DIRECT OLIGONUCLEOTIDE SYNTHESIS ON CELLS AND BIOMOLECULES
The invention is directed to methods for synthesizing oligonucleotides direction on biomolecules or cells living or fixed. In some embodiments, template-free enzymatic synthesis is implemented under biological conditions with successive cycles of (i) enzymatic addition of a 3′-O-blocked nucleoside triphosphate and (ii) enzymatic deblocking of the incorporated nucleotide to regenerate a free 3′ hydroxyl. The invention has applications in single-cell cDNA library construction and analysis.
Latest DNA Script SAS Patents:
- Efficient product cleavage in template-free enzymatic synthesis of polynucleotides
- Method for preparing 3?-o-amino-2?-deoxyribonucleoside-5?-triphosphates
- EFFICIENT PRODUCT CLEAVAGE IN TEMPLATE-FREE ENZYMATIC SYNTHESIS OF POLYNUCLEOTIDES
- PROCESS FOR PREPARING 3'-O-AMINO-RIBONUCLEOTIDE
- Efficient product cleavage in template-free enzymatic synthesis of polynucleotides
The present application is a divisional of and claims priority to U.S. patent application Ser. No. 16/970,590, entitled “DIRECT OLIGONUCLEOTIDE SYNTHESIS ON CELLS AND BIOMOLECULES,” filed on Aug. 17, 2020, which is a U.S. National Stage
Entry of International Application No. PCT/EP2019/084347, entitled “DIRECT OLIGONUCLEOTIDE SYNTHESIS ON CELLS AND BIOMOLECULES,” filed on Dec. 10, 2019, which claims priority to European Application No. 19305219.8 filed on Feb. 25, 2019 and European Application No. 18306687.7 filed on Dec. 13, 2018. All above-identified applications are hereby incorporated by reference in their entireties.
There are many instances in the biological and medical sciences where large-scale analysis of biomolecules or cells can be facilitated by the use of nucleic acid tags, or barcodes, e.g. Brenner et al, Proc. Natl. Acad. Sci., 97: 1665-1670 (2000); Brenner et al, U.S. Pat. No. 7,537,897; Brenner et al, U.S. Pat. No. 8,476,018; McCloskey et al, U.S. patent publication 2007/0020640; Kinde et al, Proc. Natl. Acad. Sci., 108: 9530-9535 (2011); Fu et al, Proc. Natl. Acad. Sci., 108: 9026-9031 (2011); Nolan, U.S. patent publication 2016/0251697; Zheng et al, Nature Comm., 8:14049 (2017).
Typically such oligonucleotide labels are attached either (1) by “labeling by sampling” (also referred to as, “stochastic labeling”), where a large set of oligonucleotide labels are pre-synthesized and used to form conjugates with a much smaller population of target organisms or biomolecules to give a conjugate population of organisms or biomolecules with unique labels e.g., Brenner et al, U.S. Pat. No. 7,537,897; or Fu et al, Proc. Natl. Acad. Sci. (cited above); or (2) by “split and mix” hybridizations of a plurality of pre-synthesized oligonucleotide subunits to give a population of organisms or biomolecules all of which have substantially unique labels, e.g. Nolan (cited above); or Seelig et al, U.S. patent publication 2016/0138086. Pre-synthesized tags or tag subunits have been used in these processes because oligonucleotide synthesis has been dominated by chemical methods, such as phosphoramidite chemistry, which requires harsh non-aqueous conditions that are incompatible with biological organisms and biomolecules.
It would be highly desirable if a capability were available for direct oligonucleotide synthesis on biological organisms or biomolecules to provide such organisms or biomolecules with oligonucleotide labels, such as unique and durable barcodes or tags, for tracking and sorting. Such labeling, particularly when coupled with next-generation sequencing techniques, would be a valuable tool for large-scale cell-based analysis of a host of biological processes.
SUMMARY OF THE INVENTIONThe invention is directed to methods for synthesizing oligonucleotides directly on biomolecules and biological cells, including the application of such methods for single-cell analysis, such as single-cell transcriptome analysis.
In some embodiments the invention is directed to methods of synthesizing oligonucleotides on biological cells or biomolecules comprising the steps of: (a) providing biological cells or biomolecule having an initiator with a free 3′-hydroxyl; (b) repeating for a plurality of cycles the steps of (i) contacting under elongation conditions the initiator or elongated fragments having free 3′-O-hydroxyls with a 3′-O-blocked nucleoside triphosphate and a template-independent DNA polymerase so that the initiator or elongated fragments are elongated by incorporation of a 3′-O-blocked nucleoside triphosphate to form 3′-O-blocked elongated fragments, and (ii) deblocking the elongated fragments to form elongated fragments having free 3′-hydroxyls, thereby synthesizing on the biological cells or biomolecules a oligonucleotide of predetermined sequence. In some embodiments, such steps are carried out under conditions that maintain biological cells, especially mammalian cells, in a viable state. In some embodiments, the step of deblocking is carried out enzymatically under conditions that maintain biological cells, especially mammalian cells, in a viable state.
In some embodiments, the invention is directed to a method of generating a cell-specific cDNA library with cell-specific oligonucleotide barcodes comprising the steps of: (a) synthesizing a unique oligonucleotide barcode on a cell surface membrane of each cell in a population of cells to form a population of barcoded cells; (b) isolating each barcoded cell in a reactor; (c) lysing barcoded cells in each reactor; (d) performing reverse-transcriptase polymerase chain reaction (RT-PCR) in each reactor to produce a cDNA library with cell-specific oligonucleotide barcodes. In some embodiments, the step of synthesizing is carried out by a template-free enzymatic synthesis method of the invention. In some embodiments, the RT-PCR reaction includes attaching barcodes to cDNAs by a polymerase cycling amplification reaction.
In some embodiments, the invention is directed to methods of generating cell-specific cDNA libraries each with cell-specific oligonucleotide barcodes comprising the steps of: (a) capturing mRNA of a single cell by hybridizing the mRNA to capture oligonucleotides attached to a bead, wherein the capture oligonucleotides are complementary to segments of the mRNA and wherein the capture oligonucleotides are attached to the bead by 5-ends and have free 3′-hydroxyls; (b) extending 3′-ends of the capture oligonucleotides with a reverse transcriptase using the captured mRNAs as templates to form cell-specific cDNA libraries; (c) synthesizing a unique cell-specific oligonucleotide barcode on each cDNA of a bead by template-free enzymatic synthesis. In some embodiments, the unique cell- or bead-specific barcode is a random sequence oligonucleotide and the step of synthesizing such barcode is carried out by a “split and mix” procedure with template-free enzymatic synthesis.
In some embodiments, the invention is directed to methods of extending one or more native polynucleotides with a predetermined nucleotide sequence, comprising: providing one or more native polynucleotides in a reaction mixture under TdT reaction conditions, the native polynucleotides having free 3′-hydroxyls; and extending the one or more native polynucleotide with a predetermined sequence of nucleotides by repeated cycles of the steps (i) contacting the native polynucleotides or elongated native polynucleotides having free 3′-O-hydroxyls with a 3′-O-blocked nucleoside triphosphate and a TdT variant so that the native polynucleotides or elongated native polynucleotides are elongated by incorporation of a 3′-O-blocked nucleoside triphosphate to form 3′-O-blocked elongated native polynucleotides, and (ii) deblocking the elongated native polynucleotides to form elongated native polynucleotides having free 3′-hydroxyls, thereby synthesizing on the native polynucleotides a oligonucleotide of the predetermined sequence.
These above-characterized aspects, as well as other aspects, of the present invention are exemplified in a number of illustrated implementations and applications, some of which are shown in the figures and characterized in the claims section that follows. However, the above summary is not intended to describe each illustrated embodiment or every implementation of the present invention.
The general principles of the invention are disclosed in more detail herein particularly by way of examples, such as those shown in the drawings and described in detail. It should be understood, however, that the intention is not to limit the invention to the particular embodiments described. The invention is amenable to various modifications and alternative forms, specifics of which are shown for several embodiments. The intention is to cover all modifications, equivalents, and alternatives falling within the principles and scope of the invention.
