 8 9 10
N 6 0 0 4 2 9 13 38 61 88 101
Sum(N) 6 6 6 10 12 21 34 72 133 221 322
f .004 .004 .004 .007 .009 .015 .025 .052 .096 .160 .233
L 11 12 13 14 15 16 17 18 19 20 21
N 118 154 150 118 125 105 84 61 46 42 16
SN 440 594 744 862 987 1092 1176 1237 1283 1325 1341
f .318 .430 .538 .623 .714 .790 .850 .894 .928 .958 .970
L 22 23 24 25 26 27 28 29 30 31 32
N 17 7 9 2 1 0 2 1 0 0 0
SN 1358 1365 1374 1376 1377 1377 1379 1380 1380 1380 1380
f .982 .987 .993 .995 .996 .996 .997 .998 .998 .998 .998
L 33 34 35 36 37 38 39 40 41 42 43
N 0 0 0 0 1 0 0 0 0 1 0
SN 1380 1380 1380 1380 1381 1381 1381 1381 1381 1382 1382
f .998 .998 .998 .998 .999 .999 .999 .999 .999 .999 .999
L 44 45 46
N 0 0 1
SN 1382 1382 1383
f .999 .999 1.0
Median =
12.65
Distribution of lengths from end of FR3 to WG motif with assigned D.
L 0 1 2 3 4 5 6 7 8 9 10
N 3 0 0 0 0 0 3 9 21 15 39
SN 3 3 3 3 3 3 6 15 36 51 90
f .004 .004 .004 .004 .004 .004 .008 .019 .046 .065 .115
L 11 12 13 14 15 16 17 18 19 20 21
N 64 77 97 72 77 75 63 45 35 38 15
SN 154 231 328 400 477 552 615 660 695 733 748
f .196 .294 .418 .510 .608 .703 .783 .841 .885 .934 .953
L 22 23 24 25 26 27 28 29 30 31 32
N 15 6 9 2 1 0 1 1 0 0 0
SN 763 769 778 780 781 781 782 783 783 783 783
f .972 .980 .991 .994 .995 .995 .996 .997 .997 .997 .997
L 33 34 35 36 37 38 39 40 41 42 43
N 0 0 0 0 1 0 0 0 0 0 0
SN 783 783 783 783 784 784 784 784 784 784 784
f .997 .997 .997 .997 .999 .999 .999 .999 .999 .999 .999
L 44 45 46
N 0 0 1
SN 784 784 785
f .999 .999 1.0
Median =
13.90
Distribution of lengths from end of FR3 to WG motif with no assigned D.
L 0 1 2 3 4 5 6 7 8 9 10
N 3 0 0 4 2 9 10 29 40 73 62
SN 3 3 3 7 9 18 28 57 97 170 232
f .005 .005 .005 .012 .015 .030 .047 .095 .162 .284 .388
L 11 12 13 14 15 16 17 18 19 20 21
N 54 77 53 46 48 30 21 16 11 4 1
SN 286 363 416 462 510 540 561 577 588 592 593
f .478 .607 .696 .773 .853 .903 .938 .965 .983 .990 .992
L 22 23 24 25 26 27 28 29 30 31 32
N 2 1 0 0 0 0 1 0 0 0 0
SN 595 596 596 596 596 596 597 597 597 597 597
f .995 .997 .997 .997 .997 .997 .998 .998 .998 .998 .998
L 33 34 35 36 37 38 39 40 41 42
N 0 0 0 0 0 0 0 0 0 1
SN 597 597 597 597 597 597 597 597 597 598
f .998 .998 .998 .998 .998 .998 .998 .998 .998 1.0
Median =
11.17
L is the length
N is the number of examples
Sum(N) = SN is the sum of the Ns
f is the cumulative fraction seen
TABLE 9P
Tally of left-aligned CDR3 sequences
A C D E F G H I K L M #
1 74 6 278 109 11 319 50 18 11 60 8 1383 GDERVASLHTNQPIWYFKMCX
2 50 9 64 32 29 249 43 42 41 109 22 1377 GRPSLDVYTANHIQKEFMWCX
3 81 18 74 39 25 214 29 42 16 83 19 1377 GSYRTVLADPIWEQHNFMCK|
4 70 23 92 49 50 228 23 58 21 70 16 1373 GSYDRVALTIPFEWNCHQKMX
5 86 28 106 32 59 217 21 41 16 72 19 1371 GYSDAVTLRFIPWNECHMQK|X
6 88 17 104 28 94 171 17 48 12 50 17 1362 GYSDFATVRWPLINEQCHMK|
7 69 15 110 21 89 176 22 50 15 81 12 1349 GSYDFVLTAPRWINHEQCKM|X
8 53 19 141 17 90 150 18 47 17 68 11 1311 YSGDFLTVWAPIRNCHEKQM|
9 44 21 120 24 102 174 24 36 20 71 11 1250 YGSDFLNVRTAWPIEHCKQM|
10 39 31 129 23 124 116 23 42 9 58 32 1162 YDFGSLIARPTVWNMCEHQK
11 36 12 158 17 137 83 13 18 10 40 21 1061 YDFGSPLVANWMTRIEHCKQX
12 34 11 164 10 82 74 34 30 1 31 20 943 YDFGPSVAHLINMRTWCEQKX
13 32 2 121 6 84 56 10 26 7 43 32 789 YDFGLSPVAMIWRTHNKQEC
14 23 131 5 59 65 10 16 4 25 34 639 YDGFMVLAPISWNRHTQEKX
15 15 4 107 5 43 42 1 23 20 34 521 YDFGVMILWAPRSENCQTH|
16 4 2 80 3 33 26 4 5 1 10 29 396 YDVFMGPSLNTRIWAHECQ|K
17 3 1 63 19 19 9 13 12 21 291 DYVMFGILHPSTWAQRCNX
18 3 47 16 13 1 4 7 23 207 DYVMFGPSLTIAHN
19 5 1 39 1 4 13 3 3 1 14 146 DYVMGAFHINRSCELPQW
20 2 17 4 5 3 4 12 100 VYDMGFLIPSARWQ
21 17 3 8 1 1 4 58 DVGYMFHINTW
22 1 7 6 1 1 5 42 VDFMYSAGITW
23 9 1 1 1 1 25 DVYGILMPS
24 1 2 1 1 1 18 VYDAHLMPT
25 1 3 9 GVDPSY
26 2 2 7 GMSTV
27 2 1 1 6 DKMST
28 1 1 1 6 VADGS
29 1 4 DPSV
30 1 3 FST
31 1 1 3 KLV
32 1 1 3 FGP
33 1 3 PG
34 1 1 1 3 HLS
35 3 AVW
36 1 1 3 DFP
37 3 PSY
38 1 2 LS
39 1 1 2 AK
40 2 PS
41 2 ST
42 2 S
43 1 1 K
44 1 S
45 1 T
46 1 S
816 220 2186 421 1166 2428 358 568 205 920 421
N P Q R S T V W Y | X #
1 35 23 31 108 63 50 94 16 13 6 1383 GDERVASLHTNQPIWYFKMCX
2 44 114 42 169 114 59 62 21 60 2 1377 GRPSLDVYTANHIQKEFMWCX
3 26 73 37 110 140 97 89 42 122 1 1377 GSYRTVLADPIWEQHNFMCK|
4 48 51 22 79 141 65 77 49 139 2 1373 GSYDRVALTIPFEWNCHQKMX
5 37 41 18 61 157 75 85 38 158 2 2 1371 GYSDAVTLRFIPWNECHMQK|X
6 32 54 23 67 152 80 78 64 165 1 1362 GYSDFATVRWPLINEQCHMK|
7 44 59 18 58 157 73 85 54 139 1 1 1349 GSYDFVLTAPRWINHEQCKM|X
8 38 48 14 41 167 68 59 59 185 1 1311 YSGDFLTVWAPIRNCHEKQM|
9 52 40 14 47 123 45 48 41 192 1 1250 YGSDFLNVRTAWPIEHCKQM|
10 33 37 12 39 73 36 36 35 235 1162 YDFGSLIARPTVWNMCEHQK
11 33 49 7 20 68 21 37 29 251 1 1061 YDFGSPLVANWMTRIEHCKQX
12 30 53 10 19 45 19 42 18 215 1 943 YDFGPSVAHLINMRTWCEQKX
13 10 34 7 22 40 15 33 25 184 789 YDFGLSPVAMIWRTHNKQEC
14 13 22 6 12 15 10 26 14 148 1 639 YDGFMVLAPISWNRHTQEKX
15 5 12 2 12 12 3 40 20 119 1 521 YDFGVMILWAPRSENCQTH|
16 10 24 3 6 12 7 49 5 82 2 396 YDVFMGPSLNTRIWAHECQ|K
17 1 8 3 2 8 5 42 4 58 1 291 DYVMFGILHPSTWAQRCNX
18 1 13 8 5 31 35 207 DYVMFGPSLTIAHN
19 2 1 1 2 2 24 1 29 146 DYVMGAFHINRSCELPQW
20 3 1 2 3 23 2 19 100 VYDMGFLIPSARWQ
21 1 1 14 1 7 58 DVGYMFHINTW
22 2 1 12 1 5 42 VDFMYSAGITW
23 1 1 5 5 25 DVYGILMPS
24 1 1 5 5 18 VYDAHLMPT
25 1 1 2 1 9 GVDPSY
26 1 1 1 7 GMSTV
27 1 1 6 DKMST
28 1 2 6 VADGS
29 1 1 1 4 DPSV
30 1 1 3 FST
31 1 3 KLV
32 1 3 FGP
33 2 3 PG
34 1 3 HLS
35 1 1 3 AVW
36 1 1 3 DFP
37 1 1 3 PSY
38 1 2 LS
39 2 AK
40 1 1 2 PS
41 1 1 2 ST
42 2 2 S
43 1 K
44 1 1 S
45 1 1 T
46 1 1 S
495 769 270 876 1518 741 1104 540 2572 10 17 18621
TABLE 10P
Tally of right-aligned sequences
A C D E F G H I K L M
5 1 1 G
6 1 S
7 1 1 G
8 1 1 G
9 2 RV
10 2 RV
11 1 1 2 GI
12 2 V
13 2 TY
14 1 1 3 DGN
15 1 3 ISY
16 1 3 DSY
17 1 3 APY
18 1 1 1 3 DFM
19 2 1 3 DG
20 1 1 3 ILV
21 3 WP
22 3 4 GS
23 2 1 6 GHQSV
24 1 3 1 6 GALR
25 1 2 1 7 DTAIS
26 1 1 1 1 1 1 1 9 ACDGKLMST
27 2 5 1 2 1 1 18 DAGVEILNQRS
28 2 2 3 1 2 25 TGQSDELPRIV
29 3 5 6 7 1 1 1 42 GEDVAPQRSKLMTY|
30 2 9 1 9 1 4 5 2 58 DGRLSIVPAMQTFHNY
31 4 2 19 9 2 18 1 2 1 3 100 DGSERVYALPTCFINHKW
32 10 5 18 5 3 16 3 3 2 14 1 146 DGLRVAPYSTCEQFHINWKM
33 20 18 10 7 34 7 8 2 6 1 207 GARDPSYTEVIFHLQWKM
34 13 4 31 18 9 37 8 16 4 14 4 291 GDRYPVEILASTFHQWCKMNX|
35 17 5 32 23 10 70 12 10 6 25 1 396 GRSDYLEVTPAHNFIWKCQM|
36 23 6 51 21 9 79 19 15 14 36 9 521 GDSYRLTVPAEHIKNFMWCQ|
37 35 12 56 23 15 110 14 17 5 24 4 639 GYDVRSTAPLEIFHNCWQKMX
38 28 19 68 27 29 133 26 31 12 43 7 789 GSYDVRLPTIFAEHCNWKQM
39 51 25 80 27 33 162 16 30 18 55 15 943 GSDRYVLATPFWIECKHMQNK
40 44 14 73 36 46 161 27 32 17 59 8 1061 GSRDYVTLPFAEIWHQNKCM
41 54 21 74 25 23 178 23 52 15 57 11 1162 GSYTDRVLPAIWNQEFHCKMX|
42 57 13 82 40 42 190 14 39 15 82 15 1250 GSYDLVRTANPFEIWQKMHC|
43 75 18 54 25 35 242 13 29 18 49 12 1311 GYSTARVPDLWNFIQECKHM|
44 63 17 79 15 43 197 20 38 14 76 8 1349 YGSTDLRAPVWNFIQHCEKM
45 59 16 69 35 55 165 26 23 23 75 9 1362 YGSLRTDNAFPVWEHIKCQM
46 41 19 125 26 27 208 31 14 16 38 8 1371 YGDSNRWATLPHFECQCKIM
47 160 10 24 13 53 332 36 16 11 40 10 1373 GYAWPSFRLHTVNDIEKCMQX
48 21 4 8 5 680 27 4 44 5 145 288 1377 FMLISGVYPAWTDNQREKCHX
49 23 2 1181 29 1 30 15 4 2 8 1 1377 DGEAHNQSYVLPTIRCKW|FMX
50 7 7 15 42 3 41 135 3 59 4 1383 YVIPSLFHNDTACXMGKQRW|
816 220 2186 421 1166 2428 358 568 205 920 421
N P Q R S T V W Y | X #
5 1 1 G
6 1 S
7 1 G
8 1 G
9 1 1 2 RV
10 1 1 2 RV
11 2 GI
12 2 2 V
13 1 1 2 TY
14 1 3 DGN
15 1 1 3 ISY
16 1 1 3 DSY
17 1 1 3 APY
18 3 DFM
19 3 DG
20 1 3 ILV
21 1 2 3 WP
22 1 4 GS
23 1 1 1 6 GSQSV
24 1 6 GALR
25 1 2 7 DTAIS
26 1 1 9 ACDGKLMST
27 1 1 1 1 2 18 DAGVEILNQRS
28 2 3 2 3 4 1 25 TGQSDELPRIV
29 3 3 2 2 1 5 1 1 42 GEDVAPQRSKLMTY|
30 1 3 2 7 5 2 4 1 58 DGRLSIVPAMQTFHNY
31 2 3 7 10 3 7 1 6 100 DGSERVYALPTCFINHKW
32 3 9 4 12 8 6 12 3 9 146 DGLRVAPYSTCEQFHINWKM
33 16 6 19 15 12 10 3 13 207 GARDPSYTEVIFHLQWKM
34 2 20 5 31 12 12 20 5 23 1 2 291 GDRYPVEILSASTFHQWCKMNX|
35 12 18 5 39 35 19 23 7 26 1 396 GRSDYLEVTPAHNFIWKCQM|
36 11 24 6 42 47 29 28 7 44 1 521 GDSYRLTVPAEHIKNFMWCQ|
37 14 33 9 54 52 37 55 11 58 1 639 GYDVRSTAPLEIFHNCWQKMX
38 18 33 12 46 77 32 58 17 73 789 GSYDVRLPTIFAEHCNWKQM
39 11 38 12 70 94 42 61 33 68 2 943 GSDRYVLATPFWIECKHMQNX
40 24 52 27 74 140 61 66 29 71 1061 GSRDYVTLPFAEIWHQNKCM
41 31 55 29 70 146 76 61 51 97 1 2 1162 GSYTDRVLPAIWNQEFHCKMX|
42 48 47 24 68 171 68 70 39 125 1 1250 GSYDLVRTANPFEIWQKMHC|
43 38 58 28 73 164 76 66 43 194 1 1311 GYSTARVPDLWNFIQECKHM|
44 48 60 24 69 131 86 57 52 252 1349 YGSTDLRAPVWNFIQHCEKM
45 62 51 16 75 116 74 50 39 324 1362 YGSLRTDNAFPVWEHIKCQM
46 97 38 21 55 110 39 26 55 377 1371 YGDSNRWATLPHFEVQCKIM
47 25 54 9 44 54 34 32 122 292 2 1373 GYAWPSFRLHTVNDIEKCMQX
48 8 22 7 6 28 10 25 16 23 1 1377 FMLISGVYPAWTDNQREKCHX
49 15 6 13 4 13 5 9 2 11 2 1 1377 DGEAHNQSYVLPTIRCKW|FMX
50 23 122 3 3 67 9 350 3 480 1 6 1383 YVIPSLFHNDTACXMGKQRW|
50 495 769 270 876 1518 741 1104 540 2572 10 17 18621
TABLE 11P
Tallies of AA-frequencies in all CDR3 by length
Tally of sequences of length 7 # = 38
A C D E F G H I K L M #
1 1 8 1 1 14 1 1 5 38 GDLRWAEFHKS
2 1 1 2 6 3 2 1 1 38 RGNHVFKTYADLMW
3 1 4 1 5 1 2 2 38 GSDWYPVILTAFHN
4 3 1 1 12 1 1 1 38 GYSANRVDFHILPT
5 2 1 14 3 4 1 3 3 38 FIGLMARVYEKP
6 26 1 1 38 DVPTHISWY
7 1 2 2 3 1 38 YVINDHSALR
9 42 2 19 40 9 11 4 13 4
N P Q R S T V W Y | X #
1 3 1 2 38 GDLRWAEFHKS
2 6 7 2 3 1 2 38 RGNHVFKTYADLMW
3 1 3 5 2 3 4 4 38 GSDWYPVILTAFHN
4 2 1 2 4 1 2 6 38 GYSANRVDFHILPT
5 1 2 2 2 38 FIGLMARVYEKP
6 2 1 2 3 1 1 38 DVPTHISWY
7 3 1 2 7 16 38 YVINDHSALR
12 7 15 13 7 20 8 31 266
Tally of sequences of length 8 # = 61
A C D E F G H I K L M #
1 3 7 3 14 2 2 5 61 GDLTVRSAEHINWPQY
2 1 9 1 1 15 1 2 1 61 GDTNRSVKWYAEFILPQ
3 2 3 1 10 1 1 7 61 GLSTYVDPRAFHIMNQW
4 4 1 3 1 1 15 1 4 61 GYRADQDSWVCEFHNPT
5 10 2 1 9 5 1 5 1 61 AGYHLTPRVDSEKMW
6 5 1 24 2 7 5 2 61 FIALPSVYGMCQRW
7 5 37 2 4 1 2 61 DAHSELNVIP|
8 1 2 3 1 12 3 61 YISFLVDNAHPRT
31 2 63 8 30 65 14 24 3 32 4
N P Q R S T V W Y | X #
1 2 1 1 4 4 5 5 1 1 61 GDLTVRSAEHINWPQY
2 6 1 1 4 3 8 3 2 2 61 GDTNRSVKWYAEFILPQ
3 1 3 1 3 7 7 5 1 7 61 GLSTYVDPRAFHIMNQW
4 1 1 4 5 3 1 2 3 11 61 GYRALQDSWVCEFHNPT
5 4 4 2 5 4 1 7 61 AGYHLTPRVDSEKMW
6 3 1 1 3 3 1 3 61 FIALPSVYGMCQRW
7 2 1 4 2 1 61 DAHSELNVIP|
8 2 1 1 7 1 3 24 61 YISFLVDNAHPRT
14 15 8 22 33 27 27 10 55 1 488
Tally of sequences of length 9 # = 88
A C D E F G H I K L M #
1 9 12 4 21 1 1 2 5 88 GDARNVLEQTKWHIPSY
2 2 2 3 3 13 4 3 7 2 88 GPSRLNTHEFKYADMQW
3 4 2 3 3 3 15 1 1 88 GTPSQNRVWYADEFCLM
4 5 1 6 3 6 22 2 4 1 6 1 88 GSDFLARITYENPWHVCKM
5 7 1 4 3 4 14 2 7 2 88 GSYALNDFVERWHMQTCP
6 13 2 1 3 13 6 2 1 4 1 88 YAGHNLPSVFTWDIEKMQR
7 4 2 41 2 3 1 14 5 88 FLMAPWIDGSVKNQTY
8 1 1 73 2 2 1 2 88 DEGLSACHNQRV
9 1 1 4 1 3 8 2 88 YVISFHPLNTCDGF
45 6 105 19 64 103 19 18 8 48 12
N P Q R S T V W Y | X #
1 7 1 3 8 1 3 7 2 1 88 GDARNVLEQTKWHIPSY
2 5 11 2 10 11 5 2 3 88 GPSRLNTHEFKYADMQW
3 5 7 6 5 7 11 5 5 5 88 GTPSQNRVWYADEFCLM
4 3 3 5 7 4 2 3 4 88 GSDFLARITYENPWHVCKM
5 6 1 2 3 12 2 4 3 11 88 GSYALNDFVERWHMQTCP
6 5 4 1 1 4 3 4 3 17 88 YAGHNLPSVFTWDIEKMQR
7 1 4 1 2 1 2 4 1 88 FLMAPWIDGSVKNQTY
8 1 1 1 2 1 88 DEGLSACHNQRV
9 2 3 1 8 2 9 43 88 YVISFHPLNTCDGR
35 34 16 34 54 31 34 22 85 792
Tally of sequences of length 10 # = 101
A C D E F G H I K L M #
1 8 1 19 7 1 16 3 2 3 2 101 DGNAERTSQVHLWKMYCF
2 3 8 3 5 13 5 15 2 101 LGRDSPVFINTAEQYMW
3 6 9 1 26 1 3 1 4 1 101 GSYDAVTLNRIPWFHKMQ
4 7 6 1 25 1 5 4 1 101 GSYARDINPLTVWQFHM
5 6 5 9 4 16 1 3 4 101 GYTESANDPRFLVKQWH
6 6 1 6 5 4 23 2 4 3 3 1 101 GYRSWADEFINKLTHCMQV
7 13 3 1 5 9 3 1 4 1 101 YASGPRWFTVLDHNEIMQ
8 2 1 1 57 3 4 15 4 101
9 3 78 2 6 1 1 1 101
10 3 4 4 13 1 101
54 3 137 28 82 137 15 36 10 54 12
N P Q R S T V W Y | X #
1 9 4 6 5 6 4 3 2 101 DGNAERTSQVHLWKMYCF
2 5 6 3 11 8 4 6 1 3 101 LGRDSPVFINTAEQYMW
3 4 3 1 4 14 5 6 2 10 101 GSYDAVTLNRIPWFHKMQ
4 5 5 3 7 11 4 4 4 8 101 GSYARDINPLTVWQFHM
5 6 5 2 5 8 10 4 2 11 101 GYTESANDPRFLVKQWH
6 4 1 8 7 3 1 7 12 101 GYRSWADEFINKLTHCMQV
7 2 7 1 7 11 5 5 6 17 101 YASGPRWFTVLDHNEIMQ
8 2 2 4 2 3 1 101 FLIMSGWANPVCEY
9 2 1 3 1 1 1 101 DGAQENIKLPRSW
10 4 8 7 5 52 101 YIPSVFHNDL
43 37 18 49 76 37 37 29 116 1010
Tally of sequences of length 11 # = 118
A C D E F G H I K L M #
1 7 1 21 11 23 5 2 7 118 GDEVRALQHSPTINCWY
2 1 2 9 1 1 24 5 6 2 7 3 118 GSRDYLPIVHQTMNCKWAEFX
3 4 4 2 4 13 2 3 1 7 2 118 SGTVRLYWADFNQIEHMKP
4 10 3 3 2 25 1 2 4 3 118 SGARTWYLVDEMQFINPH
5 5 2 10 1 4 24 2 1 5 1 118 GSVYDTNALRFWCHQEKM
6 6 4 2 7 19 2 3 1 5 1 118 GSYWTFAVLRDINEHQKMP
7 4 1 8 5 2 20 4 1 2 1 118 GYSNRDWTEPAHFLQVCIM
8 13 2 6 1 8 12 4 2 7 118 YAGWFLDPRSTHCKVE
9 2 2 68 2 5 14 7 118 FLMYVITADGP
10 2 1 100 5 3 2 1 1 118 DEGAHCLMNPQ
11 2 6 1 7 1 6 1 118 YPVISFLNDHKM
54 9 169 31 102 165 28 29 8 65 20
N P Q R S T V W Y | X #
1 2 4 7 8 5 3 10 1 1 118 GDEVRALQHSPTINCWY
2 3 7 4 10 11 4 6 2 9 1 118 GSRDYLPIVHQTMNCKWAEFX
3 4 1 4 8 25 12 9 6 7 118 SGTVRLYWADFNQIEHMKP
4 2 2 3 9 26 8 4 6 5 118 SGARTWYLVDEMQFINPH
5 6 2 5 15 9 11 4 11 118 GSVYDTNALRFWCHQEKM
6 3 1 2 5 16 9 6 11 15 118 GSYWTFAVLRDINEHQKMP
7 9 5 2 9 11 6 2 7 19 118 GYSNRDWTEPAHFLQVCIM
8 6 5 5 5 2 11 29 118 YAGWFLDPRSTHCKVE
9 1 4 6 7 118 FLMYVITADGP
10 1 1 1 118 DEGAHCLMNPQ
11 3 13 7 11 60 118 YPVISFLNDHKM
33 41 25 59 121 60 67 48 163 1 1298
Tally of sequences of length 12 # = 154
A C D E F G H I K L M #
1 5 31 12 37 6 1 1 7 3 154 GDRESVLHAPMNQTWYIK
2 5 1 7 6 1 25 3 7 3 13 2 154 GSRLPDIQEAVYHKNTMWCF
3 10 2 7 5 1 19 5 4 12 2 154 GRSYLATVPDQEIKWCMNF
4 8 9 6 8 27 6 5 6 1 154 GVSDNAFRTYEILKWPQM
5 18 1 8 5 6 42 1 9 1 7 3 154 GSAIDYLFPTEQVMNWCHK
6 13 12 4 10 23 1 7 8 1 154 GAVDSFYTLPRWINEQHM
7 11 2 4 3 10 15 1 4 12 154 YGSPLRAFWTNVDIECQH
8 3 2 18 3 3 25 4 2 5 6 154 YGDSNLTKRWHPAEFCIQV
9 15 1 2 8 33 4 7 1 5 1 154 GYWARFISPLHTDQCKMN
10 1 1 2 1 79 1 2 5 1 19 26 154 FMLIPYDHVWACEGKNQRST
11 2 135 2 4 2 154 DGYAEHSVNR
12 1 1 6 1 9 16 4 154 YVPIHFSLNCDGW
91 11 236 47 132 252 33 69 21 99 39
N P Q R S T V W Y | X #
1 3 4 3 14 10 3 10 2 2 154 GDRESVLHAPMNQTWYIK
2 3 11 7 22 24 3 5 2 4 154 GSRLPDIQEAVYHKNTMWCF
3 2 8 6 17 17 9 9 4 15 154 GRSYLATVPDQEIKWCMNF
4 9 4 4 7 17 7 18 5 7 154 GVSDNAFRTYEILKWPQM
5 3 6 4 20 6 4 2 8 154 GSAIDYLFPTEQVMNWCHK
6 5 8 3 8 11 9 13 8 10 154 GAVDSFYTLPRWINEQHM
7 5 14 2 12 15 6 5 9 24 154 YGSPLRAFWTNVDIECQH
8 10 4 2 5 15 6 2 5 34 154 YGDSNLTKRWHPAEFCIQV
9 1 6 2 10 7 3 18 30 154 GYWARFISPLHTDQCKMN
10 1 4 1 1 1 1 2 2 3 154 FMLIPYDHVWACEGKNQRST
11 1 1 2 2 3 154 DGYAEHSVNR
12 2 18 5 32 1 58 YVPIHFSLNCDGW
45 87 34 97 144 53 102 58 198 1848
Tally of sequences of length 13 # = 150
A C D E F G H I K L M #
1 4 2 28 9 3 37 8 3 3 5 150 GDTESHRVLPAQFIKCNW
2 11 4 4 1 2 32 3 1 5 11 3 150 GRSPALTKVCDYHMQWFEIN
3 7 2 8 4 4 23 11 1 4 6 2 150 GSYHQTDPRAVLEFKNCMWI
4 6 2 6 4 6 30 1 8 6 1 150 GSWYTIADFLPVEQRCHMNX
5 8 10 4 2 28 1 2 22 3 150 GLSYDATWPREQMNVFIH
6 10 2 11 1 6 21 2 2 5 1 150 GYSPTDAQVFRLNWCIKEM
7 5 1 8 1 4 19 1 6 5 21 2 150 LGYSTDPIRVAKFNWMQCEH
8 7 5 22 5 3 12 3 3 3 8 1 150 YDSGLARTCEQVNPFHIKWM
9 1 2 12 3 1 26 7 2 4 7 2 150 NGYDSWHLPRKETVCIMAFQ
10 19 1 2 2 17 24 5 2 5 1 150 YGAFWHLPTNSVDEIQRCM
11 1 1 105 2 2 1 13 14 150 FMLYGIVAEKPQRSWX
12 130 3 5 1 150 DGYEQNHT
13 1 2 5 5 14 18 1 150 YVLIPSFHTDAMN
80 21 243 38 158 259 46 46 27 127 31
N P Q R S T V W Y | X #
1 2 5 4 8 9 11 8 1 150 GDTESHRVLPAQFIKCNW
2 1 13 3 20 17 7 5 3 4 150 GRSPALTKVCDYEMQWFEIN
3 3 8 11 8 16 11 7 2 12 150 GSYHQTDPRAVLEFKNCMWI
4 1 6 4 4 18 10 6 16 14 1 150 GSWYTIADFLPVEQRCHMNX
5 3 6 4 5 19 8 3 7 15 150 GLSYDATWPREQMNVFIH
6 3 15 8 6 15 13 8 3 17 150 GYSPTDAQVFRLNWCIKEM
7 4 7 2 6 15 14 6 4 19 150 LGYSTDPIRVAKFNWMQCEH
8 4 4 5 7 15 7 5 2 29 150 YDSGLARTCEQVNPFHIKWM
9 31 5 1 5 10 3 3 9 16 150 NGYDSWHLPRKETVCIMAFQ
10 3 5 2 2 3 4 3 15 35 150 YGAFWHLPTNSVDEIQRCM
11 1 1 1 1 2 1 3 1 150 FMLYGIVAEKPQRSWX
12 2 3 1 5 150 GDYEQNHT
13 1 14 13 4 21 51 150 YVLIPSFHTDAMN
58 89 48 72 152 93 77 63 220 2 1950
Tally of sequences of length 14 # = 118
A C D E F G H I K L M #
1 6 29 7 2 32 8 1 1 2 118 GDVHERTAFLPSIKNQ
2 4 10 1 5 22 7 3 4 7 118 GPDRYSVHLFAKIQTENW
3 11 2 7 2 3 25 5 1 9 2 118 GVARYLSDITFWCEMPK
4 5 2 7 7 3 12 4 4 3 6 118 SGVYPDELRTANHIFKWC
5 6 5 12 2 18 2 2 2 4 1 118 GYSDTVARCLPFHIKNWMQ
6 6 10 5 4 16 5 3 2 1 118 YGSTDRAEIFVKWLPQMN
7 4 4 1 4 32 2 2 2 1 118 GSVTYNADFHIKPQRWEM
8 6 1 5 1 4 18 2 5 3 2 118 GSYTWAPRDIFNVLHMCE
9 5 2 4 1 2 11 2 1 5 9 1 118 YSGTLVAKNRDWCFHPEIM
10 2 5 9 2 3 21 2 2 4 118 YGSDNTCQLRFWAEIKPV
11 12 1 3 5 25 2 2 1 118 YGWAPVFNEHLTDMQR
12 1 64 5 1 5 12 16 118 FMLGIPSVAHQTY
13 3 97 4 5 1 1 1 1 118 DGEANQHIKLV
14 2 3 4 12 6 118 YVPILHFANS
73 17 195 34 104 242 35 48 24 67 25
N P Q R S T V W Y | X #
1 1 2 1 7 2 7 10 118 GDVHERTAFLPSIKNQ
2 1 13 2 10 8 2 8 1 10 118 GPDRYSVHLFAKIQTENW
3 2 11 8 4 13 3 10 118 GVARYLSDITFWCEMPK
4 5 8 6 13 6 12 3 12 118 SGVYPDELRTANHIFKWC
5 2 3 1 6 15 10 7 2 18 118 GYSDTVARCLPFHIKNWMQ
6 1 2 2 7 16 12 4 3 19 118 YGSTDRAEIFVKWLPQMN
7 5 2 2 2 18 12 13 2 10 118 GSVTYNADFHIKPQRWEM
8 4 6 6 16 12 4 9 14 118 GSYTWAPRDIFNVLHMCE
9 5 2 5 14 10 8 4 27 118 YSGTLVAKNRDWCFHPEIM
10 6 2 5 4 13 6 2 3 27 118 YGSDNTCQLRFWAEIKPV
11 4 7 1 1 2 6 14 32 118 YGWAPVFNEHLTDMQR
12 4 1 4 1 3 1 118 FMLGIPSVAHQTY
13 2 2 1 118 DGEANQHILKV
14 2 14 2 20 53 118 YVPILHFANS
38 67 17 65 129 84 111 44 233 1652
TABLE 12P
Alignment and tabulation of sequences having 3-22 D segments
D3:3-22_Phz0 YYYDSSGYYY (SEQ ID NO: 448) = GLG
Entry Seq1 L1 Seq2 L2 JH P Score
1 hs3d6hcv GRDYYDSGGYFT 12 GRDYYDSGGYFTVAFDI 17 3 6 1.76D + 13
(SEQ ID NO: 334) (SEQ ID NO: 335)
2 hs6d4xb7 DRHNYYDSSGSYS 13 DRHNYYDSSGSYSDY 15 4 9 4.40D + 12
(SEQ ID NO: 336) (SEQ ID NO: 337)
3 hs6d4xg3 DCPAPAKMYYYGSGICT 17 DCPAPAKMYYYGSGICT 20 4 3 6.55D + 04
(SEQ ID NO: 338) FDY
(SEQ ID NO: 339)
4 hs83x6f2 AFYDSAD 7 AFYDSADDY 9 4 −4 2.62D + 05
(SEQ ID NO: 340) (SEQ ID NO: 341)