The practice of the present invention may employ, unless otherwise indicated, conventional techniques and descriptions of organic chemistry, molecular biology (including recombinant techniques), cell biology, and biochemistry, which are within the skill of the art. Such conventional techniques may include, but are not limited to, preparation and use of synthetic peptides, synthetic polynucleotides, monoclonal antibodies, nucleic acid cloning, amplification, sequencing and analysis, and related techniques. Protocols for such conventional techniques can be found in product literature from manufacturers and in standard laboratory manuals, such as Genome Analysis: A Laboratory Manual Series (Vols. I-IV); PCR Primer: A Laboratory Manual; and Molecular Cloning: A Laboratory Manual (all from Cold Spring Harbor Laboratory Press); Lutz and Bomscheuer, Editors, Protein Engineering Handbook (Wiley-VCH, 2009); Hermanson, Bioconjugate Techniques, Second Edition (Academic Press, 2008); and like references.
The invention is directed to methods for directly synthesizing oligonucleotides on cells or biomolecules using template-free enzymatic oligonucleotide synthesis techniques. Such techniques can be applied directly to biomolecules extracted from their natural settings (e.g. DNAs or RNAs), to biomolecules (e.g. proteins) modified by the attachment of an initiator, or to biomolecules (e.g. nucleic acids, polysaccharides, polypeptides, etc.) produced synthetically. Such techniques may be applied in any circumstances where the mild conditions of an enzymatic reaction are necessary or useful. In particular, the template-free enzymatic synthesis techniques may be employed in hybrid chemical-enzymatic polynucleotide synthesis wherein a precursor polynucleotide is synthesized chemically, then the precursor is further modified by additions of components enzymatically, such as labeled nucleotides, that may be altered in, or not survive, the harsh conditions of chemical synthesis. Such hybrid synthesis methods may include several alterations between chemical additions and enzymatic additions of nucleotides or analogs thereof. Such hybrid synthesis techniques may pair enzymatic synthesis with a variety of different chemical synthesis approaches including, but not limited to, phosphoramidite, phosphodiester, phosphotriester, phosphite triester, H-phosphonate chemistries, e.g. Narang, Editor, Synthesis and applications of DNA and RNA (Academic Press, Inc., 1987).
In some embodiments, template-free enzymatic synthesis techniques require the presence of an initiator oligonucleotide having a free 3′-hydroxyl which may be part of a biomolecule, in the case of polynucleotides of cDNAs, or it may be readily added by a variety of chemical techniques, e.g. using readily available click chemistry reactions, in the case of cellular membrane proteins, antibodies, or the like. With the availability of an initiator, enzymatic oligonucleotide synthesis may be implemented by repeated cycles of (i) extension of the initiator (or previously extended strand) having a free 3′-hydroxyl by a single nucleotide using a template-free polymerase, such as a terminal deoxynucleotidyl transferase (TdT), in the presence of a 3′-O-blocked nucleoside triphosphate, and (ii) de-blocking recently incorporated 3′-O-blocked nucleotides to regenerate new extendable 3′-hydroxyls. Cycles are continued until an oligonucleotide having a desired sequence is synthesized. In some embodiments, unique oligonucleotide barcodes may be synthesized directly on biological cells, such as mammalian cells, of a population by a “split and mix” synthesis strategy. In some embodiments, capping steps may be included in which non-extended free hydroxyls are reacted with compounds that prevents any further extensions of the capped strand. In some embodiments, such compound may be a dideoxynucleoside triphosphate. In other embodiments, non-extended strands with free 3′-hydroxyls may be degraded by treating them with a 3′-exonuclease activity, e.g. Exo I, as described by Jensen et al, Biochemistry, 57: 1821-1832 (2018).
In some embodiments, the invention is directed to methods of synthesizing oligonucleotides on biological cells or biomolecules comprising the steps of (a) providing biological cells or biomolecule having an initiator with a free 3′-hydroxyl; (b) repeating for a plurality of cycles the steps of (i) contacting under elongation conditions the initiator or elongated fragments having free 3′-O-hydroxyls with a 3′-O-blocked nucleoside triphosphate and a template-independent DNA polymerase so that the initiator or elongated fragments are elongated by incorporation of a 3′-O-blocked nucleoside triphosphate to form 3′-O-blocked elongated fragments, and (ii) deblocking the elongated fragments to form elongated fragments having free 3′-hydroxyls, thereby synthesizing on the biological cells or biomolecules a oligonucleotide of predetermined sequence. In some embodiments, the biological cells are provided and deblocking is carried out enzymatically. In some embodiments, the 3′-O-blocked nucleoside triphosphate is a 3′-phosphate-nucleoside triphosphate and the step of deblocking is carried out by treating said 3′-O-blocked elongated fragments with a 3′-phosphatase activity. In some embodiments, the 3′-phophatase activity is provided by T4 polynucleotide kinase, recombinant shrimp alkaline phosphatase, or a calf intestinal alkaline phosphatase. In some embodiments, the 3′-O-blocked nucleoside triphosphate is a 3′-ester-nucleoside triphosphate and the step of deblocking is carried out by treating said 3′-O-blocked elongated fragments with an esterase activity. In some embodiments, the esterase activity is a lipase activity, such as, a proteinase K activity. In some embodiments, the 3′-O-blocked nucleoside triphosphate is a 3′-acetyl-nucleoside triphosphate and the step of deblocking is carried out by treating said 3′-O-blocked elongated fragments with an acetylesterase activity. In some embodiments, the template-independent DNA polymerase is a terminal deoxynucleotidyl transferase (TdT) variant having an amino acid sequence at least sixty percent identical to any one of the amino acid sequences of SEQ ID NOs 2-15 with substitutions at a first arginine at position 207 of SEQ ID NO: 2 or a functionally equivalent position in the amino acid sequences of SEQ ID NOs 3-15 and at a second arginine at 325 of SEQ ID NO: 2 or a functionally equivalent position in the amino acid sequences of SEQ ID NOs 3-15, wherein the variant TdT (i) is capable of synthesizing a nucleic acid fragment without a template and (ii) is capable of incorporating a 3′-O-modified nucleotide onto a free 3′-hydroxyl of a nucleic acid fragment.
In some embodiments, methods of the invention for synthesizing oligonucleotides on a viable cell may be carried out with the following steps: (a) providing an initiator with a free 3′-hydroxyl attached to a cell surface molecule of the cell or anchored in the cell surface membrane of the cell; (b) repeating under biological conditions for a plurality of cycles the steps of (i) contacting the initiator or elongated fragments having free 3′-O-hydroxyls with a 3′-O-blocked nucleoside triphosphate and a template-independent DNA polymerase so that the initiator or elongated fragments are elongated by incorporation of a 3′-O-blocked nucleoside triphosphate to form 3′-O-blocked elongated fragments, and (ii) enzymatically deblocking the elongated fragments to form elongated fragments having free 3′-hydroxyls, thereby synthesizing the oligonucleotide of predetermined sequence.