5 hsa230644 RDYYDSSGPEAG 12 RDYYDSSGPEAGFDI 15 3 3 6.87D + 10
(SEQ ID NO: 342) (SEQ ID NO: 343)
6 hsa239386 DGTLIDTSAYYYL 13 DGTLIDTSAYYYLY 14 4 6 6.87D + 10
(SEQ ID NO: 344) (SEQ ID NO: 345)
7 hsa234232 NSSDSS 6 NSSDSSVLDV 10 6 −4 6.55D + 04
(SEQ ID NO: 346) (SEQ ID NO: 347)
8 hsa239378 DQVFDSGGYNHR 12 DQVFDSGGYNHRFDS 15 4 3 1.07D + 09
(SEQ ID NO: 348) (SEQ ID NO: 349)
9 hsa239367 DLEYYYDSGGHYSP 14 DLEYYYDSGGHYSPFHY 17 4 9 1.10D + 12
(SEQ ID NO: 350) (SEQ ID NO: 351)
10 hsa239339 DDSSGY 6 DDSSGYYYIDY 11 4 −10 1.72D + 10
(SEQ ID NO: 352) (SEQ ID NO: 353)
11 hsa245311 GHYYDSPGQYSYS 13 GHYYDSPGQYSYSEY 15 4 3 1.07D + 09
(SEQ ID NO: 354) (SEQ ID NO: 355)
12 hsa240578 GGFRPPPYDYESSAYRTYR 19 GGFRPPPYDYESSAYRT 22 4 21 2.75D + 11
(SEQ ID NO: 356) YRLDF
(SEQ ID NO: 357)
13 hsa245359 DSDTRAY 7 DSDTRAYYWYFDL 13 2 −7 1.68D + 07
(SEQ ID NO: 358) (SEQ ID NO: 359)
14 hsa245028 GRHYYDSSGYYSTPE 15 GRHYYDSSGYYSTPENY 20 4 6 1.80D + 16
(SEQ ID NO: 360) FDY
(SEQ ID NO: 361)
15 hsa245019 DPSYYYDSSGLPL 13 DPSYYYDSSGLPLHGMDV 18 6 9 4.40D + 12
(SEQ ID NO: 362) (SEQ ID NO: 363)
16 hsa244991 TYYYDSSGYLLTR 13 TYYYDSSGYLLTRYFQH 17 1 3 4.50D + 15
(SEQ ID NO: 364) (SEQ ID NO: 365)
17 hsa244945 NAPHYDSSGYYQT 13 NAPHYDSSGYYQTFDY 16 4 6 7.04D + 13
(SEQ ID NO: 366) (SEQ ID NO: 367)
18 hsa244943 GYHSSSYA 8 GYHSSSYADAFDI 13 3 −7 6.71D + 07
(SEQ ID NO: 368) (SEQ ID NO: 369)
19 hsa245289 PIGYCSGGSC 10 PIGYCSGGSCYSFDY 15 4 −4 2.62D + 05
(SEQ ID NO: 370) (SEQ ID NO: 371)
20 hsa240554 THGTYVTSGYYPKI 14 THGTYVTSGYYPKI 14 4 6 2.68D + 08
(SEQ ID NO: 372) (SEQ ID NO: 373)
21 hsa279533 GATYYYESSGNYP 13 GATYYYESSGNYPDY 15 4 9 7.04D + 13
(SEQ ID NO: 374) (SEQ ID NO: 375)
22 hsa389177 AFYHYDSTGYPNRRY 15 AFYHYDSTGYPNRRYYFDY 19 4 6 4.29D + 09
(SEQ ID NO: 376) (SEQ ID NO: 377)
23 hsa7321 SYSYYYDSSGYWGG 14 SYSYYYDSSGYWGGYFDY 18 4 9 4.50D + 15
(SEQ ID NO: 378) (SEQ ID NO: 379)
24 hsaj2772 LSPYYYDSSSYH 12 LSPYYYDSSSYHDAFDI 17 3 6 2.62D + 05
(SEQ ID NO: 380) (SEQ ID NO: 381)
25 hsb7g4f08 EEDYYDSSGQAS 12 EEDYYDSSGQASYNWFXP 18 5 6 2.75D + 11
(SEQ ID NO: 382) (SEQ ID NO: 383)
26 hsb7g3b02 ETNYYDSGGYPG 12 ETNYYDSGGYPGFDF 15 4 6 4.40D + 12
(SEQ ID NO: 384) (SEQ ID NO: 385)
27 hsb7g3c12 GDHYYDRSGYRH 12 GDHYYDRSGYRHSYYYY 21 6 6 2.75D + 11
(SEQ ID NO: 386) AMDV
(SEQ ID NO: 387)
28 hsb8g3b07 DRSSGN 6 DRSSGNYFDGMDV 13 6 −10 6.55D + 04
(SEQ ID NO: 388) (SEQ ID NO: 389)
29 hsfoglh GRSRYSGYG 9 GRSRYSGYGFYSGMDV 16 6 −4 2.62D + 05
(SEQ ID NO: 390) (SEQ ID NO: 391)
30 hsgvh0209 DDTSGYGP 8 DDTSGYGPYYFYYGMDV 17 6 −10 2.68D + 08
(SEQ ID NO: 392) (SEQ ID NO: 393)
31 hsgvh55 RAYYDTSFYFEY 12 RAYYDTSFYFEYY 13 4 3 1.72D + 10
(SEQ ID NO: 394) (SEQ ID NO: 395)
32 hsgvh0304 DRIDYYKSGYYLGSA 15 DRIDYYKSGYYLGSADS 17 4 6 1.68D + 07
(SEQ ID NO: 396) (SEQ ID NO: 397)
33 hsgvh0332 DTDSSSHYG 9 DTDSSSHYGRFDP 13 5 −7 1.68D + 07
(SEQ ID NO: 398) (SEQ ID NO: 399)
34 hsgvh0328 VSISHYDSSGRPQRVF 16 VSISHYDSSGRPQRVFY 21 6 9 1.07D + 09
(SEQ ID NO: 400) GMDV
(SEQ ID NO: 401)
35 hsgvh536 QARENVFYDSSGPTAP 16 QARENVFYDSSGPTAPFDH 19 4 15 1.72D + 10
(SEQ ID NO: 402) (SEQ ID NO: 403)
36 hshcmg42 VPAGNYYDTSGPDN 14 VPAGNYYDTSGPDNAD 16 4 12 1.72D + 10
(SEQ ID NO: 404) (SEQ ID NO: 405)
37 hsig001vh WYYFDTSGYYPRNFYYMDV 19 WYYFDTSGYYPRNFYYMDV 19 4 3 2.81D + 14
(SEQ ID NO: 406) (SEQ ID NO: 407)
38 hsig13g10 GYYYDSGGNYNG 12 GYYYDSGGNYNGDY 14 4 3 1.10D + 12
(SEQ ID NO: 408) (SEQ ID NO: 409)
39 hsighpat3 DLRSYDPSGYYN 12 DLRSYDPSGYYNDGFDI 17 3 6 2.75D + 11
(SEQ ID NO: 410) (SEQ ID NO: 411)
40 hsigh13g7 GYYYDRGGNCNG 12 GYYYDRGGNCNGDY 14 4 3 6.87D + 10
(SEQ ID NO: 412) (SEQ ID NO: 413)
41 hsighl3g1 GYYYDRGGNYNG 12 GYYYDRGGNYNGDY 14 4 3 1.10D + 12
(SEQ ID NO: 414) (SEQ ID NO: 415)
42 hsighxx20 THYDSSGL 8 THYDSSGLDAFDI 13 3 −4 1.72D + 10
(SEQ ID NO: 416) (SEQ ID NO: 417)
43 hsihr9 DDSSGS 6 DDSSGSYYFDY 11 4 −10 1.07D + 09
(SEQ ID NO: 418) (SEQ ID NO: 419)
44 hsihv11 LSGGYYS 7 LSGGYYSDFDY 11 4 −13 2.68D + 08
(SEQ ID NO: 420) (SEQ ID NO: 421)
45 hs ej1f GDYSDSSDSYI 11 GDYSDSSDSYIDAFDV 16 3 3 1.10D + 12
(SEQ ID NO: 422) (SEQ ID NO: 423)
46 hsmvh51 GETYYYDSRGYA 12 GETYYYDSRGYAFDH 15 4 6 2.62D + 05
(SEQ ID NO: 424) (SEQ ID NO: 425)
47 hsmvh517 PTRDSSGY 8 PTRDSSGYYVGY 12 4 −4 1.07D + 09
(SEQ ID NO: 426) (SEQ ID NO: 427)
48 hsmvh0406 GSFYYDSSGYPP 12 GSFYYDSSGYPPFDC 15 4 6 6.87D + 10
(SEQ ID NO: 428) (SEQ ID NO: 429)
49 hst14x14 GPYYYDSSGYYL 12 GPYYYDSSGYYLLDY 15 4 6 1.80D + 16
(SEQ ID NO: 430) (SEQ ID NO: 431)
50 hsvhig2 EEGYYDSSGYYSLGA 15 EEGYYDSSGYYSLGASDY 18 4 6 4.50D + 15
(SEQ ID NO: 432) (SEQ ID NO: 433)
51 hsvhia2 RPDSSGSRW 9 RPDSSGSRWYFDY 13 4 −7 6.71D + 07
(SEQ ID NO: 434) (SEQ ID NO: 435)
52 hsy14936 GYYDISGYYF 10 GYYDISGYYFDAFNI 15 3 −4 2.81D + 14
(SEQ ID NO: 436) (SEQ ID NO: 437)
53 hsy14934 DRGYDSSGYYGN 12 DRGYDSSGYYGNLDC 15 4 3 1.76D + 13
(SEQ ID NO: 438) (SEQ ID NO: 439)
54 hsy14935 DRGYDSIGYYGN 12 DRGYDSIGYYGNLDC 15 4 3 1.10D + 12
(SEQ ID NO: 440) (SEQ ID NO: 441)
55 hsz80519 AEDLTYYYDRSGWGVHGLL 19 AEDLTYYYDRSGWGVHG 24 4 15 4.40D + 12
(SEQ ID NO: 442) LLYYFDY
(SEQ ID NO: 443)
56 hsz80429 LYPHYDSSGYYYV 13 LYPHYDSSGYYYVLDY 16 4 6 4.50D + 15
(SEQ ID NO: 444) (SEQ ID NO: 445)
57 hsz80461 DRVGYYDSSGYPPGSP 16 DRVGYYDSSGYPPGSPLDY 19 4 9 1.76D + 13
(SEQ ID NO: 446) (SEQ ID NO: 447)
Frequency of each AA type at each position in 57 Sequences having D3-22 segments
Pos A C D E F G H I K L M N P Q R S T V W Y | X #
1 1 1
2 1 1
3 1 1 1 3
4 1 1 1 1 4
5 5 1 1 2 1 1 1 12
6 3 3 4 6 3 1 2 2 2 1 1 28 x
7 1 5 4 1 7 2 1 1 1 3 5 3 4 1 1 1 41 x
8 2 1 4 1 5 3 1 4 4 1 3 1 3 1 14 48 x
9 4 2 3 5 1 1 1 2 2 2 1 28 52 Y
10 1 4 2 1 1 1 1 4 1 40 56 Y
11 46 2 1 1 1 2 1 3 57 D
12 1 1 1 1 1 1 4 39 7 1 57 S
13 1 8 1 1 1 1 43 1 57 S
14 3 2 1 45 1 1 3 56 G
15 2 2 2 5 3 2 1 4 1 33 55 Y
16 2 1 1 1 2 3 1 1 1 6 3 1 1 1 24 49 x
17 3 1 1 1 5 2 1 4 6 6 2 7 2 1 1 3 46 x
18 8 1 1 2 2 2 4 3 1 3 27
19 2 1 1 1 3 4 1 13
20 2 1 2 1 1 1 1 9
21 1 1 1 3
22 1 1 2
23 1 1 2
24 1 1
25 1 1
Average Dseg = 11.9 Average DJ = 15.7
Median D = 12 12 Shortest 6 Longest 19
Median DJ = 15 15 Shortest 9 Longest 24
TABLE 13P
Frequency of D-segments. “|” stands for a stop codon.
D seg “0” % C % GLG “1” % C % GLG “2” % C % GLG
1-01 1 0.13 0 VQLERX 4 0.53 0.22 GTTGTX 5 0.66 0.34 YNWND
(SEQ ID NO: 132) (SEQ ID NO: 133) (SEQ ID NO: 134)
1-07 0 0 0 V|LELX 3 0.4 0.11 GITGTX 9 1.19 0.34 YNWNY
(SEQ ID NO: 135) (SEQ ID NO: 136) (SEQ ID NO: 137)
1-20 0 0 0 V|LERX 1 0.13 0.22 GITGTX 4 0.53 0.45 YNWND
(SEQ ID NO: 138) (SEQ ID NO: 139) (SEQ ID NO: 140)
1-26 4 0.53 0 V|WELLX 13 1.72 0.90 GIVGATX 36 4.76 0.78 YSGSYY
(SEQ ID NO: 141) (SEQ ID NO: 142) (SEQ ID NO: 143)
2-02 31 4.1 2.47 GYCSSTSCYT 4 0.53 0.22 RIL||YQLLYX 9 1.19 2.47 DIVVVPAAIX
(SEQ ID NO: 144) (SEQ ID NO: 145) (SEQ ID NO: 146)
2-08 5 0.66 0.56 GYCTNGVCYT 0 0 0 RILY|WCMLYX 3 0.4 0.56 DIVLMVYAIX
(SEQ ID NO: 147) (SEQ ID NO: 148) (SEQ ID NO: 149)
2-15 29 3.83 1.57 GYCSGGSCYS 2 0.26 0.11 RIL|WW|LLLX 7 0.92 1.57 DIVVVVAATX
(SEQ ID NO: 150) (SEQ ID NO: 151) (SEQ ID NO: 152)
2-21 16 2.11 0.67 AYCGGDCYS 0 0 0 SILWW|LLFX 7 0.92 0.67 HIVVVTAIX
(SEQ ID NO: 153) (SEQ ID NO: 154) (SEQ ID NO: 155)
3-03 32 4.23 2.80 YYDFWSGYYT 7 0.92 0.90 VLRFLEWLLYX 27 3.57 1.12 ITIFGVVIIX
(SEQ ID NO: 156) (SEQ ID NO: 157) (SEQ ID NO: 158)
3-09 13 1.72 1.35 YYDILTGYYN 5 0.66 0.78 VLRYFDWLL|X 0 0 0 ITIF|LVIIX
(SEQ ID NO: 159) (SEQ ID NO: 160) (SEQ ID NO: 161)
3-10 42 5.55 4.26 YYYGSGSYYN 13 1.72 0.89 VLLWFGELL|X 11 1.45 2.91 ITMVRGVIIX
(SEQ ID NO: 162) (SEQ ID NO: 163) (SEQ ID NO: 164)
3-16 18 2.38 0.67 YYDYVWGSYRYT 8 1.06 0 VL|LRLGELSLYX 5 0.66 0.34 IMITFGGVIVIX
(SEQ ID NO: 165) (SEQ ID NO: 166) (SEQ ID NO: 167)
3-22 57 7.53 3.36 YYYDSSGYYY 1 0.13 0.11 VLL|||WLLLX 6 0.79 0.34 ITMIVVVITX
(SEQ ID NO: 168) (SEQ ID NO: 169) (SEQ ID NO: 170)
4-04 5 0.66 0.28 DYSNY 2 0.26 0 |LQ|LX 2 0.26 0.06 TTVTX
(SEQ ID NO: 171) (SEQ ID NO: 172) (SEQ ID NO: 173)
4-17 29 3.83 1.45 DYGDY 0 0 0 |LR|LX 20 2.64 0.90 TTVTX
(SEQ ID NO: 174) (SEQ ID NO: 175) (SEQ ID NO: 176)
4-23 10 1.32 0.56 DYGGNS 1 0.13 0 |LRW|LX 4 0.53 0.56 TTVVTX
(SEQ ID NO: 177) (SEQ ID NO: 178) (SEQ ID NO: 179)
5-05 3 0.4 0.06 WIQLWLX 10 1.32 0.39 VDTAMVX 31 4.1 0.73 GYSYGY
(SEQ ID NO: 180) (SEQ ID NO: 181) (SEQ ID NO: 182)
5-12 0 0 0 WI|WLRLX 8 1.06 0.45 VDIVATIX 14 1.85 1.12 GYSGYDY
(SEQ ID NO: 183) (SEQ ID NO: 184) (SEQ ID NO: 185)
5-24 11 1.45 0 |RWLQLX 5 0.66 0.34 VEMATIX 13 1.72 0.44 RDGYNY
(SEQ ID NO: 186) (SEQ ID NO: 187) (SEQ ID NO: 188)
6-06 11 1.45 0.78 SIAARX 9 1.19 0.48 EYSSSS 1 0.13 0.11 V|QLVX
(SEQ ID NO: 189) (SEQ ID NO: 190) (SEQ ID NO: 191)
6-13 19 2.51 1.01 GIAAAGX 35 4.62 2.13 GYSSSWY 2 0.26 0.31 V|QQLVX
(SEQ ID NO: 192) (SEQ ID NO: 193) (SEQ ID NO: 194)
6-19 14 1.85 2.12 GIAVAGX 48 6.34 2.02 GYSSGWY 4 0.53 0.56 V|QWLVX
(SEQ ID NO: 195) (SEQ ID NO: 196) (SEQ ID NO: 197)
D7: 1 0.13 0 |LGX 2 0.26 0.68 LTGX 2 0.26 0.22 NWG
7-27 (SEQ ID NO: 198)
Total = 757
TABLE 14P
Possible library components.
Component L f
D2_2-02_Phz0 xxxYCSSTSCxxx 13, 31, (SEQ ID NO: 199)
D3_3-16_Phz0 xxxxYVWGSYxxx 13, 18, (SEQ ID NO: 200)
D5_5-12_Phz2 xxxxxxxSGYxxx 13, 14, (SEQ ID NO: 201)
D3_3-09_Phz0 xxxYDILIGYYxx 13, 13, (SEQ ID NO: 202)
D2_2-02_Phz2 xxxVVVPAAxxxx 13, 9, (SEQ ID NO: 203)
D3_3-22_Phz0 xxxYYDSSGYxx 12, 57, (SEQ ID NO: 204)
D3_3-03_Phz0 xxxDFWSGxxxx 12, 32, (SEQ ID NO: 205)
D3_3-03_Phz2 xxxTIFGVxxxx 12, 27, (SEQ ID NO: 206)
D5_5-12_Phz1 xxxxIVATxxxx 12, 8, (SEQ ID NO: 207)
D3_3-10_Phz0 xxxYGSGSYYx 11, 42, ! could add one x
at either end
(SEQ ID NO: 208)
D5_5-05_Phz2 xxxxYSYGxxx 11, 31, (SEQ ID NO: 209)
D2_2-15_Phz0 xxxCSGxxCYx 11, 29, (SEQ ID NO: 210)
D6_6-13_Phz0 xxxxAAAGxxx 11, 19, (SEQ ID NO: 211)
D4_4-23_Phz0 xGxxxGGNxxx 11, 10, (SEQ ID NO: 212)
D1_1-26_Phz2 xxxSGSYxxx 10, 35, (SEQ ID NO: 213)
D6_6-13_Phz1 xxxSSSWxxx 10, 35, (SEQ ID NO: 214)
D4_4-17_Phz2 xxxxTTVTTx 10, 20, (SEQ ID NO: 215)
D2_2-21_Phz0 xxxC(SG)GDxCx 10, 16, (SEQ ID NO: 216)
D6_6-19_Phz0 xxx(IV)AVAGxx 10, 14, (SEQ ID NO: 217)
D3_3-10_Phz1 xxLWFGELxx 10, 13, (SEQ ID NO: 218)
D5_5-24_Phz0 GxxWLxxxxF 10, 11, (SEQ ID NO: 219)
D5_5-05_Phz1 xxxDTxMVxx 10, 10, (SEQ ID NO: 220)
D3_3-16_Phz1 xxxxxGExxx 10, 8, (SEQ ID NO: 221)
D6_6-19_Phz1 xxxxSGWxx 9, 48, (SEQ ID NO: 222)
D5_5-24_Phz2 xxxxGYNxx 9, 13, (SEQ ID NO: 223)
D3_3-10_Phz2 xxxVRGVxx 9, 11, (SEQ ID NO: 224)
D6_6-06_Phz0 xxxIAAxxx 9, 11, (SEQ ID NO: 225)
D1_1-07_Phz2 xxYxWNxxx 9, 9, (SEQ ID NO: 226)
D4_4-17_Phz0 xxxYGDxx 8, 29, (SEQ ID NO: 227)
D1_1-26_Phz1 xxVGATxx 8, 13, (SEQ ID NO: 228)
D6_6-06_Phz1 xxxYSSSx 8, 9, (SEQ ID NO: 229)
TABLE 15P
Lengths of CDRs: 1095 actual VH domains and 51 VH GLGs.
Length 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
CDR1 0 0 10 0 1 820 38 175 1 1 5 1 11 0 23 1 7 0
GLG 0 0 0 0 0 38 3 10 0 0 . . .
CDR2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 464 579
GLG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 17 28
CDR3 0 0 0 4 2 8 6 28 40 65 77 90 117 117 88 105 86 81
Length 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 (33 or more)
CDR2 9 31 1 3 3 1 0 0 0 0 2 0 0 . . .
GLG 1 4 0 0 . . .
CDR3 45 36 36 16 16 8 8 2 3 0 2 1 0 0 1 5
TABLE 16P
Library of HC CDR3
Component Fraction of Length #X Complexity library Adjusted
1: YYCA21111YFDYWG. 8 4 2.6 E 5 .10 (0-8) .02
(2 = KR; SEQ ID NO: 6)
2: YYCA2111111YFDYWG. 10 6 9.4 E 7 .14 (9-10) .14
(2 = KR; SEQ ID NO: 7)
3: YYCA211111111YFDYTG. 12 8 3.4 E 10 .25 (11 + 12 + .25
(2 = KR; SEQ ID NO: 8) 13/2)
4: YYCAR111S2S3111YFDYWG. 14 6 1.9 e 8 .13 (14 + 13/2) .14
(2 = SG 3 = YW;
SEQ ID NO: 9)
5: YYCA2111CSG11CY1YFDYWG. 15 6 9.4 E 7 .13 (15 + 16/2) .14
(2 = KR; SEQ ID NO: 10)
6: YYCA211S1TIFG11111YFDYWG. 17 8 1.7 E 10 .11 (17 + 16/2) .12
(2 = KR; SEQ ID NO: 11)
7: YYCAR111YY2S33YY111YFDYWG. 18 6 3.8 E 8 .04 (18) .08
(2 = D|G; 3 = S|G;
SEQ ID NO: 12)
8: YYCAR1111YC2231CY111YFDYWG. 19 8 2.0 E 11 .10 (19 on) .11
(2 = S|G; 3 = T|D|G;
SEQ ID NO: 13)
Allowed lengths: 8, 10, 12, 14, 15, 17, 18, & 19
TABLE 17P
vgDNA encoding the CDR3 elements of the library
! CDR3 library components
(Ctop25) 5′-gctctggtcaa C|TTA|AGg|gct|gag|g-3′ (SEQ ID NO: 40)
(CtprmA) 5′-gctctggtcaa C|TTA|AGg|gct|gag|gac-
! AflII...
|acc|gct|gtc|tac|tac|tgc|gcc-3′ (SEQ ID NO: 41)
!
(CBprmB)[RC] 5′-|tac|ttc|gat|tac|ttg|ggc|caa|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′(SEQ ID NO: 42)
! BstEII...
(CBot25)[RC] 5′-|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′(SEQ ID NO: 43)
!
! N.B. [RC] means the the actual oligonucleotide is the reverse complement
! of the one shown.
! N.B. The 20 bases at 3′ end of CtprmA are identical to the most 5′ 20 bases
! of each of the vgDNA molecules.
! N.B. Ctop25 is identical to the most 5′ 25 bases of CtprmA.
! N.B. The 23 most 3′ bases of CBprmB are the reverse complement of the
! most 3′ 23 bases of each of the vgDNA molecules.
! N.B. CBot25 is identical to the 25 bases at the 5′ end of CBprmB.
!
(C1t08) 5′-cc|gct|gtc|tac|tac|tgc|B|-
<2>|<1>|<1>|<1>|<1>-
|tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 44)
! 2 = KR, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C
!
(C2t10) 5′-cc|gct|gtc|tac|tac|tgc|gcc|-
<2>|<1>|<1>|<1>|<1>|<1>|<1>|-
tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 45)
! 2 = KR, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C
!
(C3t12) 5′-cc|gct|gtc|tac|tac|tgc|gcc|-
<2>|<1>|<1>|<1>|<1>|<1>|<1>|<1>|<1>|-
tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 46)
! 2 = KR, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C
!
(C4t14) 5′-cc|gct|gtc|tac|tac|tgc|gcc|cgt|-
|<1>|<1>|<1>|tct|<2>|tct|<3>|<1>|<1>|<1>|-
tac|ttc|gat|tac|ttg|ggc|caa|GG-3 (SEQ ID NO: 47)
! 2 = SG, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C, 3 = YW
!
(C5t15) 5′-cc|gct|gtc|tac|tac|tgc|gcc|-
<2>|<1>|<1>|<1>|tgc|tct|ggt|<1>|<1>|tgc|tat|<1>|-
tac|ttc|gat|tac|ttg|ggc|caa|GG-3 (SEQ ID NO: 48)
! 2 = KR, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C
!
(C6t17) 5′-cc|gct|gtc|tac|tac|tgc|gcc|-
<2>|<1>|<1>|tct|<1>|act|atc|ttc|ggt|<1>|<1>|<1>|<1>|<1>|-
tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 49)
! 2 = KR, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C
!
(C7t18) 5′-cc|gct|gtc|tac|tac|tgc|gcc|cgt|-
|<1>|<1>|<1>|tat|tac|<2>|tct|<3>|<3>|tac|tat|<1>|<1>|<1>|-
tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 50)
! 2 = DG, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C, 3 = SG
!
(c8t19) 5′-cc|gct|gtc|tac|tac|tgc|gcc|cgt|-
|<1>|<1>|<1>|<1>|tat|tgc|<2>|<2>|<3>|<1>|tgc|tat|<1>|<1>|<1>|-
tac|ttc|gat|tac|ttg|ggc|caa|GG-3′ (SEQ ID NO: 51)
! 2 = SG, 1 = 0.27Y + 0.27G + 0.027{ADEFHIKLMNPQRSTVW} no C, 3 = TDG
!
TABLE 19
Names of 1398 GeneBank entries examined
haj10335 hsa006165 hsa234190 hsa234288 hsa239366 hsa240594 hsa244963
hs201e3 hsa006167 hsa234191 hsa234290 hsa239367 hsa240595 hsa244965
hs201g1 hsa006169 hsa234193 hsa234291 hsa239368 hsa240599 hsa244966
hs201m2 hsa006171 hsa234194 hsa234294 hsa239369 hsa240604 hsa244967
hs202e2 hsa006173 hsa234196 hsa234296 hsa239370 hsa241344 hsa244968
hs202g3 hsa131921 hsa234197 hsa234298 hsa239371 hsa241345 hsa244969
hs202g9 hsa132847 hsa234199 hsa235649 hsa239372 hsa241346 hsa244970
hs202m3 hsa132849 hsa234202 hsa235658 hsa239373 hsa241347 hsa244971
hs203e1 hsa132850 hsa234203 hsa235662 hsa239375 hsa241348 hsa244972
hs203g1 hsa132851 hsa234205 hsa235664 hsa239376 hsa241349 hsa244973
hs203m5 hsa132852 hsa234206 hsa235665 hsa239377 hsa241350 hsa244974
hs204e1 hsa224746 hsa234207 hsa235667 hsa239378 hsa241351 hsa244975
hs204g1 hsa225092 hsa234208 hsa235671 hsa239379 hsa241353 hsa244976
hs3d6hcv hsa225093 hsa234209 hsa235675 hsa239380 hsa241354 hsa244977
hs6d4xa7 hsa230634 hsa234211 hsa235677 hsa239381 hsa241355 hsa244978
hs6d4xb7 hsa230635 hsa234212 hsa238036 hsa239382 hsa241356 hsa244979
hs6d4xf1 hsa230636 hsa234214 hsa238037 hsa239383 hsa241357 hsa244980
hs6d4xf2 hsa230637 hsa234217 hsa238038 hsa239384 hsa241420 hsa244981
hs6d4xg3 hsa230638 hsa234221 hsa238039 hsa239385 hsa241421 hsa244982
hs6d4xh5 hsa230639 hsa234224 hsa238040 hsa239386 hsa242555 hsa244983
hs83x6b2 hsa230640 hsa234227 hsa238326 hsa239387 hsa242556 hsa244984
hs83x6b5 hsa230641 hsa234229 hsa238327 hsa239388 hsa243108 hsa244985
hs83x6c3 hsa230643 hsa234230 hsa238328 hsa239390 hsa243110 hsa244986
hs83x6c4 hsa230644 hsa234232 hsa239330 hsa239391 hsa244928 hsa244987
hs83x6c5 hsa230645 hsa234235 hsa239331 hsa240553 hsa244929 hsa244988
hs83x6d4 hsa230646 hsa234238 hsa239332 hsa240554 hsa244930 hsa244989
hs83x6f1 hsa230647 hsa234239 hsa239333 hsa240555 hsa244931 hsa244990
hs83x6f2 hsa230648 hsa234242 hsa239334 hsa240556 hsa244932 hsa244991
hs83x6f3 hsa230649 hsa234245 hsa239335 hsa240557 hsa244933 hsa244992
hs83x6f5 hsa230650 hsa234248 hsa239336 hsa240558 hsa244934 hsa244993
hs83x6h3 hsa230651 hsa234249 hsa239337 hsa240559 hsa244935 hsa244994
hs83x9a6 hsa230652 hsa234251 hsa239338 hsa240560 hsa244936 hsa244995
hs83x9b6 hsa230653 hsa234252 hsa239339 hsa240561 hsa244937 hsa244996
hs83x9b9 hsa230654 hsa234255 hsa239340 hsa240562 hsa244938 hsa244997
hs83x9c8 hsa230655 hsa234256 hsa239341 hsa240563 hsa244939 hsa244998
hs83x9d6 hsa230656 hsa234257 hsa239342 hsa240564 hsa244940 hsa244999
hs83x9d7 hsa230657 hsa234258 hsa239343 hsa240565 hsa244941 hsa245000
hs83x9e6 hsa230658 hsa234259 hsa239344 hsa240566 hsa244942 hsa245001
hs83x9e8 hsa234156 hsa234260 hsa239345 hsa240567 hsa244943 hsa245002
hs83x9e9 hsa234158 hsa234262 hsa239346 hsa240568 hsa244944 hsa245003
hs83x9f6 hsa234160 hsa234263 hsa239347 hsa240569 hsa244945 hsa245004
hs83x9g6 hsa234161 hsa234264 hsa239348 hsa240570 hsa244946 hsa245005
hs9d4x10 hsa234163 hsa234266 hsa239349 hsa240571 hsa244947 hsa245006
hs9d4x7 hsa234164 hsa234268 hsa239350 hsa240572 hsa244948 hsa245007
hs9d4x8 hsa234166 hsa234269 hsa239351 hsa240573 hsa244949 hsa245008
hs9d4x9 hsa234168 hsa234270 hsa239353 hsa240575 hsa244950 hsa245009
hs9d4xa6 hsa234169 hsa234272 hsa239354 hsa240576 hsa244951 hsa245010
hs9d4xa7 hsa234171 hsa234273 hsa239355 hsa240578 hsa244952 hsa245011
hs9d4xb6 hsa234172 hsa234274 hsa239356 hsa240580 hsa244953 hsa245012
hs9d4xc2 hsa234175 hsa234276 hsa239357 hsa240581 hsa244954 hsa245013
hs9d4xd6 hsa234178 hsa234277 hsa239358 hsa240582 hsa244955 hsa245014
hs9d4xe6 hsa234180 hsa234279 hsa239359 hsa240585 hsa244956 hsa245015
hs9d4xf3 hsa234181 hsa234281 hsa239360 hsa240586 hsa244957 hsa245016
hs9d4xh4 hsa234183 hsa234282 hsa239361 hsa240588 hsa244958 hsa245017
hs9d4xh5 hsa234184 hsa234283 hsa239362 hsa240589 hsa244959 hsa245018
hsa005975 hsa234186 hsa234284 hsa239363 hsa240590 hsa244960 hsa245019
hsa005977 hsa234187 hsa234286 hsa239364 hsa240592 hsa244961 hsa245020
hsa006161 hsa234189 hsa234287 hsa239365 hsa240593 hsa244962 hsa245021
hsa245022 hsa245217 hsa245305 hsa279524 hsabhiv8 hsb8g2g08 hsevh52a1
hsa245023 hsa245218 hsa245307 hsa279526 hsadeigvh hsb8g3b07 hsevh52a2
hsa245024 hsa245219 hsa245309 hsa279527 hsaj2768 hsb8g3c07 hsevh52a3
hsa245025 hsa245220 hsa245311 hsa279528 hsaj2769 hsb8g3c08 hsevh52a4
hsa245026 hsa245221 hsa245312 hsa279529 hsaj2771 hsb8g3c12 hsevh52a5
hsa245027 hsa245222 hsa245313 hsa279530 hsaj2772 hsb8g3d03 hsevh52b1
hsa245028 hsa245223 hsa245315 hsa279531 hsaj2773 hsb8g3d04 hsevh53a1
hsa245029 hsa245224 hsa245317 hsa279532 hsaj2776 hsb8g3d07 hsevh53a2
hsa245030 hsa245225 hsa245318 hsa279533 hsaj2777 hsb8g3d08 hsfog1h
hsa245031 hsa245226 hsa245319 hsa279535 hsaj4083 hsb8g3e02 hsfog3h
hsa245032 hsa245228 hsa245320 hsa279536 hsaj4899 hsb8g3e03 hsfogbh
hsa245033 hsa245229 hsa245321 hsa279537 hsasighc hsb8g3f03 hsfom1h
hsa245034 hsa245230 hsa245322 hsa279543 hsavh510 hsb8g3g01 hsfs10hc
hsa245035 hsa245231 hsa245323 hsa279544 hsavh512 hsb8g3g03 hsfs11hc
hsa245036 hsa245232 hsa245325 hsa279545 hsavh513 hsb8g3g05 hsfs9whc
hsa245037 hsa245233 hsa245326 hsa279552 hsavh514 hsb8g3g10 hsgad2h
hsa245039 hsa245234 hsa245338 hsa389169 hsavh515 hsb8g3h01 hsgvh0117
hsa245040 hsa245235 hsa245342 hsa389170 hsavh516 hsb8g4c02 hsgvh0118
hsa245041 hsa245236 hsa245343 hsa389171 hsavh517 hsb8g4e01 hsgvh0119
hsa245042 hsa245237 hsa245345 hsa389172 hsavh519 hsb8g4e05 hsgvh0120
hsa245043 hsa245238 hsa245346 hsa389173 hsavh520 hsb8g4f11 hsgvh0121
hsa245044 hsa245239 hsa245347 hsa389174 hsavh523 hsb8g4h09 hsgvh0122
hsa245045 hsa245240 hsa245348 hsa389175 hsavh524 hsb8g4h10 hsgvh0123
hsa245046 hsa245241 hsa245349 hsa389176 hsavh526 hsb8g5d10 hsgvh0124