The above process is illustrated in
After cDNAs are cleavably or releasably attached to a solid support leaving their 3′-hydroxyls free, enzymatic synthesis can proceed to generate an oligonucleotide of a predeterminded sequence on the free 3′ ends, which is illustrated diagrammatically in
In some embodiments, oligonucleotides may be synthesized on other biomolecules, such as antibodies, by a process similar to that of
In some embodiments, the invention is directed to methods of generating cDNA libraries each with a oligonucleotide label comprising the steps of: (a) capturing mRNA by hybridizing the mRNA to capture oligonucleotides attached to one or more solid supports, wherein the capture oligonucleotides are complementary to segments of the mRNA and wherein the capture oligonucleotides are attached to the one or more solid supports by 5-ends and have 3′-ends with free 3′-hydroxyls; (b) extending 3′-ends of the capture oligonucleotides with a reverse transcriptase using the captured mRNAs as templates to form cDNA libraries on the one or more solid supports; and (c) synthesizing a oligonucleotide label on each cDNA on the one or more solid support by template-free enzymatic synthesis. In some embodiments, the step of synthesizing comprises repeating cycles of (i) contacting under elongation conditions said cDNAs with a 3′-O-blocked nucleoside triphosphate and a template-independent DNA polymerase so that said cDNAs or elongated cDNAs with free 3′-hydroxyls are elongated by incorporation of a 3′-O-blocked nucleoside triphosphate to form 3′-O-blocked elongated cDNAs, and (ii) deblocking the elongated cDNA to form elongated cDNAs having free 3′-hydroxyls. In some embodiments, each of said cycles further comprises splitting said cDNAs or elongated cDNAs with free 3′-hydroxyls among separate reaction mixtures in which said cDNAs or elongated cDNAs with free 3′-hydroxyls are elongated by a different kind of nucleoside triphosphate to form said elongated cDNAs after which said elongated cDNAs of the separate reaction mixtures are combined. In some embodiments, the step of capturing includes capturing mRNA of a single cell on a bead to form the cDNA libraries that are cell-specific cDNA libraries and wherein the oligonucleotide labels are unique cell-specific oligonucleotide barcodes. In some embodiments, the step of synthesizing a unique cell-specific barcode is implemented by a split and mix synthesis method.
Template-Free Enzymatic Synthesis of Oligonucleotides
Generally, methods of template-free (or equivalently, “template-independent”) enzymatic DNA synthesis comprise repeated cycles of steps, such as are illustrated in
Initiator polynucleotides (1000) are provided, for example, attached to solid support (1020), which have free 3′-hydroxyl groups (1030). To the initiator polynucleotides (1000) (or elongated initiator polynucleotides in subsequent cycles) are added a 3′-O-protected-dNTP and a template-free polymerase, such as a TdT or variant thereof (e.g. Ybert et al, WO/2017/216472; Champion et al, WO2019/135007) under conditions (1040) effective for the enzymatic incorporation of the 3′-O-protected-dNTP onto the 3′ end of the initiator polynucleotides (1000) (or elongated initiator polynucleotides). This reaction produces elongated initiator polynucleotides whose 3′-hydroxyls are protected (1060). If the elongated sequence is not complete, then another cycle of addition is implemented (1080). If the elongated initiator polynucleotide contains a competed sequence, then the 3′-O-protection group may be removed, or deprotected, and the desired sequence may be cleaved from the original initiator polynucleotide (1100). Such cleavage may be carried out using any of a variety of single strand cleavage techniques, for example, by inserting a cleavable nucleotide at a predetermined location within the original initiator polynucleotide. An exemplary cleavable nucleotide may be a uracil nucleotide which is cleaved by uracil DNA glycosylase.
If the elongated initiator polynucleotide does not contain a completed sequence, then the 3 ′-O-protection groups are removed to expose free 3′-hydroxyls (1030) and the elongated initiator polynucleotides are subjected to another cycle of nucleotide addition and deprotection.
As used herein, an “initiator” (or equivalent terms, such as, “initiating fragment,” “initiator nucleic acid,” “initiator oligonucleotide,” or the like) usually refers to a short oligonucleotide sequence with a free 3′-end, which can be further elongated by a template-free polymerase, such as TdT. In one embodiment, the initiating fragment is a DNA initiating fragment. In an alternative embodiment, the initiating fragment is an RNA initiating fragment.
In some embodiments, an initiating fragment possesses between 3 and 100 nucleotides, in particular between 3 and 20 nucleotides. In some embodiments, the initiating fragment is single-stranded. In alternative embodiments, the initiating fragment is double-stranded. In some embodiments, an initiator may comprise a non-nucleic acid compound having a free hydroxyl to which a TdT may couple a 3′-O-protected dNTP, e.g. Baiga, U.S. patent publications US2019/0078065 and US2019/0078126.
Returning to
When the sequence of polynucleotides on a synthesis support includes reverse complementary subsequences, secondary intra-molecular or cross-molecular structures may be created by the formation of hydrogen bonds between the reverse complementary regions. In some embodiments, base protecting moieties for exocyclic amines are selected so that hydrogens of the protected nitrogen cannot participate in hydrogen bonding, thereby preventing the formation of such secondary structures. That is, base protecting moieties may be employed to prevent the formation of hydrogen bonds, such as are formed in normal base pairing, for example, between nucleosides A and T and between G and C. At the end of a synthesis, the base protecting moieties may be removed and the polynucleotide product may be cleaved from the solid support, for example, by cleaving it from its initiator.
3′-O-blocked dNTPs without base protection may be purchased from commercial vendors or synthesized using published techniques, e.g. U.S. Pat. No. 7,057,026; Guo et al, Proc. Natl. Acad. Sci., 105(27): 9145-9150 (2008); Benner, U.S. Pat. Nos. 7,544,794 and 8,212,020; International patent publications WO2005/005667, WO91/06678; Canard et al, Gene (cited herein); Metzker et al, Nucleic Acids Research, 22: 4259-4267 (1994); Meng et al, J. Org. Chem., 14: 3248-3252 (3006); U.S. patent publication 2005/037991. 3′-O-blocked dNTPs with base protection may be synthesized as described below.
When base-protected dNTPs are employed the above method of
The above method may also include capping step(s) as well as washing steps after the reacting, or extending, step, as well as after the deprotecting step. As mentioned above, in some embodiments, capping steps may be included in which non-extended free 3′-hydroxyls are reacted with compounds that prevents any further extensions of the capped strand. In some embodiments, such compound may be a dideoxynucleoside triphosphate. In other embodiments, non-extended strands with free 3′-hydroxyls may be degraded by treating them with a 3′-exonuclease activity, e.g. Exo I. For example, see Hyman, U.S. Pat. No. 5,436,143. Likewise, in some embodiments, strands that fail to be deblocked may be treated to either remove the strand or render it inert to further extensions.
In some embodiments, reaction conditions for an extension or elongation step may comprising the following: 2.0 μM purified TdT; 125-600 μM 3′-O-blocked dNTP (e.g. 3′-O—NH2-blocked dNTP); about 10 to about 500 mM potassium cacodylate buffer (pH between 63 and 7.5) and from about 0.01 to about 10 μM of a divalent cation (e.g. CoCl2 or MnCl2), where the elongation reaction may be carried out in a 50 μI, reaction volume, at a temperature within the range RT to 45° C., for 3 minutes. In embodiments, in which the 3′-O-blocked dNTPs are 3′-O—NH2-blocked dNTPs, reaction conditions for a deblocking step may comprise the following: 700 mM NaNO2; 1 M sodium acetate (adjusted with acetic acid to pH in the range of 4.8-6.5), where the deblocking reaction may be carried out in a 50 μl, volume, at a temperature within the range of RT to 45° C. for 30 seconds to several minutes.
Depending on particular applications, the steps of deblocking and/or cleaving may include a variety of chemical or physical conditions, e.g. light, heat, pH, presence of specific reagents, such as enzymes, which are able to cleave a specified chemical bond. Guidance in selecting 3′-O-blocking groups and corresponding de-blocking conditions may be found in the following references, which are incorporated by reference: Benner, U.S. Pat. Nos. 7,544,794 and 8,212,020; U.S. Pat. Nos. 5,808,045; 8,808,988; International patent publication WO91/06678; and references cited below. In some embodiments, the cleaving agent (also sometimes referred to as a de-blocking reagent or agent) is a chemical cleaving agent, such as, for example, dithiothreitol (DTT). In alternative embodiments, a cleaving agent may be an enzymatic cleaving agent, such as, for example, a phosphatase, which may cleave a 3′-phosphate blocking group. It will be understood by the person skilled in the art that the selection of deblocking agent depends on the type of 3′-nucleotide blocking group used, whether one or multiple blocking groups are being used, whether initiators are attached to living cells or organisms or to solid supports, and the like, that necessitate mild treatment. For example, a phosphine, such as tris(2-carboxyethyl)phosphine (TCEP) can be used to cleave a 3′O-azidomethyl groups, palladium complexes can be used to cleave a 3′O-allyl groups, or sodium nitrite can be used to cleave a 3′O-amino group. In particular embodiments, the cleaving reaction involves TCEP, a palladium complex or sodium nitrite.