hsa245047 hsa245246 hsa245350 hsa389177 hsavh529 hsb8g5h08 hsgvh0201
hsa245048 hsa245251 hsa245352 hsa389178 hsavh53 hsbel1 hsgvh0202
hsa245049 hsa245255 hsa245353 hsa389179 hsavh56 hsbel14 hsgvh0203
hsa245050 hsa245258 hsa245355 hsa389180 hsb3g4a07 hsbel28 hsgvh0204
hsa245051 hsa245260 hsa245356 hsa389181 hsb73g04n hsbel29 hsgvh0205
hsa245052 hsa245261 hsa245357 hsa389182 hsb74a08n hsbel3 hsgvh0206
hsa245053 hsa245262 hsa245358 hsa389183 hsb7g1a11 hsbel34 hsgvh0207
hsa245054 hsa245263 hsa245359 hsa389184 hsb7g2b01 hsbel43 hsgvh0208
hsa245055 hsa245265 hsa249378 hsa389185 hsb7g3a01 hsbel45 hsgvh0209
hsa245056 hsa245266 hsa249628 hsa389186 hsb7g3a05 hsbel5 hsgvh0210
hsa245057 hsa245268 hsa249629 hsa389187 hsb7g3a10 bsbel54 hsgvh0211
hsa245058 hsa245272 hsa249630 hsa389188 hsb7g3b02 bsbel69 hsgvh0213
hsa245059 hsa245273 hsa249631 hsa389190 hsb7g3b03 hsbo1vhig hsgvh0214
hsa245060 hsa245275 hsa249632 hsa389191 hsb7g3b05 hsbo3vhig hsgvh0215
hsa245061 hsa245277 hsa249633 hsa389192 hsb7g3c03 hsbr1vhig hsgvh0216
hsa245062 hsa245278 hsa249634 hsa389193 hsb7g3c12 hsbradh3 hsgvh0217
hsa245063 hsa245279 hsa249635 hsa389194 hsb7g3d07 hscal4ghc hsgvh0218
hsa245064 hsa245280 hsa249636 hsa389195 hsb7g3e01 hsd4xd10 hsgvh0219
hsa245065 hsa245281 hsa249637 hsa389927 hsb7g3f02 hsd4xf21 hsgvh0220
hsa245066 hsa245282 hsa271600 hsa389929 hsb7g3f10 hsd4xg2 hsgvh0221
hsa245067 hsa245283 hsa271601 hsa6351 hsb7g3g02 hsd4xi10 hsgvh0222
hsa245068 hsa245284 hsa271602 hsa7321 hsb7g3g04 hsd4xi4 hsgvh0223
hsa245069 hsa245285 hsa271603 hsa7322 hsb7g4a08 hsd4xk9 hsgvh0224
hsa245071 hsa245286 hsa271604 hsa7323 hsb7g4c05 hsd4xl3 hsgvh0302
hsa245072 hsa245287 hsa279513 hsa7325 hsb7g4d09 hsd5hc hsgvh0304
hsa245073 hsa245288 hsa279514 hsa7326 hsb7g4f08 hsdo1vhig hsgvh0306
hsa245201 hsa245289 hsa279515 hsa7328 hsb7g4g07 hseliepa1 hsgvh0307
hsa245203 hsa245290 hsa279516 hsa7438 hsb7g5g03 hseliepa3 hsgvh0308
hsa245204 hsa245291 hsa279517 hsa7440 hsb8g1c04 hseliepa4 hsgvh0309
hsa245208 hsa245292 hsa279519 hsa7441 hsb8g1e04 hseliepb2 hsgvh0310
hsa245209 hsa245294 hsa279520 hsa7442 hsb8g1f03 hseliepd2 hsgvh0311
hsa245210 hsa245298 hsa279521 hsa7443 hsb8g1g04 hselilpb1 hsgvh0312
hsa245214 hsa245299 hsa279522 hsa7444 hsb8g1h02 hsevh51a1 hsgvh0314
hsa245215 hsa245301 hsa279523 hsaarma1 hsb8g2f09 hsevh51b1 hsgvh0315
hsgvh0318 hsig001vh hsighpat5 hsigvhc07 hsimghc1 hsmvh0401 hsrou233
hsgvh0320 hsig030vh hsighpat6 hsigvhc08 hsimghc2 hsmvh0403 hsrt792hc
hsgvh0321 hsig033vh hsighpat7 hsigvhc09 hsimghc3 hsmvh0404 hsrt79hc
hsgvh0322 hsig039vh hsighpat8 hsigvhc10 hsimghc4 hsmvh0405 hssm1vhig
hsgvh0323 hsig040vh hsighpat9 hsigvhc11 hsimghcS hsmvh0406 hssp46a
hsgvh0324 hsig055vh hsighpt11 hsigvhc12 hsin42p5 hsmvh0501 hst14vh
hsgvh0325 hsig057vh hsighpt12 hsigvhc14 hsin51p7 hsmvh0502 hst14x1
hsgvh0326 hsig1059 hsighpta1 hsigvhc16 hsin51p8 hsmvh0503 hst14x10
hsgvh0327 hsig10610 hsighvb5 hsigvhc17 hsin78 hsmvh0504 hst14x11
hsgvh0328 hsig13g10 hsighvca hsigvhc18 hsin87 hsmvh0505 hst14x12
hsgvh0329 hsig473 hsighvcb hsigvhc19 hsin89p2 hsmvh0506 hst14x13
hsgvh0330 hsig7sa11 hsighvcc hsigvhc20 hsin92 hsmvh0507 hst14x14
hsgvh0331 hsigaehc hsighvcd hsigvhc21 hsin98p1 hsmvh0508 hst14x15
hsgvh0332 hsigaf2h2 hsighvce hsigvhc22 hsjac10h hsmvh0509 hst14x16
hsgvh0333 hsigashc hsighvm hsigvhc23 hsjhba1f hsmvh0510 hst14x17
hsgvh0334 hsigathc hsighxx1 hsigvhc24 hsjhbr2f hsmvh0511 hst14x18
hsgvh0335 hsigdvrhc hsighxx10 hsigvhc25 hsjhej1f hsmvh0513 hst14x19
hsgvh0336 hsigg1kh hsighxx11 hsigvhc26 hsld1110 hsmvh0515 hst14x20
hsgvh0419 hsigg1kl hsighxx12 hsigvhc27 hsld1117 hsmvh0529 hst14x21
hsgvh0420 hsigg1lh hsighxx14 hsigvhc28 hsld152 hsmvh51 hst14x22
hsgvh0421 hsigghc85 hsighxx16 hsigvhc29 hsld21 hsmvh510 hst14x23
hsgvh0422 hsigghcv3 hsighxx18 hsigvhc30 hsld217 hsmvh511 hst14x24
hsgvh0423 hsigghevr hsighxx2 hsigvhc31 hsld218 hsmvh512 hst14x25
hsgvh0424 hsiggvdj1 hsighxx20 hsigvhc32 hsld25 hsmvh515 hst14x3
hsgvh0428 hsiggvdj2 hsighxx21 hsigvhc33 hsmad2h hsmvh516 hst14x6
hsgvh0429 hsiggvhb hsighxx22 hsigvhc35 hsmbcl5h4 hsmvh517 hst14x7
hsgvh0430 hsiggvhc hsighxx23 hsigvhc36 hsmica1h hsmvh53 hst14x8
hsgvh0517 hsigh10g1 hsighxx25 hsigvhc37 hsmica3h hsmvh54 hst14x9
hsgvh0519 hsigh10g2 hsighxx26 hsigvhc38 hsmica4h hsmvh55 hst22x1
hsgvh0522 hsigh10g3 hsighxx28 hsigvhc39 hsmica5h hsmvh56 hst22x11
hsgvh0523 hsigh10g4 hsighxx29 hsigvhc40 hsmica6h hsmvh57 hst22x12
hsgvh0526 hsigh10g5 hsighxx3 hsigvhc41 hsmica7h hsmvh58 hst22x13
hsgvh0527 hsigh10g7 hsighxx30 hsigvhc42 hsmt11ige hsmvh59 hst22x14
hsgvh0531 hsigh10g8 hsighxx31 hsigvhc43 hsmt12ige hsnamembo hst22x15
hsgvh511 hsigh10g9 hsighxx32 hsigvhls hsmt13ige hsnpb346e hst22x18
hsgvh512 hsigh13g1 hsighxx34 hsigvhttd hsmt14ige hsoak3h hst22x20
hsgvh513 hsigh13g7 hsighxx36 hsigvp151 hsmt15ige hsog31h hst22x21
hsgvh515 hsigh14g1 hsighxx37 hsigvp152 hsmt16ige hspag1h hst22x22
hsgvh519 hsigh14g2 hsighxx38 hsigvp153 hsmt17ige hsrael hst22x23
hsgvh521 hsigh2f2 hsighxx5 hsigvp154 hsmt21ige hsregah hst22x25
hsgvh526 hsigh3135 hsighxx6 hsigvp155 hsmt22ige hsrfabh37 hst22x26
hsgvh530 hsigh35 hsighxx7 hsigvp156 hsmt23ige hsrighvja hst22x27
hsgvh533 hsigh44 hsighxx8 hsigvp157 hsmt24ige hsrighvjb hst22x28
hsgvh534 hsigh4c2 hsighxx9 hsigvp158 hsmt25ige hsrou10 hst22x30
hsgvh535 hsigh9e1 hsigkrf hsigvp251 hsmt26ige hsrou11 hst22x9
hsgvh536 hsighadi2 hsigmhavh hsigvp255 hsmt27ige hsrou111 hsu24687
hsgvh55 hsighadi3 hsigrhe15 hsigvp256 hsmutuiem hsrou112 hsu24688
hsh217e hsighcvr hsigtgk1h hsigvp257 hsmvh0001 hsrou119 hsu24690
hsh241e hsighcza hsigtgk4h hsigvp360 hsmvh0002 hsrou122 hsu24691
hsh28e hsighczb hsigtgl9h hsigvp363 hsmvh0003 hsrou126 hsv52a512
hsha3d1ig hsighczc hsigvarh1 hsigvp369 hsmvh0004 hsrou127 hsvdj10h
hshambh hsighczd hsigvhc hsigvp39 hsmvh0005 hsrou129 hsvdj12h
hshcmg42 hsighczf hsigvhc01 hsihr8 hsmvh0006 hsrou13 hsvgcg1
hshcmg43 hsighczg hsigvhc02 hsihr9 hsmvh0007 hsrou131 hsvgcm1
hshcmg44 hsigheavy hsigvhc03 hsihv1 hsmvh0009 hsrou18 hsvgcm2
hshcmg46 hsighpat2 hsigvhc04 hsihv11 hsmvh0010 hsrou219 hsvh1djh6
hshcmt42 hsighpat3 hsigvhc05 hsihv18 hsmvh0011 hsrou221 hsvh3djh4
hshcmt47 hsighpat4 hsigvhc06 hsim9vch hsmvh0012 hsrou222 hsvh4dj
hsvh4djh6 hsvhic11 hsww1p10e hsy14935 hsz80377 hsz80424 hsz80482
hsvh4r hsvhic2 hsx98932 hsy14936 hsz80378 hsz80426 hsz80483
hsvh52a43 hsvhic3 hsx98933 hsy14937 hsz80383 hsz80427 hsz80487
hsvh52a55 hsvhid1 hsx98934 hsy14938 hsz80385 hsz80429 hsz80489
hsvh5dj hsvhid5 hsx98935 hsy14939 hsz80386 hsz80433 hsz80492
hsvh5djh5 hsvhid7 hsx98936 hsy14940 hsz80388 hsz80436 hsz80495
hsvh710p1 hsvhid9 hsx98938 hsy14943 hsz80390 hsz80438 hsz80496
hsvheg7 hsvhie4 hsx98939 hsy14945 hsz80391 hsz80439 hsz80499
hsvhfa2 hsvhif10 hsx98940 hsy18120 hsz80392 hsz80441 hsz80500
hsvhfa7 hsvhif3 hsx98941 hsz74663 hsz80393 hsz80442 hsz80502
hsvhfb5 hsvhif7 hsx98943 hsz74665 hsz80394 hsz80443 hsz80504
hsvhfc2 hsvhig2 hsx98944 hsz74668 hsz80397 hsz80445 hsz80507
hsvhfd7 hsvhp2 hsx98945 hsz74671 hsz80400 hsz80458 hsz80509
hsvhfe5 hsvhp29 hsx98946 hsz74672 hsz80403 hsz80459 hsz80512
hsvhfg9 hsvhp30 hsx98947 hsz74682 hsz80406 hsz80460 hsz80513
hsvhgd8 hsvhp32 hsx98948 hsz74688 hsz80407 hsz80461 hsz80517
hsvhgd9 hsvhp34 hsx98950 hsz74690 hsz80409 hsz80462 hsz80519
hsvhgh7 hsvhp4 hsx98951 hsz74693 hsz80411 hsz80463 hsz80520
hsvhha10 hsvhp46 hsx98952 hsz74695 hsz80412 hsz80465 hsz80527
hsvhia2 hsvhp48 hsx98953 hsz80363 hsz80414 hsz80466 hsz80534
hsvhia5 hsvhp53 hsx98954 hsz80364 hsz80415 hsz80473 hsz80538
hsvhib12 hsvhp7 hsx98955 hsz80365 hsz80416 hsz80474 hsz80544
hsvhib6 hsvigd9 hsx98956 hsz80367 hsz80417 hsz80475 hsz80545
hsvhib8 hswad35vh hsx98958 hsz80368 hsz80418 hsz80476
hsvhic1 hswanembo hsx98963 hsz80372 hsz80421 hsz80477
hsvhic10 hswo1vhig hsy14934 hsz80375 hsz80422 hsz80480
TABLE 20P
Human GLG CDR1 & CDR2 AA seqs
CDR1 1 1 1
Name 1234567 CDR2 1234567890123456789
1-02 GYY-MH (SEQ ID NO: 230) WINPNSGG--TNYAQKFQG (SEQ ID NO: 231)
1-03 SYA--MH (SEQ ID NO: 232) WINAGNGN--TKYSQKFQG (SEQ ID NO: 233)
1-08 SYD--IN (SEQ ID NO: 234) WMNPNSGN--TGYAQKFQG (SEQ ID NO: 235)
1-18 SYG--IS (SEQ ID NO: 236) WISAYNGN--TNYAQKLQG (SEQ ID NO: 237)
1-24 ELS--MH (SEQ ID NO: 238) GFDPEDGE--TIYAQKFQG (SEQ ID NO: 239)
1-45 YRY--LH (SEQ ID NO: 240) WITPFNGN--TNYAQKFQD (SEQ ID NO: 241)
1-46 SYY--MH (SEQ ID NO: 242) IINPSGGS--TSYAQKFQG (SEQ ID NO: 243)
1-58 SSA--VQ (SEQ ID NO: 244) WIVVGSGN--TNYAQKFQE (SEQ ID NO: 245)
1-69 SYA--IS (SEQ ID NO: 246) GIIPIFGT--ANYAQKFQG (SEQ ID NO: 247)
1-e SYA--IS (SEQ ID NO: 248) GIIPIFGT--ANYAQKFQG (SEQ ID NO: 249)
1-f DYY--MH (SEQ ID NO: 250) LVDPEDGE--TIYAEKFQG (SEQ ID NO: 251)
2-05 TSGVGVG (SEQ ID NO: 252) LIYWNDDK---RYSPSLKS (SEQ ID NO: 253)
2-26 NARMGVS (SEQ ID NO: 254) HIFSNDEK---SYSTSLKS (SEQ ID NO: 255)
2-70 TSGMRVS (SEQ ID NO: 256) RIDWDDDK---FYSTSLKT (SEQ ID NO: 257)
3-07 SYW--MS (SEQ ID NO: 258) NIKQDGSE--KYYVDSVKG (SEQ ID NO: 259)
3-09 DYA--MH (SEQ ID NO: 260) GISWNSGS--IGYADSVKG (SEQ ID NO: 261)
3-11 DYY--MS (SEQ ID NO: 262) YISSSGST--IYYADSVKG (SEQ ID NO: 263)
3-13 SYD--MH (SEQ ID NO: 264) AIGTAGD---TYYPGSVKG (SEQ ID NO: 265)
3-15 NAW--MS (SEQ ID NO: 266) RIKSKIDGGITDYAAPVKG (SEQ ID NO: 267)
3-20 DYG--MS (SEQ ID NO: 268) GINWNGGS--TGYADSVKG (SEQ ID NO: 269)
3-21 SYS--MN (SEQ ID NO: 270) SISSSSSY--IYYADSVKG (SEQ ID NO: 271)
3-23 SYA--MS (SEQ ID NO: 272) AISGSGGS--TYYADSVKG (SEQ ID NO: 273)
3-30 SYG--MH (SEQ ID NO: 274) VISYDGSN--KYYADSVKG (SEQ ID NO: 275)
3303 SYA--MH (SEQ ID NO: 276) VISYDGSN--KYYADSVKG (SEQ ID NO: 277)
3305 SYG--MH (SEQ ID NO: 278) VISYDGSN--KYYADSVKG (SEQ ID NO: 279)
3-33 SYG--MH (SEQ ID NO: 280) VIWYDGSN--KYYADSVKG (SEQ ID NO: 281)
3-43 DYT--MH (SEQ ID NO: 282) LISWDGGS--TYYADSVKG (SEQ ID NO: 283)
3-48 SYS--MN (SEQ ID NO: 284) YISSSSST--IYYADSVKG (SEQ ID NO: 285)
3-49 DYA--MS (SEQ ID NO: 286) FIRSKAYGGTTEYTASVKG (SEQ ID NO: 287)
3-53 SNY--MS (SEQ ID NO: 288) VIYSGGS---TYYADSVKG (SEQ ID NO: 289)
3-64 SYA--MH (SEQ ID NO: 290) AISSNGGS--TYYANSVKG (SEQ ID NO: 291)
3-66 SNY--MS (SEQ ID NO: 292) VIYSGGS---TYYADSVKG (SEQ ID NO: 293)
3-72 DHY--MD (SEQ ID NO: 294) RTRNKANSYTTEYAASVKG (SEQ ID NO: 295)
3-73 GSA--MH (SEQ ID NO: 296) RIRSKANSYATAYAASVKG (SEQ ID NO: 297)
3-74 SYW--MH (SEQ ID NO: 298) RINSDGSS--TSYADSVKG (SEQ ID NO: 299)
3-d SNE--MS (SEQ ID NO: 300) SISGGS----TYYADSRKG (SEQ ID NO: 301)
4-04 SSNW-WS (SEQ ID NO: 302) EIYHSGS---TNYNPSLKS (SEQ ID NO: 303)
4-28 SSNW-WG (SEQ ID NO: 304) YIYYSGS---TYYNPSLKS (SEQ ID NO: 305)
4301 SGGYYWS (SEQ ID NO: 306) YIYYSGS---TYYNPSLKS (SEQ ID NO: 307)
4302 SGGYSWS (SEQ ID NO: 308) YIYHSGS---TYYNPSLKS (SEQ ID NO: 309)
4304 SGDYYWS (SEQ ID NO: 310) YIYYSGS---TYYNPSLKS (SEQ ID NO: 311)
4-31 SGGYYWS (SEQ ID NO: 312) YIYYSGS---TYYNPSLKS (SEQ ID NO: 313)
4-34 GYY--WS (SEQ ID NO: 314) EINHSGS---TNYNPSLKS (SEQ ID NO: 315)
4-39 SSSYYWG (SEQ ID NO: 316) SIYYSGS---TYYNPSLKS (SEQ ID NO: 317)
4-59 SYY--WS (SEQ ID NO: 318) YIYYSGS---TNYNPSLKS (SEQ ID NO: 319)
4-61 SGSYYWS (SEQ ID NO: 320) YIYYSGS---TNYNPSLKS (SEQ ID NO: 321)
4-b SGYY-WG (SEQ ID NO: 322) SIYHSGS---TYYNPSLKS (SEQ ID NO: 323)
5-51 SYW--IG (SEQ ID NO: 324) IIYPGDSD--TRYSPSFQG (SEQ ID NO: 325)
5-a SYW--IS (SEQ ID NO: 326) RIDPSDSY--TNYSPSFQG (SEQ ID NO: 327)
6-1 SNSAAWN (SEQ ID NO: 328) RTYYRSKWY-NDYAVSVKS (SEQ ID NO: 329)
74.1 SYA--MN (SEQ ID NO: 330) WINTNIGN--PTYAQGFIG (SEQ ID NO: 331)
CDR1 of human GLGs
A C D E F G H I K L M N P Q R S T V W Y — Consens.