As noted above, in some embodiments it is desirable to employ two or more blocking groups that may be removed using orthogonal de-blocking conditions. The following exemplary pairs of blocking groups may be used in parallel synthesis embodiments (Table 1). It is understood that other blocking group pairs, or groups containing more than two, may be available for use in these embodiments of the invention.
Synthesizing oligonucleotides on living cells requires mild deblocking, or deprotection, conditions, that is, conditions that do not disrupt cellular membranes, denature proteins, interfere with key cellular functions, or the like. In some embodiments, deprotection conditions are within a range of physiological conditions compatible with cell survival. In such embodiments, enzymatic deprotection is desirable because it may be carried out under physiological conditions. In some embodiments specific enzymatically removable blocking groups are associated with specific enzymes for their removal. For example, ester- or acyl-based blocking groups may be removed with an esterase, such as acetylesterase, or like enzyme, and a phosphate blocking group may be removed with a 3′ phosphatase, such as T4 polynucleotide kinase. By way of example, 3′-O-phosphates may be removed by treatment with as solution of 100 mM Tris-HCl (pH 6.5) 10 mM MgCl2, 5 mM 2-mercaptoethanol, and one Unit T4 polynucleotide kinase. The reaction proceeds for one minute at a temperature of 37° C.
A “3′-phosphate-blocked” or “3′-phosphate-protected” nucleotide refers to nucleotides in which the hydroxyl group at the 3′-position is blocked by the presence of a phosphate containing moiety. Examples of 3′-phosphate-blocked nucleotides in accordance with the invention are nucleotidyl-3′-phosphate monoester/nucleotidyl-2′,3′-cyclic phosphate, nucicotidyl-2′-phosphate monoester and nucleotidyl-2′ or 3′-alkylphosphate diester, and nucleotidyl-2′ or 3′-pyrophosphate. Thiophosphate or other analogs of such compounds can also be used, provided that the substitution does not prevent dephosphorylation resulting in a free 3′-OH by a phosphatase.
Further examples of synthesis and enzymatic deprotection of 3′-O-ester-protected dNTPs or 3′-O-phosphate-protected dNTPs are described in the following references: Canard et al, Proc. Natl. Acad. Sci., 92:10859-10863 (1995); Canard et al, Gene, 148: 1-6 (1994); Cameron et al, Biochemistry, 16(23): 5120-5126 (1977); Rasolonjatovo et al, Nucleosides & Nucleotides, 18(4&5): 1021-1022 (1999); Ferrero et al, Monatshefte fur Chemie, 131: 585-616 (2000); Taunton-Rigby et al, J. Org. Chem., 38(5): 977-985 (1973); Uemura et al, Tetrahedron Lett., 30(29): 3819-3820 (1989); Becker et al, J. Biol. Chem., 242(5): 936-950 (1967); Tsien, International patent publication WO1991/006678.
In some embodiments, the modified nucleotides comprise a modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety having a removable 3′-OH blocking group covalently attached thereto, such that the 3′ carbon atom has attached a group of the structure:
—O—Z
wherein —Z is any of —C(R′)2—O—R″, —C(R′)2—N(R″)2, —C(R′)2—N(H)R″, —C(R′)2—S—R″ and —C(R′)2—F, wherein each R″ is or is part of a removable protecting group; each R′ is independently a hydrogen atom, an alkyl, substituted alkyl, arylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclic, acyl, cyano, alkoxy, aryloxy, heteroaryloxy or amido group, or a detectable label attached through a linking group; with the proviso that in some embodiments such substituents have up to 10 carbon atoms and/or up to 5 oxygen or nitrogen heteroatoms; or (R′)2 represents a group of formula ═C(R′″)2 wherein each R′″ may be the same or different and is selected from the group comprising hydrogen and halogen atoms and alkyl groups, with the proviso that in some embodiments the alkyl of each R′″ has from 1 to 3 carbon atoms; and wherein the molecule may be reacted to yield an intermediate in which each R″ is exchanged for H or, where Z is —(R′)2—F, the F is exchanged for OH, SH or NH2, preferably OH, which intermediate dissociates under aqueous conditions to afford a molecule with a free 3′-OH; with the proviso that where Z is —C(R′)2—S—R″, both R′ groups are not H. In certain embodiments, R′ of the modified nucleotide or nucleoside is an alkyl or substituted alkyl, with the proviso that such alkyl or substituted alkyl has from 1 to 10 carbon atoms and from 0 to 4 oxygen or nitrogen heteroatoms. In certain embodiments, —Z of the modified nucleotide or nucleoside is of formula —C(R′)2—N3. In certain embodiments, Z is an azidomethyl group.
In some embodiments, Z is a cleavable organic moiety with or without heteroatoms having a molecular weight of 200 or less. In other embodiments, Z is a cleavable organic moiety with or without heteroatoms having a molecular weight of 100 or less. In other embodiments, Z is a cleavable organic moiety with or without heteroatoms having a molecular weight of 50 or less. In some embodiments, Z is an enzymatically cleavable organic moiety with or without heteroatoms having a molecular weight of 200 or less. In other embodiments, Z is an enzymatically cleavable organic moiety with or without heteroatoms having a molecular weight of 100 or less. In other embodiments, Z is an enzymatically cleavable organic moiety with or without heteroatoms having a molecular weight of 50 or less. In other embodiments, Z is an enzymatically cleavable ester group having a molecular weight of 200 or less. In other embodiments, Z is a phosphate group removable by a 3′-phosphatase. In some embodiments, one or more of the following 3′-phosphatases may be used with the manufacturer's recommended protocols: T4 polynucleotide kinase, calf intestinal alkaline phosphatase, recombinant shrimp alkaline phosphatase (e.g. available from New England Biolabs, Beverly, MA)
In a further embodiment, the 3′-blocked nucleotide triphosphate is blocked by either a 3′-O-azidomethyl, 3′-O—NH2 or 3′-O-allyl group.
In still other embodiments, 3′-O-blocking groups of the invention include 3′-O-methyl, 3′-O-(2-nitrobenzyl), 3′-O-allyl, 3′-O-amine, 3′-O-azidomethyl, 3′-O-tert-butoxy ethoxy, 3′-O-(2-cyanoethyl), and 3′-O-propargyl.
In some embodiments, 3′-O— protection groups are electrochemically labile groups. That is, deprotection or cleavage of the protection group is accomplished by changing the electrochemical conditions in the vicinity of the protection group which result in cleavage. Such changes in electrochemical conditions may be brought about by changing or applying a physical quantity, such as a voltage difference or light to activate auxiliary species which, in turn, cause changes in the electrochemical conditions at the site of the protection group, such as an increase or decrease in pH. In some embodiments, electrochemically labile groups include, for example, pH-sensitive protection groups that are cleaved whenever the pH is changed to a predetermined value. In other embodiments, electrochemically labile groups include protecting groups which are cleaved directly whenever reducing or oxidizing conditions are changed, for example, by increasing or decreasing a voltage difference at the site of the protection group.
In some embodiments, enzymatic synthesis methods employ TdT variants that display increased incorporation activity with respect to 3′-O-modified nucleoside triphosphates. For example, such TdT variants may be produced using techniques described in Champion et al, U.S. Pat. No. 10,435,676, which is incorporated herein by reference. In some embodiments, a TdT variant is employed having an amino acid sequence at least 60 percent identical to SEQ ID NO: 2 and a substitution at a first arginine at position 207 and a substitution at a second arginine at position 325, or functionally equivalent residues thereof. In some embodiments, a terminal deoxynucleotidyl transferase (TdT) variant is employed that has an amino acid sequence at least sixty percent identical to an amino acid sequence selected from SEQ ID NO: 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 with a substitution of arginine (“first arginine”) at position 207 with respect to SEQ ID NOs 2, 3, 4, 6, 7, 9, 12 and 13, at position 206 with respect to SEQ ID NO 5, at position 208 with respect to SEQ ID NOs 8 and 10, at position 205 with respect to SEQ ID NO 11, at position 216 with respect to SEQ ID NO 14 and at position 210 with respect to SEQ ID NO 15; and a substitution of arginine (“second arginine”) at position 325 with respect to SEQ ID NOs 2, 9 and 13, at position 324 with respect to SEQ ID NOs 3 and 4, at position 320 with respect to SEQ ID NO 320, at position 331 with respect to SEQ ID NOs 6 and 8, at position 323 with respect to SEQ ID NO 11, at position 328 with respect to SEQ ID NOs 12 and 15, and at position 338 with respect to SEQ ID NO 14; or functionally equivalent residues thereof; wherein the TdT variant (i) is capable of synthesizing a nucleic acid fragment without a template and (ii) is capable of incorporating a 3′-O-modified nucleotide onto a free 3′-hydroxyl of a nucleic acid fragment. In some embodiments, the above percent identity value is at least 80 percent identity with the indicated SEQ ID NOs; in some embodiments, the above percent identity value is at least 90 percent identity with the indicated SEQ ID NOs; in some embodiments, the above percent identity value is at least 95 percent identity with the indicated SEQ ID NOs; in some embodiments, the above percent identity value is at least 97 percent identity; in some embodiments, the above percent identity value is at least 98 percent identity; in some embodiments, the above percent identity value is at least 99 percent identity. As used herein, the percent identity values used to compare a reference sequence to a variant sequence do not include the expressly specified amino acid positions containing substitutions of the variant sequence; that is, the percent identity relationship is between sequences of a reference protein and sequences of a variant protein outside of the expressly specified positions containing substitutions in the variant. Thus, for example, if the reference sequence and the variant sequence each comprised 100 amino acids and the variant sequence had mutations at positions 25 and 81, then the percent homology would be in regard to sequences 1-24, 26-80 and 82-100.
In regard to (ii), such 3′-O-modified nucleotide may comprise a 3′-O—NH2-nucleoside triphosphate, a 3′-O-azidomethyl-nucleoside triphosphate, a 3′-O-allyl-nucleoside triphosphate, a 3′O-(2-nitrobenzyl)-nucleoside triphosphate, or a 3′-O-propargyl-nucleoside triphosphate.
In some embodiments, the above TdT variants have substitutions at the first and second arginines as shown in Table 2.
In some embodiments, further TdT variants for use with methods of the invention include one or more of the further substitutions of methionine, cysteine or glutamic acid, as shown in Table 1.
Further specific TdT variants that may be used in methods of the invention are set forth in Table 3. Each of the TdT variants DS1001 through DS1018 of Table 2 comprises an amino acid sequence at least 60 percent identical to SEQ ID NO 2 and comprises the substitutions at the indicated positions. In some embodiments, TdT variants DS1001 through DS1018 comprises an amino acid sequence at least 80 percent identical to SEQ ID NO 2 and comprises the substitutions at the indicated positions; in some embodiments, TdT variants DS1001 through DS1018 comprises an amino acid sequence at least 90 percent identical to SEQ ID NO 2 and comprises the substitutions at the indicated positions; in some embodiments, TdT variants DS1001 through DS1018 comprises an amino acid sequence at least 95 percent identical to SEQ ID NO 2 and comprises the substitutions at the indicated positions; in some embodiments, TdT variants DS1001 through DS1018 comprises an amino acid sequence at least 97 percent identical to SEQ ID NO 2 and comprises the substitutions at the indicated positions; in some embodiments, TdT variants DS1001 through DS1018 comprises an amino acid sequence at least 98 percent identical to SEQ ID NO 2 and comprises the substitutions at the indicated positions; in some embodiments, TdT variants DS1001 through DS1018 comprises an amino acid sequence at least 99 percent identical to SEQ ID NO 2 and comprises the substitutions at the indicated positions.
TdT variants of the invention as described above each comprise an amino acid sequence having a percent sequence identity with a specified SEQ ID NO, subject to the presence of indicated substitutions. In some embodiments, the number and type of sequence differences between a TdT variant of the invention described in this manner and the specified SEQ ID NO may be due to substitutions, deletion and/or insertions, and the amino acids substituted, deleted and/or inserted may comprise any amino acid. In some embodiments, such deletions, substitutions and/or insertions comprise only naturally occurring amino acids. In some embodiments, substitutions comprise only conservative, or synonymous, amino acid changes, as described in Grantham, Science, 185: 862-864 (1974). That is, a substitution of an amino acid can occur only among members of its set of synonymous amino acids. In some embodiments, sets of synonymous amino acids that may be employed are set forth in Table 4A.
In some embodiments, sets of synonymous amino acids that may be employed are set forth in Table 4B.
Biomolecules on which oligonucleotides may be synthesized in accordance with the invention include, but are not limited to, polynucleotides, peptides, proteins, glycans, polysaccharides, and the like. Virtually any biomolecule or other material to which an initiator can be attached can have an oligonucleotide synthesized on it by methods of the invention. As noted above, for polynucleotides, such as cDNAs, genomic fragments, or the like, a variety of different initiator attachment schemes are available, including schemes resulting in a covalent bond between an initiator and a biomolecule or surface and schemes resulting in a non-covalent bond between an initiator and biomolecule or surface, such as the formation of a duplex between the initiator and another complementary oligonucleotide attached to a surface or biomolecule, or the formation of a complex between a capture moiety and its complementary moiety, such as a biotin and streptavidin.
Polynucleotides to which an oligonucleotide has been synthesized may be detached from a solid support in a variety of ways. Initiators hybridized to a capture oligonucleotide may simply be melted or dehybridized from the capture oligonucleotide, or the duplex may be designed to include a restriction endonuclease or nickase recognition site. In embodiments in which an initiator is covalently attached to a surface, several techniques are available to cleave a single strand, e.g. inserting a uracil at a predetermined location in an initiator, Delort et al, Nucleic Acids Research, 13: 319-335 (1985).
Oligonucleotide initiators may be attached to proteins, such as antibodies, using well-known techniques, such as described in the following references: Hermanson (cited above); Baskin et al, Proc. Natl. Acad. Sci., 104(43): 16793-16797 (2007); Gong et al, Bioconjugate Chemistry, 27: 217-225 (2016); Horisawa, Frontiers in Physiology, 5: 1-6 (2014); Jewett et al, Chem. Soc. Rev., 39(4): 1272-1279 (2010); U.S. Pat. No. 5,665,539; and the like.
Once an initiator is attached, then enzymatic synthesis may be performed to extend the initiator. In some embodiments, proteins are reversibly attached to a solid support prior to synthesis. As with polynucleotides, such attachment may be covalent or non-covalent. If the protein is a recombinant protein attachment may be by way of a peptide tag, such as a poly-histidine tag, or like method. In some embodiments, proteins may be immobilized on a solid support by capture and binding to an antibody attached to the solid support.
Synthesizing Oligonucleotides on Biological CellsThe value of single cell measurements has been long appreciated for assessing rare subpopulations which otherwise would be undetectable from ensemble measurements, which provide only averages of cellular parameters from many cells, e.g. Di Carlo et al, Methods in Molecular Biology, 853: 1-9 (2012). As a result, a range of technologies has been developed for high-throughput single cell analysis, e.g. reviewed in Shapiro et al, Nature Reviews Genetics, 14: 618-630 (2013). A common approach in many of these technologies has included the formation of single cell-containing reactors by stochastically distributing cells of a population into small reaction volumes for analysis. Although such stochastic methods permit handling cells in “bulk” mixtures, the methods allow only limited control of the numbers of cells that end up in the small volumes, e.g. Koster et al, LabChip, 8: 1110-1115 (2008), so that typically the higher the concentration of cells in the starting population, the greater the number of small volumes that end up with two or more cells. Since successful single-cell analysis depends on having only one cell in each reaction volume, very low cellular concentrations of starting populations are selected to avoid the occurrence of cellular doublets. Unfortunately, this creates significant inefficiencies in analyses conducted downstream of such stochastic isolation steps. This problem is exacerbated when cell-specific barcodes are delivered to cells by coalescing droplets carrying cells with droplets carrying barcoded beads, which are also stochastically distributed in the droplets. Thus, the availability of a technique to directly synthesis a unique barcode on a cell would obviate the requirement of delivering a single bead to a single cell.