1 7 1 3 2 35 2 1 Sd x
2 2 6 1 1 4 1 7 29 Ysg x
3 11 3 1 10 2 1 6 1 5 11 YAGS x
4 1 2 1 2 7 38 —
5 1 2 1 1 5 41 —
6 6 1 28 4 12 Mwi
7 1 5 16 5 1 23 SHng
CDR2 of human GLGs
1 3 2 1 5 1 2 3 1 7 4 6 7 9 X
2 1 46 1 2 1 I
3 4 1 1 2 2 8 3 12 1 1 1 15 ysn x
4 2 2 4 1 10 1 11 2 1 5 12 ysp x
5 1 8 2 1 6 2 4 8 1 17 1 sd x
6 3 7 2 26 3 8 2 Gsd x
7 4 1 17 1 2 24 1 1 SG x
8 1 3 3 3 10 9 4 1 2 15 -ns
9 2 3 46 —
10 1 3 47 —
11 2 4 5 1 1 35 3 T
12 1 2 2 1 3 2 1 11 2 3 1 22 Yn x
13 51 Y
14 31 11 1 6 1 1 An x
15 4 16 1 1 1 14 11 2 1 dpq x
16 1 11 1 38 Sk
17 13 15 1 22 Vlf
18 37 13 1 Kq
19 1 1 34 14 1 GS
TABLE 21P
Tallies of Amino-acid frequencies in mature CDR1 and CDR2
Tally of 23 examples with length 14
A C D E F G H I K L M N P Q R S T V W Y | X
1 8 2 13
2 3 15 3 2
3 2 1 14 1 5
4 2 2 11 5 3
5 7 1 1 13 1
6 1 4 3 12 2 1
7 3 1 1 2 1 5 10
8 6 1 1 2 1 6 4 2
9 1 5 1 3 1 4 7 1
10 1 8 3 1 2 1 4 1 2
11 1 1 1 1 2 1 16
12 1 2 1 1 1 1 1 1 14
13 4 2 17
14 4 1 5 4 5 4
Tally of 11 examples with length 12
A C D E F G H I K L M N P Q R S T V W Y | X
1 4 7
2 1 4 4 2
3 7 4
4 1 1 1 5 2 1
5 1 9 1
6 2 1 3 2 3
7 3 1 3 1 3
8 1 3 2 1 2 2
9 1 1 9
10 1 10
11 11
12 2 1 7 1
Tally of 175 examples with length 7
A C D E F G H I K L M N P Q R S T V W Y | X
1 2 1 1 2 1 3 2 153 10
2 3 2 1 87 1 10 1 5 61 2 2
3 3 26 1 54 1 5 1 2 76 3 1 2
4 6 1 1 6 1 2 1 11 1 145
5 5 2 13 2 2 3 6 2 140
6 1 1 1 13 159
7 2 1 67 1 10 88 5 1
Tally of 38 examples with length 6
A C D E F G H I K L M N P 4 R S T V W Y | X
1 2 34 2
2 1 2 1 8 4 22
3 3 26 9
4 1 1 29 7
5 38
6 10 3 3
Tally of 820 examples with length 5
A C D E F G H I K L M N P Q R S T V W Y Seen
1 8 81 10 151 4 8 5 3 100 4 15 364 55 8 4 SGNDT x 15
2 7 5 12 24 1 30 1 1 5 26 1 1 23 2 681 Y 15
3 202 4 24 13 13 133 10 2 7 5 2 3 32 14 13 112 231 YAGW x 17
4 6 172 2 7 409 3 16 205 MWI 8
5 8 6 1 1 49 241 2 79 1 3 367 56 2 4 SHNTx 14
CDR2
Tally of 31 examples with CDR2 of length 19
A C D E F G H I K L M N P Q R S T V W Y X RF x
1 11 1 1 1 15 1 1 I
2 1 28 2 Rk
3 9 1 18 1 1 1 S
4 1 2 6 21 1 K x
5 1 1 1 22 1 1 1 1 1 1 A x
6 16 1 1 1 1 3 1 6 1 y x
7 1 9 7 3 1 10 G
8 23 1 1 5 1 G
9 2 18 1 1 1 7 1 T
10 4 1 1 1 1 1 21 1 T
11 1 3 1 26 x
12 2 11 9 1 1 1 1 2 1 2 Y
13 1 1 29 A
14 29 1 1 A
15 25 3 1 1 1 Sp
16 1 10 20 V
17 1 1 29 K
18 1 27 1 2 G
19 1 30
Tally of 579 (n > 50, bold; over 400, underscored) examples with length 17
A C D E F G H I K L M N P Q R S T V W Y X
1 44 1 1 2 11 81 5 69 1 14 6 41 1 4 34 30 19 118 66 31 VGIW x
2 7 522 1 10 17 1 3 3 8 10 I
3 3 1 22 5 7 6 51 25 1 76 8 262 19 1 46 46 SNIx
4 39 2 8 6 16 64 9 3 2 3 15 178 23 6 50 11 8 16 120 PYGx
5 3 194 6 1 70 6 44 6 4 1 55 4 8 133 9 7 1 27 DSGN x
6 3 1 75 4 45 326 1 6 43 1 63 8 1 2 GDS x
7 8 24 5 226 3 3 3 4 24 2 11 245 14 6 1 SG x
8 4 2 57 37 5 22 4 18 18 2 2 161 1 4 11 106 90 2 1 32 NST x
9 56 11 2 63 157 1 3 3 11 5 13 4 242 8 TKIA x
10 1 14 2 13 30 23 6 29 2 3 110 3 52 20 10 1 1 259 YNR x
11 2 7 5 1 4 3 5 551 Y
12 405 1 2 18 1 6 2 3 1 89 8 44 A
13 7 323 22 7 4 1 4 66 138 3 1 3 DQP x
14 2 5 6 3 123 4 2 7 421 1 2 2 SK x
15 1 1 188 2 1 22 3 1 357 2 1 VF
16 1 13 1 1 332 3 2 1 1 199 21 4 KQ x
17 11 1 565 1 1 G
Tally of 464 (over 50, bold; over 400, underscored)
A C D E F G H I K L M N P Q R S T V W Y X
1 5 13 184 8 1 7 1 2 15 6 3 26 65 9 14 105 EYSL x
2 6 429 3 4 1 2 19 I
3 1 13 13 4 10 5 154 1 12 1 250 YN x
4 1 12 2 6 199 2 1 3 4 5 2 19 28 15 165 YH x
5 5 20 1 1 18 4 9 1 22 365 16 1 1 S x
6 13 8 439 1 1 1 1 G
7 20 2 14 2 4 2 26 1 12 357 20 1 2 1 S x
8 13 2 4 8 1 2 4 3 6 420 1 T
9 10 4 1 10 1 8 1 245 13 9 3 1 1 157 NY x
10 6 2 2 2 1 7 444 Y
11 14 3 1 1 8 408 4 21 2 2 N
12 4 13 4 2 1 418 14 7 1 P
13 2 2 6 452 1 1 S
14 2 2 441 1 18 L
15 18 413 3 5 11 10 1 2 1 K
16 1 1 31 2 2 3 419 5 S
TABLE 22P
Tally of VH types
1-02 16 1-03 16 1-08 13 1-18 27 1-24 5
1-45 0 1-46 14 1-58 1 1-69 37 1-e 16
1-f 1 2-05 13 2-26 1 2-70 2 3-07 33
3-09 13 3-11 15 3-13 4 3-15 10 3-20 4
3-21 25 3-23 85 3-30 55 3303 59 3305 0
3-33 42 3-43 1 3-48 24 3-49 11 3-53 12
3-64 4 3-66 4 3-72 3 3-73 3 3-74 12
3-d 0 4-04 29 4-28 3 4301 46 4302 7
4304 37 4-31 0 4-34 184 4-39 65 4-59 45
4-61 9 4-b 11 5-51 55 5-a 13 6-1 7
74.1 3
TABLE 23P
Oligonucleotides used to variegate CDR1 and CDR2 of human HC
!(name) 5′-....DNA sequence....-3′
!everything to right of an exclamation point is commentary
![RC] means “reverse complement” of sequence shown
! If last non-comment and non-blank character is “-”, then continue
!on next line.
! Ignore case, “a” = “A”, “c” = “C”, etc.
! Ignore “I” and blanks.
! <number> means incorporate trinucleotide mixtue of given number.
!-------------------------------------------------------------------------
!
! CDR1
(ON-R1V1vg) 5′- ct|TCC|GGA|ttc|act|ttc|tct|-
<1>|tac|<1>|atg|<1>|- ! CDR1 of length 5, ON = 55 bases
tgg|gtt|cgC|CAa|gct|ccT|GG-3′ (SEQ ID NO: 27)
! <1> = ADEFGHIKLMNPQRSTVWY no C
!
(ON-R1top) 5′-cctactgtct |TCC|GGA|ttc|act|ttc|tct-3′ (SEQ ID NO: 28)
(ON-R1bot)[RC] 5′-tgg|gtt|cgC|CAa|gct|ccT|GG ttgctcactc-3′ (SEQ ID NO: 29)
(ON-R1V2vg) 5′- ct|TCC|GGA|ttc|act|ttc|tct|-
<6>|<7>|<7>|tac|tac|tgg|<7>|- ! CDR1 of length 7, ON = 61 bases
tgg|gtt|cgC|CAa|gct|ccT|GG-3′ (SEQ ID NO: 30)
! <6> = ST, 1:1
! <7> = 0.2025(SG) + 0.035(ADEFHIKLMNPQRTVWY) no C
(ON-R1V3vg) 5′-ct|TCC|GGA|ttc|act|ttc|tct|-
|atc|agc|ggt|ggt|tct|atc|tcc|<1>|<1>|<1>|tac|tac|tgg|<1>|- ! CDR1, L = 14
tgg|gtt|cgC|CAa|gct|ccT|GG-3′(SEQ ID NO: 31) ! ON = 82 bases
! CDR2
(ON-R2V1vg) 5′-ggt|ttg|gag|tgg|gtt|tct|-
<2>|atc|<2>|<3>|tct|ggt|ggc|<1>|act|<1>|-
tat|gct|gac|tcc|gtt|aaa|gg-3′ (SEQ ID NO: 32)! ON = 68
bases, CDR2 = 17 AA
(ON-R2top) 5′-ct|tgg|gtt|cgC|CAa|gct|ccT|GGt|aaa|ggt|ttg|gag|tgg|gtt|tct-3′
(SEQ ID NO: 33)
(ON-R2bot)[RC] 5 -tat|gct|gac|tcc|gtt|aaa|ggt|-
cgc|ttc|act|atc|TCT|AGA|ttcctgtcac-3′ (SEQ ID NO: 34)! XbaI plus 10
bases of scab
(ON-R2V2vg) 5′-ggt|ttg|gag|tgg|gtt|tct|-
<1>|atc|<4>|<1>|<1>|ggt|<5>|<1>|<1>|<1>|-
tat|gct|gac|tcc|gtt|aaa|gg-3′ (SEQ ID NO: 35)! ON = 68
bases, CDR2 = 17 AA
! <4> = DINSWY, equimolar ! <5> = SGDN, equimolar
(ON-R2V3vg) 5′-ggt|ttg|gag|tgg|gtt|tct|-
<1>|atc|<4>|<1>|<1>|ggt|<5>|<1>|<1>|-
tat|aac|cct|tcc|ctt|aag|gg-3′ (SEQ ID NO: 36)! ON = 65
bases, CDR2 = 16 AA
(ON-R2bo3)[RC] 5′-tat|aac|cct|tcc|ctt|aag|ggt|-
cgc|ttc|act|atc|TCT|AGA|ttcctgtcac-3′ (SEQ ID NO: 37)! XbaI plus 10
bases of scab
(ON-R2V4vg) 5′-ggt|ttg|gag|tgg|gtt|tct|-
<1>|atc|<8>|agt|<1>|<1>|<1>|ggt|ggt|act|act|<1>
tat|gcc|gct|tcc|gtt|aag|gg-3′ (SEQ ID NO: 38)! ON = 74
bases, CDR2 = 19 AA
(ON-R2bo4)[RC] 5′--tat|gcc|gct|tcc|gtt|aag|ggt|-
cgc|ttc|act|atc|TCT|AGA|ttcctgtcac-3′ (SEQ ID NO: 39) ! XbaI plus
10 bases of scab
TABLE 25P
Lengths of CDRs in 285 human kappa chains
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
CDR1 0 0 0 0 0 0 0 0 0 0 0 154 73 3 0 0 28 27 0 0
CDR2 0 0 0 0 0 0 0 285 0 0 0 0 0 0 0 0 0 0 0 0
CDR3 0 5 0 0 1 0 3 2 28 166 63 12 1 1 0 0 0 0 0 1
TABLE 26P
Tally of kappa types: V and J
V genes:
O12 59 O2 0 O18 0 O8 0 A20 0
A30 0 L14 0 L1 2 L15 0 L4 2
L18 0 L5 4 L19 0 L8 4 L23 0
L9 1 L24 0 L11 4 L12 8 O11 10
O1 0 A17 5 A1 0 A18 3 A2 0
A19 13 A3 0 A23 4 A27 79 A11 26
L2 28 L16 0 L6 11 L20 0 L25 0
B3 22 B2 0 A26 0 A10 0 A14 0
JH# 1 2 3 4 5
tally 105 64 29 78 9
TABLE 27P
Names of Kappa chains analyzed
AB022651
AB022653
AB022654
AB022656
AF007572
AF021036
AF103499
AF103500
AF103527
AF103873
AF107244
AF107245
AF107246
AF107247
AF115361
AF165099
AF165101
AF165103
AF165108
AF165110
AF165111
AF184763
AF184767
hsa004955
hsa004956
hsa011133
HSA241367
HSA241375
HSA388639
HSA388640
HSA388641
HSA388642
HSA388643
HSA388644
HSA388645
HSA388646
HSA388647
HSA388648
HSA388650
HSA388651
HSA388652
HSA388653
HSA388654
HSA388655
HSA388656
HSA388657
hsew1vk
hsew3vk
hsew4vk
hsigdpk13
hsigg1kl
HSIGGVKA
hsigk123
hsigk319
hsigklc14
hsigklc28
hsigklc5
hsigklg31
hsigklv01
hsigklv02
hsigklv03
hsigklv04
hsigklv05
hsigklv06
hsigklv07
hsigklv09
hsigklv10
hsigklv12
hsigklv13
hsigklv14
hsigklv15
hsigklv16
hsigklv17
hsigklv18
hsigklv19
hsigklv20
hsigklv21
hsigklv22
hsigklv23
hsigklv24
hsigklv25
hsigklv27
hsigklv28
hsigklv29
hsigklv31
hsigklv32
hsigklv33
hsigklv34
hsigklv35
hsigklv36
hsigklv37
hsigklv38
hsigklv39
hsigklv40
hsigklv41
hsigklv42
hsigklv43
hsigklv44
hsigklv45
hsigklv46
hsigklv49
hsigklv50
hsigklv51
hsigklv52
hsigklv53
hsigklv54a
hsigklv56
hsigklv57
hsigklv58
hsigklv59
hsigklv60
hsigklv61
hsigklv62
hsigklv63
hsigklv65
hsigklv66
hsigklv68
hsigklv69
hsigklv71
hsigkvba
hsigkvbb
hsigkvbc
hsigkvbd
hsigkvbe
hsigkvbf
hsigkvc01
hsigkvc03
hsigkvc06
hsigkvc11
hsigkvc12
hsigkvc20
hsigkvc23
hsigkvc27
hsigkvc29
hsigrklc
hsikcvjp1
hsikcvjp2
hsikcvjp3
hsikcvjp6
hsikcvjp7
hsld110vl
hsld117vl
hsld128vl
hsld140vl
hsld152vl
hsld184vl
hsld198vl
hsld24vl
hsmbcl1k1
hsmbcl1k2
hsmbcl2k2
hsmbcl5k4
hss10avl
hss17bvl
hss1a15vl
HSU44792
HSU44794
HSU94422
hsz84852
hsz84853
humigk1dm
humigk3am
humigk3bm
humigk3cm
humigkacoa
humigkacob
humigkacoc
humigkacoe
humigkacof
humigkb1aa
humigkb1ab
humigkb1ac
humigkvra
humigkvrb
humigkvrc
humigkvrd
humigkvre
humigkvrg
humigkvrh
humigkvri
humigkx
humigky1
humigky2
humigky4
humigky5
humigky6
humigl3ac
humikc
humikca
humikcad
humikcaf
humikcag
humikcah
humikcai
humikcaj
humikcal
humikcam
humikcan
humikcas
humikcau
humikcav
humikcaw
humikcax
humikcay
humikcaz
humikcb
humikcba
humikcbb
humikcbc
humikcbd
humikcbe
humikcbf
humikcbg
humikcbh
humikcbi
humikcbj
humikcbl
humikcbm
humikcbn
humikcbo
humikcbp
humikcbq
humikcbs
humikcbt
humikcbu
humikcbv
humikcbw
humikcbx
humikcbz
humikcc
humikcca
humikccb
humikccc
humikccd
humikcce
humikccf
humikccg
humikcch
humikcci
humikccj
humikcck
humikcco
humikccp
humikccq
humikccr
humikccs
humikcct
humikccu
humikccv
humikccw
humikcd
humikcf
humikcg
humikch
humikci
humikck
humikcm
humikcn
humikco
humikcp
humikcq
humikcr
humikcs
humikct
humikcu
humikcv
humikcva
humikcvb
humikcvc
humikcvd
humikcve
humikcvf
humikcvg
humikcvh
humikcvi
humikcvj
humikcw
humikcx
humikcy
humikcz
S46248
S82746
S82747
SU96396
SU96397
TABLE 28P
AA types seen in 154 kappa sequences having CDR1 of length 11 Tally
A C D E F G H I K L M N P Q R S T V W Y
1 11 143 R
2 148 1 2 2 1 A
3 152 2 S
4 1 3 3 147 Q
5 12 1 27 7 3 99 4 1 S
6 1 81 1 71 V
7 2 4 18 5 1 2 9 12 97 3 1 S
8 3 5 1 2 1 31 1 10 87 12 1 S
9 2 7 10 1 6 29 1 8 13 77 Y
10 2 150 1 1 L
11 96 4 2 46 2 1 3 A
TABLE 30P
Synthetic Kappa light chain gene
!
!
! A27::JH1 with all CDRs replaced by stuffers.
! Each stuffer contains at least one stop codon and a
! restriction site that will be unique within the diversity vector.
!
1 GAGGACCATt GGGCCCC ctccgagact
! Scab...... EcoO109I
! ApaI.
!-----------------------------------
!
28 CTCGAG cgca
! XhoI..
!-----------------------------------
!
38 acgcaatTAA TGTgagttag ctcactcatt aggcacccca ggcTTTACAc tttatgcttc
! ..-35.. Plac ..−10.
!-----------------------------------
!
98 cggctcgtat gttgtgtgga attgtgagcg gataacaatt tc
!-----------------------------------
!
140 acacagga aacagctatgac
!-----------------------------------
!
160 catgatta cgCCAAGCTT TGGagccttt tttttggaga ttttcaac (SEQ ID NO: 54)
! PflMI.......
! Hind3.
!-----------------------------------
!
! M13 III signal sequence (AA seq)--------------------------->
! 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
! M K K L L F A I P L V V P F Y
206 gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac
!----------------------------------
!
! --Signal--> FR1------------------------------------------->
! 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
! S H S A Q S V L T Q S P G T L
251 |agc|cat|aGT|GCA|Caa|tcc|gtc|ctt|act|caa|tct|cct|ggc|act|ctt|
! ApaLI...
!----------------------------------
!
! ----- FR1 ------------------------------------->| CDR1------>
! 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
! S L S P G E R A T L S C R A S (SEQ ID NO: 55)
! |tcG|CTA|AGC|CCG|GGt|gaa|cgt|gct|acC|TTA|AGt|tgc|cgt|gct|tcc|(SEQ ID NO: 54;
! EspI..... AflII...
! XmaI....
!
!----------------------------------
! For CDR1:
! <1> ADEFGHIKLMNPQRSTVWY equimolar
! <2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)
! <3> Y(0.2) ADEFGHIKLMNPQRSTVW (0.044 each)
! In a preferred embodiment, we omit codon 52 in vgDNA for CDR1.
!
! ------- CDR1 --------------------->|--- FR2 --------------->
! <1> <2> <2> xxx <3>
! 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
! Q S V S S S Y L A W Y Q Q K P
|cag|tct|gtt|tcc|tct|tct|tat|ctt|gct|tgg|tat|caa|cag|aaA|CCT|
! SexAI...
!-----------------------------------
! For CDR2:
! <1> ADEFGHIKLMNPQRSTVWY equimolar
! <2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)
! <4> A(0.2) DEFGHIKLMNPQRSTVWY (0.044 each)
! ----- FR2 ------------------------->|------- CDR2 ---------->
! <1> <2> <4>
! 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
! G Q A P R L L I Y G A S S R A
|GGT|caG|GCG|CCg|cgt|tta|ctt|att|tat|ggt|gct|tct|tcc|cgc|gct|
! SexAI.... KasI.... (CDR1 installed as AFlII-(SexAI or KasI) cassette.)
!
!-----------------------------------
!
! CDR2-->|--- FR3 ----------------------------------------------->
! <1>
! 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
! T G I P D R F S G S G S G T D
|act|gGG|ATC|CCG|GAC|CGt|ttc|tct|ggc|tct|ggt|tca|ggt|act|gac|
! BamHI...
! RsrII.....
! (CDR2 installed as (SexAI or KasI) to (BamHI or RsrII) cassette.)
!-----------------------------------
!
! ------ FR3 ------------------------------------------------->
! 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
! F T L T I S R L E P E D F A V
477 |ttt|acc|ctt|act|att|TCT|AGA|ttg|gaa|cct|gaa|gac|ttc|gct|gtt|
! XbaI...
!
!-----------------------------------
!
! ----------->|----CDR3-------------------------->|-----FR4--->
! <3> <1> <1> <1> <1>
! 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
! Y Y C Q Q Y G S S P E T F G Q
|tat|tat|tgC|CAa|cag|taT|GGt|tct|tct|cct|gaa|act|ttc|ggt|caa|
! BstXI...........
!
!-----------------------------------
!
! -----FR4------------------->| <------- Ckappa ------------
! 121 122 123 124 125 126 127 128 129 130 131 132 133 134
! G T K V E I K R T V A A P S
510 |ggt|aCC|AAG|Gtt|gaa|atc|aag| |CGT|ACG|gtt|gcc|gct|cct|agt|
! StyI.... BsiWI..
!
! (CDR3 installed as XbaI to (StyI or BsiWI) cassette.)
!
! 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149
! V F I F P P S D E Q L K S G T
552 |gtg|ttt|atc|ttt|cct|cct|tct|gac|gaa|CAA|TTG|aag|tca|ggt|act|
! MfeI...
!
! 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164
! A S V V C L L N N F Y P R E A
597 |gct|tct|gtc|gta|tgt|ttg|ctc|aac|aat|ttc|tac|cCT|CGT|Gaa|gct|
! BssSI...
!
! 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
! K V Q W K V D N A L Q S G N S
642 |aaa|gtt|cag|tgg|aaa|gtc|gat|aAC|GCG|Ttg|cag|tcg|ggt|aac|agt|
! MluI....
!
! 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194
! Q E S V T E Q D S K D S T Y S
687 |caa|gaa|tcc|gtc|act|gaa|cag|gat|agt|aag|gac|tct|acc|tac|tct|
!
! 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209
! L S S T L T L S K A D Y E K H
732 |ttg|tcc|tct|act|ctt|act|tta|tca|aag|gct|gat|tat|gag|aag|cat|
!
! 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224
! K V Y A C E V T H Q G L S S P
777 |aag|gtc|tat|GCt|TGC|gaa|gtt|acc|cac|cag|ggt|ctG|AGC|TCc|cct|
! SacI....
!
! 225 226 227 228 229 230 231 232 233 234
! V T K S F N R G E C . . (SEQ ID NO: 332)
822 |gtt|acc|aaa|agt|ttc|aaC|CGT|GGt|gaa|tgc|taa|tag GGCGCGCC
! DsaI.... AscI....
! BssHII
!
866 acgcatctctaa GCGGCCGC aacaggaggag (SEQ ID NO: 333)
! NotI....
! EagI..
TABLE 31P
Tally of 285 CDR2s of length 7 in human kappa
Tally A C D E F G H I K L M N P Q R S T V W Y
1 51 62 7 95 1 11 15 2 1 2 6 6 3 22 1 x
2 225 18 5 5 2 1 1 3 16 9 A
3 2 9 1 2 267 2 1 1 S
4 2 1 5 4 9 1 77 4 93 80 2 7 Sx
5 1 2 80 200 2 R
6 162 7 36 4 4 1 3 3 63 2 Ax
7 5 1 3 1 1 2 2 1 125 144 x
TABLE 32P
Tally of 166 CDR3s of length 9 from human kappa.
Tally A C D E F G H I K L M N P Q R S T V W Y
1 4 8 21 131 1 1 Q
2 1 9 2 1 153 Q
3 14 4 4 3 6 4 1 1 3 21 16 3 4 82 Yx
4 1 9 1 2 37 4 2 2 15 1 33 2 20 7 1 29 x
5 2 2 6 3 4 5 3 28 17 7 65 19 1 1 3 x
6 7 1 11 2 3 8 1 4 3 41 33 5 28 19 x
7 1 2 6 146 2 2 5 2 P
8 2 4 1 2 21 7 3 5 1 38 7 4 25 1 3 1 16 25 x
9 3 2 1 1 2 157 T
TABLE 33P
lengths of CDRs in 93 human lambda chains
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18+
CDR1 0 0 0 0 0 0 0 0 0 0 0 23 7 15 46 0 0 0 2
CDR2 5 0 0 1 0 0 0 80 2 0 0 1 4 0 0 0 0 0 1
CDR3 0 0 0 0 0 0 0 0 1 16 28 27 6 1 0 4 6 4 0
TABLE 34P
Tally of 46 CDR1s of length 14 from human lambda chains
Tally A C D E F G H I K L M N P Q R S T V W Y
1 2 2 1 41 T
2 43 3 G
3 2 1 1 6 36 TGx
4 1 45 S
5 5 1 40 S
6 39 1 4 2 DNx
7 8 1 37 V
8 1 42 2 1 G
9 4 1 35 1 2 3 TGx
10 1 1 3 1 2 38 Yx
11 4 1 35 6 DNx
12 3 1 2 1 1 2 36 Yx
13 1 2 43 V
14 1 4 41 S
TABLE 35P
Synthtic human lambda-chain gene
! Lambda 14-7(A) 2a2::JH2::Clambda
! AA sequence tested
!
1 GAGGACCATt GGGCCCC ttactccgtgac
! Scab...... EcoO109I
! ApaI..
!-----------------------------------------------
!
! -----------FR1-------------------------------------------->
! 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
! S A Q S A L T Q P A S V S G S P G
30 aGT|GCA|Caa|tcc|gct|ctc|act|cag|cct|GCT|AGC|gtt|tcc|gGG|TcA|CCt|GGT|
! ApaLI... NheI... BstEII...
! SexAI....
!-----------------------------------------------
!
! For CDR1,
! <1> = 0.27 T, 0.27 G, 0.027 {ADEFHIKLMNPQRSVWY} no C
! <2> = 0.27 D, 0.27 N, 0.027 {AEFGHIKLMPQRSTVWY} no C
! <3> = 0.36 Y, 0.0355{ADEFGHIKLMNPQRSTVW} no C
! T G <1> S S <2> V G
! ------FR1------------------> |-----CDR1---------------------
! 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
! Q S I T I S C T G T S S D V G
|caa|agt|atc|act|att|tct|TGT|ACA|ggt|act|tct|tct|gat|gtt|ggc|
! BsrGI..
!
! a second vg scheme for CDR1 gives segments of length 11:
! G23<2><4>L<4><4><4><3><4><4> where
! <4> = equimolar {ADEFGHIKLMNPQRSTVWY} no C
!-------------------------------------------------------
!
! <1> <3> <2> <3> V S = vg Scheme #1, length = 14
! -----CDR1------------->|--------FR2-------------------------
! 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
! G Y N Y V S W Y Q Q H P G K A
|ggt|tac|aat|tac|gtt|tct|tgg|tat|caa|caa|caC|CCG|GGc|aaG|GCG|
! XmaI.... KasI.....
! AvaI....
!-------------------------------------------------------------------
!
! <4> <4> <4> <2> R P S
! --FR2-----------------> |------CDR2--------------->|-----FR3--
! 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
! P K L M I Y E V S N R P S G V
|CCg|aag|ttg|atg|atc|tac|gaa|gtt|tcc|aat|cgt|cct|tct|ggt|gtt|
! KasI....
!-------------------------------------------------------------------
!
! -------FR3----------------------------------------------------
! 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
! S N R F S G S K S G N T A S L
|agc|aat|cgt|ttc|TCC|GGA|tct|aaa|tcc|ggt|aat|acc|gcA|AGC|TTa|
! BspEI.. | HindIII.
! BsaBI........(blunt)
!-------------------------------------------------------------------
!
! -------FR3-------------------------------------------------->|
! 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
! T I S G L Q A E D E A D Y Y C
|act|atc|tct|ggt|CTG|CAG|gct|gaa|gac|gag|gct|gac|tac|tat|tgt|
! PstI...
!
!-------------------------------------------------------------------
!
! <5> = 0.36 S, 0.0355{ADEFGHIKLMNPQRTVWY} no C
!
! <4> <5> <4> <2> <4> S <4> <4> <4> <4> V
! -----CDR3---------------------------------->|---FR4---------
! 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
! S S Y T S S S T L V V F G G G
|tct|tct|tac|act|tct|tct|agt|acc|ctt|gtt|gtc|ttc|ggc|ggt|GGT|
! KpnI...
!
!------------------------------------------------------------------------
!
! -------FR4-------------->
! 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
! T K L T V L G Q P K A A P S V
279 |ACC|aaa|ctt|act|gtc|ctc|gGT|CAA|CCT|aAG|Gct|gct|cct|tcc|gtt|
! KpnI... HindII..
! Bsu36I...
!
! 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
! T L F P P S S E E L Q A N K A
324 |act|ctc|ttc|cct|cct|agt|tct|GAA|GAG|Ctt|caa|gct|aac|aag|gct|
! SapI.....
!
! 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
! T L V C L I S D F Y P G A V T
369 |act|ctt|gtt|tgc|tTG|ATC|Agt|gac|ttt|tat|cct|ggt|gct|gtt|act|
! BClI....
!
! 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
! V A W K A D S S P V K A G V E
414 |gtc|gct|tgg|aaa|gcc|gat|tct|tct|cct|gtt|aaa|gct|ggt|gtt|GAG|
! BsmBI...
!
! 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
! T T T P S K Q S N N K Y A A S
459 |ACG|acc|act|cct|tct|aaa|caa|tct|aac|aat|aag|tac|gct|gcG|AGC|
! BsmBI.... SacI....
!
! 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
! S Y L S L T P E Q W K S H K S
504 |TCt|tat|ctt|tct|ctc|acc|cct|gaa|caa|tgg|aag|tct|cat|aaa|tcc|
! SacI...
!
! 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210
! Y S C Q V T H E G S T V E K T
549 |tat|tcc|tgt|caa|gtt|acT|CAT|GAa|ggt|tct|acc|gtt|gaa|aag|act|
! BspHI...
!
! 211 212 213 214 215 216 217 218 219
! V A P T E C S . . (SEQ ID NO: 57)
594 |gtt|gcc|cct|act|gag|tgt|tct|tag|tga|GGCGCGCC
! AscI....
! BssHII
!
629 aacgatgttc aag GCGGCCGC aacaggaggag (SEQ ID NO: 56)
! NotI.... Scab.......