Methods of the invention may be applied to a wide range of biological cells, including but not limited to, mammalian cells, yeast cells, bacterial cells, protozoan cells, fungal cells, plant cells, and the like. In some embodiments, methods of the invention are applied to mammalian cells. Such mammalian cells may be free of tissues, e.g. white blood cells, or such cells may be tissue-bound cells which have been disaggregated. During synthesis of oligonucleotides on living cells reaction conditions are selected to maintain the cells in a viable state. Such conditions (sometimes referred to herein as “biological conditions” or “viable conditions” or “cell-viable conditions”) include disposing and maintaining cells in reaction mixtures that comprise a physiological salt solution that permits a balance of osmotic presssure across cell membranes, a pH in the range of from 6.8 to 7.8, and a temperature in a range of from 15° C. to 41° C. In some embodiments, a temperature in the range of from 25° C. to 38° C. is employed. Physiological salt solutions may include sodium, calcium and/or potassium ions in an aqueous solvent at a concentration in the range of 0.8-1.0 percent (w/v). For example, 0.9 percent (w/v) of sodium chloride in distilled water is a common physiological salt solution. It is understood that such physiological conditions are averages and that in particular implementations of the invention there may be brief deviations from such conditions without significant harm to the cells or biomolecules, for example, in deprotection steps. Likewise, it is understood that some biological cells may be viable in conditions outside those mentioned above, e.g. thermophilic organisms.
Attaching initiators to cells. A first step to generating a unique cellular label is attaching initiators to cells of a target population. This is accomplished using a variety of conventional techniques including, but not limited to, attaching an initiator to one or more antibodies specific for cell surface markers, integrating an initiator into an aptamer specific for cell surface markers, using click chemistry techniques to attach initiators directly to cell surface proteins, generating initiators with 5′-lipophilic tails which insert into the membranes of the target cells. Examples of such labeling techniques are described in the following references: Weber et al, Biomacromolecules, 15: 4621-4626 (2014); Borisenko et al, Nucleic Acids Research, 37(4): e28 (2009); Sano et al, Science, 258: 120-122 (1992); Kazane et al, Proc. Natl. Acad. Sci., 109(10): 3731-3736 (2012); Nikic et al, Nature Protocols, 10: 780-791 (2015); Baskin et al, Proc. Natl. Acad. Sci., 104(43): 16793-16797 (2007); Jewitt et al, Chem. Soc. Rev., 39(4): 1272-1279 (2010); Li et al, Chem. Sci., 8: 2107 (2017).
“Split and Mix” Barcoding of Cells. In some embodiments, the invention provides methods for uniquely barcoding cells, either living cells, fixed cells, or fixed and permeabilized cells. For example, in testing or screening compounds for biological effects, such as changes in gene expression, populations of cells after cells have been exposed to different agents or compounds. Samples of such cells may be tested while viable for changes in gene expression, for example, of cell surface molecules, or such cells may be fixed and permeabilized and tested for changes in the expression of both cellular proteins and mRNA. In some embodiments, protein expression may be monitored using one or more protein-specific antibodies each linked to a distinct initiator that may be extended using the enzymatic synthesis methods of the invention. In some embodiments, mRNA expression may be monitored using mRNA-specific primers to generate cDNAs that may be extended as described in
Similar to adding unique cellular tags in the case of beads described above, the invention also may be used to attach unique position tags in the case of spatial patterns of gene expression in a tissue slice disposed on a planar surface, as illustrated in
Position tags (173) are selected (e.g. are long enough) to uniquely identify each location or region of interest. Additional segment (174) may be added to facilitate manipulation and sequencing of cDNAs (171). In some embodiments, this application of the invention may be carried out with the following steps: (a) providing an array comprising a uniform coating of capture probes each comprising a capture segment; (b) contacting a tissue sample with the array and allowing the nucleic acid of the tissue sample to interact with the capture domain of the capture probe so that the nucleic acid is captured; (c) treating the tissue sample to identify different regions of the tissue sample; (d) generating a nucleic acid molecule from the nucleic acid that interacts with the capture domain; (e) enzymatically synthesizing position tags onto the nucleic acid molecules; (f) determining the region that is associated with the nucleic acid that interacts with the capture domain; and (e) correlating the determined regions to the cDNAs. In some embodiments, the nucleic acid molecules from the tissue sample is RNA. In other embodiments, the nucleic acid molecules from the tissue sample may be genomic DNA. In other embodiments, the nucleic acid molecules from the tissue sample may be mRNA.
Similarly, as illustrated in
The UMI (1167) may comprise a random nucleotide segment. Different kinds of oligonucleotides, for example, oligonucleotides with different position tags are not required because they are synthesized later using methods of the invention. Segment (1166) may also include a cleavable linker or cleavable nucleotide for releasing antibody barcodes for analysis, such as, by sequencing. Onto array (1164) is disposed a slice or thin layer (1181) (e.g. 100-1000 μm thick) of tissue, which it is then treated (1169) (i) to identify features, such as cells or sub-tissues, of interest and to record and/or correlate such information to locations on planar array (1164), and (ii) to permeablized cells in the tissue so that antibodies can access target proteins and so that released antibody barcodes can diffuse to and be captured by oligonucleotides (1180). The image information is used to define regions on array (1164) within which common position tags are synthesized on antibody barcodes. As above, the position tags allow antibody barcodes to be harvested and sequenced in bulk, yet be related to specific regions by their position tags. After the above steps (i) and (ii), reagents for a reverse transcriptase reaction are applied in order to synthesize complements of the antibody barcodes (1171) just as mRNAs above using captured antibody barcodes (1170) as templates. Tissue slice (1181) is then removed leaving array (1164) with a pattern of different cDNAs attached to its surface. The different cDNAs at the different positions may be identified and quantified by attaching position tags to samples of antibody barcodes from regular locations by inkjet delivery of synthesis reagents for the position tags. As with cDNAs, position tags (1173) on antibody barcodes are selected (e.g. are long enough) to uniquely identify each location or region of interest.
Similarly, as illustrated in
Although
Embodiments described in
As mentioned above, cells may be labeled with a similar random barcode that, instead of consisting of a random sequence of nucleotides, consists of a random sequence of homopolymer segments, wherein each homopolymer segment comprises a different kind of nucleotide than that of a nearest neighbor homopolymer segment. The advantage of such a barcoding scheme is that 3′-blocked dNTPs do not have to be used; therefore, no deblocking step is required, which makes the synthesis process simpler and potentially less damaging to the viability of the cells. The lengths of homopolymer segments used in such barcodes may vary widely. In some embodiments, conditions including the duration of reaction are selected so that the average length of a homopolymer segment is in the range of from 1 to 100 nucleotides; in other embodiments, the average length of a homopolymer segment is in the range of from 1 to 25 nucleotides; and in still other embodiments, the average length of a homopolymer segment is in the range of from 1 to 10 nucleotides.
Binding compounds used with the invention may include a wide variety of compositions that specifically bind to predetermined cellular constituents and to which initiators may be attached for generating identifying oligonucleotides.
In some embodiments, initiator oligonucleotides with free 3′-hydroxyls are stably inserted into to the cell surface membranes of target cells by derivatizing the 5′ end of initiator oligonucleotides with a lipophilic moiety using conventional techniques, e.g. as disclosed in the following references: Weber et al, Biomacromolecules, 15: 4621-4626 (2014); Bunge et al, Langmuir, 23(8): 4455-4464 (2007); Borjesson et al, J. Amer. Chem. Soc., 131(8): 2831-2839 (2009); Bunge et al, J. Phys. Chem. B, 113(51): 16425-16434 (2009); and like references. Of particular interest is the technique disclosed by Weber (cited above) which calls for the insertion of complementary pairs of oligonucleotides each derivatized with a lipophilic moiety, one oligonucleotide of the pair on its 5′ end (a longer initiator oligonucleotide) and the other on its 3′ end (a shorter support oligonucleotide). The hybridized pairs are very stable in the cell membrane, which would minimize losses during synthesis.
As illustrated in
In some embodiments, enzymatic extension of initiators (310) may be employed to generate unique cell-specific barcodes on cells (314) by a “split and mix” synthesis strategy, as illustrated in
In some embodiments, unique oligonucleotide tags may be synthesized on viable cells by attaching tags comprising sequences of homopolymeric segments. In some embodiments, the invention is directed to methods of synthesizing on a viable cell an oligonucleotide barcode comprising the steps of: (a) providing an initiator with a free 3′-hydroxyl attached to a cell surface molecule of the cell or anchored in a cell surface membrane of the cell; (b) repeating under biological conditions a plurality of cycles of the step of contacting under elongation conditions the initiator or elongated fragments having free 3′-O-hydroxyls with a nucleoside triphosphate and a template-independent DNA polymerase so that the initiator or elongated fragments are elongated by a homopolymer segment to form elongated fragments having free 3′-hydroxyls, wherein the kind of nucleoside triphosphate added in each step after a first step is different from the kind in the immediately preceding step.
In some embodiments, each of the cycles further includes a step of removing unincorporated nucleoside triphosphates. In some embodiments, the elongation conditions include a concentration of said nucleoside triphosphates, a temperature and a reaction time to produce homopolymer segments having an average length in the range of from 1 to 100 nucleotides. In some embodiments, unique oligonucleotide tags comprising homopolymeric segments are produced using a split-and-mix procedure.
Single Cell AnalysisIn some embodiments of the invention, cells from a population are disposed in reactors each containing a single cell. This may be accomplished by a variety of large-scale single-cell reactor platforms known i the art, e,g. Clarke et al, U.S. patent publication 201010255471; Mathies et al., U.S. patent publication 2010/0285975; Edd et al., U.S. patent publication 2010/0021984; Colston et al, U.S. patent publication 2010/0173394; Love et al, International patent publication WO2009/145925; Muraguchi et al, U.S. patent publication 2009/0181859; Novak et al, Angew. Chem. Int. Ed., 50: 390-395 (2011); Chen et al, Biomed Microdevices, 11: 1223-1231 (2009); and the like, which are incorporated herein by reference. In one aspect, cells are disposed in wells of a microwell array where reactions, such as PCA reactions, take place; in another aspect, cells are disposed in micelles of a water-in-oil emulsion, where micelles serve as reactors. Micelle reactors generated by microfiuidics devices, e.g. Mathies et al (cited above) or Edd et al (cited above), are of particular interest because uniform-sized micelles may be generated with lower shear and stress on cells than in bulk emulsification processes. Compositions and techniques for emulsifications, including carrying out amplification reactions, such as PCRs, in micelles is found in the following references, which are incorporated by reference: Becher, “Emulsions: Theory and Practice,” (Oxford. University Press, 2001); Griffiths and Tawfik, U.S. Pat. No. 6,489,103; Tawfik and Griffiths, Nature Biotechnology, 16: 652-656 (1998); Nakano et al, J. Biotechnology, 102: 117-124 (2003); Dressman et al, Proc. Natl. Acad, Sci., 100: 8817-8822 (2003); Dressman et al, U.S, Pat. No, 8,048,627; Berka et al, U.S. Pat. Nos. 7,842,457 and 8,012,690; Diehl et al, Nature Methods, 3; 551-559 (2006); Williams et al, Nature Methods, 3: 545-550 (2006); Zeng et al, Analytical Chemistry, 82(8): 3183.-3190 (2010); Micellula DNA Emulsion & Purification Kit instructions (EURx, Gdansk, Poland, 2011); and the like. In one embodiment, the mixture of homogeneous sequence tags (e.g. beads) and reaction mixture is added dropwise into a spinning mixture of biocompatible oil (e.g., light mineral oil, Sigma) and allowed to emulsify. In another embodiment, the homogeneous sequence tags and reaction mixture are added dropwise into a cross-now of biocompatible oil.The oil used may be supplemented with one or more biocompatible emulsion stabilizers. These emulsion stabilizers may include Atlox 4912, Span 80, and other recognized and commercially available suitable stabilizers. in some embodiments, the emulsion is heat stable to allow thermal cycling, e.g,, to at least 94° C., at least 95° C., or at least 96° C. In sonic embodiments, the droplets formed range in size from about 5 microns to about 500 microns. In soma embodiments, droplets are formed in a range of from about 10 microns to about 350 microns, or from about 50 to 250 microns, or from about 100 microns to about 200 microns. Advantageously, cross-now fluid mixing allows for control of the droplet formation, and uniformity of droplet size.
In some embodiments, micelles are produced having a uniform distribution of volumes so that reagents available in such reactors result in similarly amplified target nucleic acids and sequence tags. That is, widely varying reactor volumes, e.g. micelle volumes, may lead to amplification failures and/or widely varying degrees of amplification. Such failures and variation would preclude or increase the difficulty of making quantitative comparisons of target nucleic acids in individual cells of a population, e.g. differences in gene expression. in one aspect, micelles are produced that have a distribution of volumes with a coefficient of variation (CV) of thirty percent or less. In some embodiments, micelles have a distribution of volumes with a CV of twenty percent of less.
Cells of a sample and homogeneous sequence tags may be suspended in a reaction mixture prior to disposition into reactors. In one aspect, a reaction mixture is a PCA reaction mixture and is substantially the same as a PCR reaction mixture with at least one pair of inner (or linking) primers and at least one pair of outer primers. A reaction mixture may comprise one or more optional components, including but not limited to, thermostable restriction endonucleases; one or more proteinase inhibitors; lysing agents to facilitate release of target nucleic acids of isolated cells, e.g. Brown et al, Interface, 5: S131-S138 (2008); and the like. In some embodiments, a step of lysing cells may be accomplished by heating cells to a temperature of 95° C. or above in the presence of a nonionic detergent, e.g. 0.1% Tween X-100, for a period prior to carrying out an amplification reaction. In one embodiment, such period of elevated temperature may be from 10-20 minutes. Alternatively, a step of lysing cells may be accomplished by one or more cycles of heating and cooling, e.g. 96° C. for 15 min followed by 10° C., for 10 min, in the presence of a nonionic detergent, e.g. 0.1% Tween X-100. In some embodiments, micelle reactors are generated and sorted in a micro fluidics device as described more fully below.
Single Cell Transcriptome AnalysisIn
Cell-containing micelle (346) is caused to coalesce with reagent micelle (348) in oil flow (354) at junction (352). Reagent micelle (348) contains lysis reagents for breaking down the cell surface membrane to expose mRNA for transcription and amplification. The result of such coalescence is micelle (356), which incubates during flow through passage (360) whose length is designed to provide a transit time sufficient for the lysis reagents carried by micelle (348) to complete lysis of the cell and produce a cellular lysate (358) ready for reverse transcription and amplification. Lysis reagents are described in the following references: Tang et al, Nature Protocol, 5(3): doi:10.1038/nprot.2009.236; Tbronhill et al, Prenatal Diagnosis, 21: 490-497 (2001); Kim et al, Fertility and Sterility, 92: 814-818 (2009); and the like. Exemplary lysis conditions for use with PCA reactions are as follows: 1) cells in H2O at 96° C. for 15 min, followed by 15 min at 10° C.; 2) 200 mM KOH, 50 mM dithiotheitol, heat to 65° C. for 10 min; 3) for 4 μL protease-based lysis buffer: 1 μL of 17 μM SDS combined with 3 μL of 125 μg/mL proteinase K, followed by incubation at 37° C. for 60 min, then 95° C. for 15 min (to inactivate the proteinase K); 4) for 10 μL of a detergent-based lysis buffer: 2 μL H2O, 2 μL 250 ng/μL polyA, 2 μL 10 mM EDTA, 2 μL 250 mM dithiothreitol, 2 μL 0.5% N-laurylsarcosin salt solution. Single-cell analysis platforms, incubation times, lysis buffer and/or PCA reaction other components, their concentrations, reactions volumes and the like, are design choices that are optimized for particular applications by one of ordinary skill in the art. In one embodiment, an alkaline lysis buffer disclosed by Kim et al, Anal. Chem., 90: 1273-1279 (2018) is employed. Such buffer comprises 20 mM NaOH, 60% (v/v) PeG-200, and 2% (v/v) Triton X-100, and may be neutralized by the buffering capacity of an RT-PCR reagents.