TABLE 36P
Tally of 23 CDR1s of length 11 from human lambda chains
Tally A C D E F G H I K L M N P Q R S T V W Y
1 1 6 10 6 x
2 1 1 21 G
3 15 1 7 DNx
4 2 1 1 3 7 1 8 X
5 7 16 L
6 11 1 2 8 1 X
7 1 1 1 2 2 1 14 1 X
8 1 10 1 1 1 2 7 X
9 2 6 15 Yx
10 11 1 11 X
11 3 7 9 2 2 X
TABLE 37P
Tally of 80 CDR2s of length 7 from human lambda chains
Tally A C D E F G H I K L M N P Q R S T V W Y
1 1 14 32 1 13 3 1 4 5 1 2 3 X
2 18 2 8 16 2 34 X
3 1 2 1 31 39 4 2 X
4 6 4 1 14 1 41 8 1 1 2 1 DNx
5 1 1 78 R
6 1 77 2 P
7 2 78 S
TABLE 38P
Tally of 27 CDR3s of length 11 from human lambda chains
Tally A C D E F G H I K L M N P Q R S T V W Y
1 4 5 6 5 4 3 X
2 3 1 2 14 5 2 Sx
3 1 7 13 6 X
4 19 2 1 1 4 DNx
5 1 4 2 2 2 1 13 2 X
6 1 3 1 21 1 S
7 1 7 12 1 4 2 X
8 2 1 10 1 6 6 1 X
9 3 1 8 10 3 1 1 X
10 1 4 1 1 1 3 1 1 6 5 3 X
11 2 25 V
TABLE 40P
Synthetic Kappa light chain gene with stuffers
!
! A27::JH1 with all CDRs replaced by stuffers.
! Each stuffer contains at least one stop codon and a
! restriction site that will be unique within the diversity vector.
!
1 GAGGACCATt GGGCCCC ctccgagact
! Scab...... EcoO109I
! ApaI.
!----------------------------------
!
28 CTCGAG cgca
! XhoI..
!----------------------------------
38 acgcaatTAA TGTgagttag ctcactcatt aggcacccca ggcTTTACAc tttatgcttc
! ..−35.. Plac ..−10.
!----------------------------------
!
98 cggctcgtat gttgtgtgga attgtgagcg gataacaatt tc
!----------------------------------
!
140 acacagga aacagctatgac
!----------------------------------
!
160 catgatta cgCCAAGCTT TGGagccttt tttttggaga ttttcaac
! PflMI.......
! Hind3.
!----------------------------------
!
! M13 III signal sequence (AA seq)--------------------------->
! 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
! M K K L L F A I P L V V P F Y
206 gtg aag aag ctc cta ttt gct atc ccg ctt gtc gtt ccg ttt tac
!----------------------------------
!
! --Signal--> FR1------------------------------------------->
! 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
! S H S A Q S V L T Q S P G T L
251 |agc|cat|aGT|GCA|Caa|tcc|gtc|ctt|act|caa|tct|cct|ggc|act|ctt|
! ApaLI...
!----------------------------------
!
! ----- FR1 --------------------------------->|-------Stuffer->
! 31 32 33 34 35 36 37 38 39 40 41 42 43
! S L S P G E R A T L S | |
296 |tcG|CTA|AGC|CCG|GGt|gaa|cgt|gct|acC|TTA|AGt|TAG|TAA|gct|ccc|
! EspI..... AflII...
! XmaI....
!----------------------------------
!
! ------- Stuffer for CDR1------------------------->|- FR2 -->
! 59 60
! K P
341 |AGG|CCT|ctt|TGA|tct| g|aaA|CCT|
! StuI... SexAI...
!----------------------------------
!
! ----- FR2 ------|-----------Stuffer for CDR2---------------->
! 61 62 63 64 65 66
! G Q A P R | |
363 |GGT|caG|GCG|CCg|cgt|TAA|TGA|a AGCGCT aa TGGCCA aca gtg
! SexAI.... KasI.... AfeI.. MscI..
!----------------------------------
!
! Stuffer-->|--- FR3 ----------------------------------------------->
! <1>
! 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
! T G I P D R F S G S G S G T D
405 |act|gGG|ATC|CCG|GAC|CGt|ttc|tct|ggc|tct|ggt|tca|ggt|act|gac|
! BamHI...
! RsrII.....
!----------------------------------
!
! ------ FR3 ---------------------STUFFER for CDR3------------------>
! 91 92 93 94 95 96 97
! F T L T I S R | |
450 |ttt|acc|ctt|act|att|TCT|AGA|TAA|TGA| GTTAAC TAG acc TACGTA acc tag
! XbaI... HpaI.. SnaBI.
!----------------------------------
!
!
! ------------------------CDR3 stuffer------------------>|-----FR4--->
! 118 119 120
! F G Q
501 |ttc|ggt|caa|
!----------------------------------
!
! -----FR4------------------->| <------- Ckappa ------------
! 121 122 123 124 125 126 127 128 129 130 131 132 133 134
! G T K V E I K R T V A A P S
510 |ggt|aCC|AAG|Gtt|gaa|atc|aag| |CGT|ACG|gtt|gcc|gct|cct|agt|
! StyI.... BsiWI..
!
!(CDR3 installed as XbaI to (StyI or BsiWI) cassette.)
!
! 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149
! V F I F P P S D E Q L K S G T (SEQ ID NO: 96)
552 |gtg|ttt|atc|ttt|cct|cct|tct|gac|gaa|CAA|TTG|aag|tca|ggt|act|
! MfeI...
!
!
866 acgcatctctaa GCGGCCGC aacaggaggag (SEQ ID NO: 95)
! NotI....
! EagI..
TABLE 41P
Variegated DNA for kappa chains
!----------------------------------------------------------------
! Kappa chains
! For CDR1:
! <1> ADEFGHIKLMNPQRSTVWY equimolar
! <2> S(0.2) ADEFGHIKLMNPQRTVWY (0.044 each)
! <3> Y(0.2) ADEFGHIKLMNPQRSTVW (0.044 each)
! <4> A(0.2) DEFGHIKLMNPQRSTVWY (0.044 each)
(Ka1vg600) 5′-gct|acC|TTA|AGt|tgc|cgt|gct|tcc|cag-
|<1>|gtt|<2>|<2>| <3>|ctt|gct|tgg|tat|caa|cag|aaA|CC-3′ (SEQ ID NO: 66)
(Ka2vg650) 5′-caG|GCG|CCg|cgt|tta|ctt|att|tat|<1>|gct|tct|<2>|cgc|<4>|-
|<1>|gGG|ATC|CCG|GAC|CGt|ttc|tct|ggt|tctcacc-3′ (SEQ ID NO: 71)
(Ka3vg670) 5′- gac|ttc|gct|gtt|-
|tat|tat|tgC|CAa|cag|<3>|<1>|<1>|<1>|cct|<1>|act|ttc|ggt|caa|-
|ggt|aCC|AAG|Gtt|g-3′ (SEQ ID NO: 77)
TABLE 42P
Variegated DNA for lambda chains
!------------------------
! For CDR1,
! <1> = 0.27 T, 0.27 G, 0.027 {ADEFHIKLMNPQRSVWY} no C
! <2> = 0.27 D, 0.27 N, 0.027 {AEFGHIKLMPQRSTVWY} no C
! <3> = 0.36 Y, 0.0355{ADEFGHIKLMNPQRSTVW} no C
! <4> = equimolar {ADEFGHIKLMNPQRSTVWY} no C
! <5> = 0.36 S, 0.0355{ADEFGHIKLMNPQRTVWY} no C
(Lm1vg710) 5′-gt|atc|act|att|tct|TGT|ACA|ggt|<1>|tct|tct|<2>|gtt|ggc|-
|<1>|<3>|<2>|<3>|gtt|tct|tgg|tat|caa|caa|caC|CC-3′ (SEQ ID NO: 83)
!-------------------------------------------------
(Lm2vg750) 5′-G|CCg|aag|ttg|atg|atc|tac|-
<4>|<4>|<4>|<2>|cgt|cct|tct|ggt|gtc|agc|aat|c-3′ (SEQ ID NO: 88)
(Lm3vg817) 5′- gac|gag|gct|gac|tac|tat|tgt|-
|<4>|<5>|<4>|<2>|<4>|tct|<4>|<4>|<4>|<4>|gtc|ttc|ggc|ggt|GGT|-
|ACC|aaa|ctt|ac-3′ (SEQ ID NO: 93)
!----------------------------------------------------------------
TABLE 43P
Constant DNA for Synthetic Library
! CDR3 library components
(Ctop25) 5′-gctctggtcaa C|TTA|AGg|gct|gag|g-3′ (SEQ ID NO: 58)
(CtprmA) 5′-gctctggtcaa C|TTA|AGg|gct|gag|gac-
! AflII...
|acc|gct|gtc|tac|tac|tgc|gcc-3′ (SEQ ID NO: 59)
!
(CBprmB)[RC] 5′-|tac|ttc|gat|tac|ttg|ggc|caa|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′(SEQ ID NO: 60)
! BstEII...
(CBot25)[Rc] 5′-|GGT|ACC|ctG|GTC|ACC|tcgctccacc-3′(SEQ ID NO: 61)
!----------------------------------------------------------------
! Kappa chains
(Ka1Top610) 5′-ggtctcagtt-
G|CTA|AGC|CCG|GGt|gaa|cgt|gct|acC|TTA|AGt|tgc|cgt|gct|tcc|cag-3′ (SEQ ID NO: 62)
(Ka1STp615) 5′-ggtctcagtt-
G|CTA|AGC|CCG|GGt|g-3′ (SEQ ID NO: 63)
(Ka1Bot620) [RC] 5′-ctt|gct|tgg|tat|caa|cag|aaA|-
CCt|GGT|caG|GCG|CC aagtcgtgtc-3′ (SEQ ID NO: 64)
(Ka1SB625) [RC] 5′-cct |GGT|caG|GCG|CC aagtcgtgtc-3′ (SEQ ID NO: 65)
!
(Ka2Tshort657) 5′-cacgagtcctA|CCT|GGT|-
caG|GC-3′ (SEQ ID NO: 68)
(Ka2Tlong655) 5′-cacgagtcctA|CCT|GGT|-
caG|GCG|CCg|cgt|tta|ctt|att|tat-3′ (SEQ ID NO: 69)
(Ka2Bshort660) [RC] 5′- |GAC|CGt|ttc|tct|ggt|tctcacc-3′ (SEQ ID NO: 70)
!---------------------------------------------------------------
(Ka3Tlon672)5′- gacgagtcct TCT|AGA|ttg|gaa|cct|gaa|gac|ttc|gct|gtt|-
|tat|tat|tgC|CAa|c -3′ (SEQ ID NO: 72)
(Ka3BotL682) [RC]5′-act|ttc|ggt|caa|-
|ggt|aCC|AAG|Gtt|gaa|atc|aag| |CGT|ACG|tcacaggtgag-3′ (SEQ ID NO: 73)
(Ka3Bsho694) [RC]5′- gaa|atc|aag| |CGT|ACG| tcacaggtgag-3′(SEQ ID NO: 74)
!-----------------------------------------------------------------
(Lm1TPri75) 5′-gacgagtcct GG|TcA|CCt|GGT|-3′ (SEQ ID NO: 78)
(Lm1TLo715) 5′-gacgagtcct GG|TcA|CCt|GGt|-
caa|agt|atc|act|att|tct|TGT|ACA|ggt-3′ (SEQ ID NO: 79)
(Lm1BLo724)[RC] 5′-gtt|tct|tgg|tat|caa|caa|caC|CCG|GGc|aaG|GCG|-
AGA TCT tcacaggtgag-3′ (SEQ ID NO: 80)
(Lm1BSh737)[RC] 5′- Gc|aaG|GCG|-
AGA TCT tcacaggtgag-3′ (SEQ ID NO: 81)
!-------------------------------------------------
(Lm2TSh757) 5′-gagcagagga C|CCG|GGc|aaG|GC-3′ (SEQ ID NO: 84)
(Lm2TLo753) 5′-gagcagagga C|CCG|GGc|aaG|GCG|CCg|aag|ttg|atg|atc|tac|-3′ (SEQ ID NO: 85)
(Lm2BLo762)[RC] 5′-cgt|cct|tct|ggt|gtc|agc|aat|cgt|ttc|TCC|GGA|tcacaggtgag-3′ (SEQ ID NO: 86)
(Lm2BSh765)[RC] 5′- cgt|ttc|TCC|GGA|tcacaggtgag-3′ (SEQ ID NO: 87)
!-------------------------------------------------
(Lm3TSh822) 5′-CTG|CAG|gct|gaa|gac|gag|gct|gac -3′ (SEQ ID NO: 89)
(Lm3TLo819) 5′-CTG|CAG|gct|gaa|gac|gag|gct|gac|tac|tat|tgt|-3′ (SEQ ID NO: 90)
(Lm3BLo825) [RC] 5′-gtc|ttc|ggc|ggt|GGT|-
|ACC|aaa|ctt|act|gtc|ctc|gGT|CAA|CCT|aAG|G acacaggtgag-3′ (SEQ ID NO: 91)
(Lm3BSh832) [RC] 5′- c|gGT|CAA|CCT|aAG|G acacaggtgag-3′ (SEQ ID NO: 92)
!----------------------------------------------------------------
TABLE 48P
Synthtic human lambda-chain gene with stuffers in place of CDRs
! Lambda 14-7(A) 2a2::JH2::Clambda
! AA sequence tested
!
1 GAGGACCATt GGGCCCC ttactccgtgac
! Scab...... EcoO109I
! ApaI..
!-----------------------------------------------
!
! -----------FR1-------------------------------------------->
! 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
! S A Q S A L T Q P A S V S G S P G
30 aGT|GCA|Caa|tcc|gct|ctc|act|cag|cct|GCT|AGC|gtt|tcc|gGG|TcA|CCt|GGT|
! ApaLI... NheI... BstEII...
! SexAI....
!-----------------------------------------------
!
! ------FR1------------------> |-----stuffer for CDR1---------
! 16 17 18 19 20 21 22 23
! Q S I T I S C T
81 |caa|agt|atc|act|att|tct|TGT|ACA|tct TAG TGA ctc
! BsrGI..
!-------------------------------------------------------
!
! -----Stuffer--------------------------->--------------------
! 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
! R S | | P | H P G K A
117 AGA TCT TAA TGA ccg tag caC|CCG|GGc|aaG|GCG|
! BglII XmaI.... KasI.....
! AvaI....
!-------------------------------------------------------------------
!
! --|-------------Stuffer ------------------------------------->
! P
150 |CCg|TAA|TGA|atc tCG TAC G ct|ggt|gtt|
! KasI.... BsiWI...
!-------------------------------------------------------------------
!
! -------FR3----------------------------------------------------
! 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
! S N R F S G S K S G N T A S L
177 |agc|aat|cgt|ttc|TCC|GGA|tct|aaa|tcc|ggt|aat|acc|gcA|AGC|TTa|
! BspEI.. | HindIII.
! BsaBI........(blunt)
!-------------------------------------------------------------------
!
! -------FR3------------->|--Stuffer-------------------------->|
! 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90
! T I S G L Q
222 |act|atc|tct|ggt|CTG|CAG|gtt ctg tag ttc CAATTG ctt tag tga ccc
! PstI... MfeI..
!-------------------------------------------------------------------
!
! -----Stuffer------------------------------->|---FR4---------
! 103 104 105
! G G G
270 |ggc|ggt|GGT|
! KpnI...
!----------------------------------------------------------------------
!
! -------FR4-------------->
! 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
! T K L T V L G Q P K A A P S V
279 |ACC|aaa|ctt|act|gtc|ctc|gGT|CAA|CCT|aAG|Gct|gct|cct|tcc|gtt|
! KpnI... HincII..
! Bsu36I...
!
! 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
! T L F P P S S E E L Q A N K A
324 |act|ctc|ttc|cct|cct|agt|tct|GAA|GAG|Ctt|caa|gct|aac|aag|gct|
! SapI.....
!
! 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
! T L V C L I S D F Y P G A V T (SEQ ID NO: 98)
369 |act|ctt|gtt|tgc|tTG|ATC|Agt|gac|ttt|tat|cct|ggt|gct|gtt|act| (SEQ ID NO: 97)
! BclI....
TABLE 50P
3-23::CDR3::JH4 Stuffers in place of CDRs
FR1(DP47/V3-23)---------------
20 21 22 23 24 25 26 27 28 29 30
A M A E V Q L L E S G
ctgtctgaac CC atg gcc gaa|gtt|CAA|TTG|tta|gag|tct|ggt|
Scab...... NcoI.... | MfeI |
--------------FR1--------------------------------------------
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
G G L V Q P G G S L R L S C A
|ggc|ggt|ctt|gtt|cag|cct|ggt|ggt|tct|tta|cgt|ctt|tct|tgc|gct|
----FR1-------------------->|...CDR1 stuffer....|---FR2------
46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
A S G F T F S S Y A | | W V R
|gct|TCC|GGA|ttc|act|ttc|tct|tCG|TAC|Gct|TAG|TAA|tgg|gtt|cgC|
| BspEI | | BsiWI| |BstXI.
-------FR2-------------------------------->|...CDR2 stuffer.
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75
Q A P G K G L E W V S | p r |
|CAa|gct|ccT|GGt|aaa|ggt|ttg|gag|tgg|gtt|tct|TAA|CCT|AGG|TAG|
...BstXI | AvrII..
.....CDR2 stuffer....................................|---FR3---
--------FR3--------------------------------------------------
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105
T I S R D N S K N T L Y L Q M
|act|atc|TCT|AGA|gac|aac|tct|aag|aat|act|ctc|tac|ttg|cag|atg|
| XbaI |
---FR3-----------..> Stuffer------------->|
106 107 108 109 110
N S L R A (SEQ ID NO: 53)
|aac|agC|TTA|AGg|gct|TAG TAA AGG cct TAA (SEQ ID NO: 52)
|AflII | StuI...
|----- FR4 ---(JH4)------------------------------------------
Y F D Y W G Q G T L V T V S S (SEQ ID NO: 26)
|tat|ttc|gat|tat|tgg|ggt|caa|GGT|ACC|ctG|GTC|ACC|gtc|tct|agt|... (SEQ ID NO: 25)
| KpnI| | BstEII |