After lysis, cell lysate in micelle (358) is coalesced at junction (368) with reagent micelle (362) from oil flow (364). Reagent micelle contains reverse transcriptase and PCR reaction components. In some embodiments, such components may comprise ingredient from a commercial RT-PCR kit, for example, ThermoFisher Invitrogen SuperScript IV One-Step RT-PCR system. In some embodiments, such components may comprise template-switching transcription components, e.g. Trombetta et al, Curr. Protocol Mol. Biol., 107: 4.22.1-4.22.17 (2014). After coalescence, droplets are collected in a temperature-control device, such as a thermocycler, which permits heat denaturation of reverse transcriptase and subsequence PCR of cDNAs and barcodes. Different embodiments of reverse transcription reactions are illustrated in
In some embodiments, after template-switching reverse transcription, polymerase cycling assembly reactions are carried out in each micelle. Polymerase cycling assembly (PCA) reactions permit a plurality of nucleic acid fragments to be fused together to form a single fusion product in one or more cycles of fragment annealing and polymerase extension, e.g. Xiang et al, FEBS Micro biol. Rev., 32: 522-540 (2008). PCA reactions come in many formats, In one format of interest, PCA follows a plurality of polymerase chain reactions (PCRs) taking place in a common reaction volume, wherein each component PCR includes at least one linking primer that permits strands from the resulting amplicon to anneal to strands from another amplicon in the reaction and to be extended to form a fusion product or a precursor of a fusion product. PCA in its various formats (and under various alternative names) is a well-known method for fragment assembly and gene synthesis, several forms of which are disclosed in the following references; Yon et al, Nucleic Acids Research, 17: 4895 (1989); Chen et al, J. Am. Chem. Soc., 116: 8799-8800 (1994); Stemmer et al, Gene, 164: 49-53 (1995); Hoover et al, Nucleic Acids Research, 30: c43 (2002); Xiong et al, Biotechnology Advances, 26: 121-134 (2008); Xiong et al, FEBS Microbial. Rev., 32: 522-540 (2008); and the like.
Multiple different target nucleic acids, such as cDNAs (460), g1, g2, . . . gn, are linked to the same barcode nucleic acid, X (462) to form (464) multiple fusion products X-g1, X-g2, X-ga (466). In some embodiments, such plurality is between 2 and 10000; and in another embodiment, it is between 2 and 1000; and in another embodiment, it is between 2 and 100. In PCA reactions of these embodiments, the concentration of inner primer (468) may be greater than those of inner primers (e.g. 471) of the various gi nucleic acids so that there is adequate quantities of the X amplicon to anneal with the many stands of the gi amplicons. In accordance with a method of the invention, the fusion products (466) may be extracted from the reaction mixture of the coalesced micelles and sequenced.
In some embodiments, a method for generating a cDNA library with cell-specific barcodes may comprise the steps of (a) synthesizing a unique oligonucleotide barcode on each cell of a population to form a population of barcoded cells; (b) disposing barcoded cells into multiple reactors each containing a single barcoded cell in a polymerase cycling assembly (PCA) reaction mixture, wherein the PCA reaction mixture comprises a pair of outer primers and one or more pairs of linking primers specific for a plurality of target nucleic acids in the barcoded cells and the oligonucleotide barcodes; (c) performing a PCA reaction in the reactors so that fusion products of the target nucleic acids and the oligonucleotide barcodes are formed in the reactors; and (d) sequencing the fusion products from the reactors to identify the target nucleic acids of each cell in the population.
An alternative application for single-cell transcriptome analysis is illustrated in
Clearly many other microfluidics device configurations may be employed to generate micelles containing a single cell and a predetermined number of homogeneous sequence tags, for example, one homogeneous sequence tag, two homogeneous sequence tags, or to selectively add reagents to a micelle by selectively coalescing micelles, by electroporation, or the like, e.g. Zagoni et al, chapter 2, Methods of Cell. Biology, 102: 25-48 (2011); Brouzes, chapter 10, Methods of Cell Biology, 102: 105439 (2011); Wiklund et al, chapter 14, Methods of Cell Biology, 102: 177-196 (2011); Le Gac et al, chapter 7, Methods of Molecular Biology, 853: 65-82 (2012); and the like.
Fixing and Permeabilizing Cells or TissuesIn some embodiments, initiators coupled to binding compounds comprising nucleic acid hybridization probes and/or protein-specific binding compounds may be directed to intracellular targets, such as intracellular proteins, messenger RNAs, and/or genomic DNAs. In some embodiments, cells are fixed and permeablilized for application of binding compounds specific for such intracellular targets. Fixing and permeablization of cells may be carried out by conventional protocols, such as used in flow cytometry. Typically such protocols include a steps of treating cells with a fixing agent followed by a step of treating cells with a permeabilizing agent. A fixing step typically immobilizes intracellular cellular targets, while retaining cellular and subcellular architecture and permitting unhindered access of antibodies and/or hybridization probes to all cells and subcellular compartments. Wide ranges of fixatives are commercially available, and the correct choice of method will depend on the nature of the targets being examined and on the properties of the antibody and/or hybridization probes used. Fixation methods fall generally into two classes: organic solvents and cross-linking reagents. Organic solvents such as alcohols and acetone remove lipids and dehydrate the cells, while precipitating the proteins on the cellular architecture. Cross-linking reagents (such as paraformaldehyde) form intermolecular bridges, normally through free amino groups, thus creating a network of linked antigens. Cross-linkers preserve cell structure better than organic solvents, but may reduce the antigenicity of some cell components, and require the addition of a permeabilization step, to allow access of the antibodies and/or hybridization probes to the intracellular targets. Exemplary fixing and permeabilizing steps include, but are not limited to, methanol-acetone fixation (fix in cooled methanol, 10 minutes at −20° C.; permeabilize with cooled acetone for 1 min at −20° C.); paraformaldehyde-triton fixation (fix in 3-4% paraformaldehyde for 10-20 min; rinse with phosphate buffered saline (PBS); permeabilize with 0.5% Triton X-100 for 2-10 min); paraformaldehyde-methanol fixation (fix in 3-4% paraformaldehyde for 10-20 min; rinse with PBS; permeabilize with cooled methanol for 5-10 min at -20° C.). Permeabilizing agents include, but are not limited to, detergents saponin, Triton X-100, Tween-20, NP40. Permeabilizing agents may also include proteinases, such as proteinase K, streptolysin O, and the like.
Chimeric Enzymatically and Chemically Synthesized Polynucleotides for User Specified ApplicationsFrequently products used in medicine and biology comprise components that may be used in every circumstance and components that must be provided anew for particular applications, the latter components sometimes being referred to as “user specified” or “user determined” components. Many nucleic acid reagents are of this character. In particular, common components of labeled hybridization probes may be manufactured in bulk and provided as kits for a user who, to obtain an operable assay, must supply a specific component, for example, a target specific component of a probe which hybridizes to a nucleic acid target of interest. Exemplary techniques that are provided in the above format include, but are not limited to, Taqman probes, CRISPR guide sequences, various kinds of PCR probes, and the like, which can be constructed as combinations of pre-existing chemically synthesized oligonucleotides and enzymatically user specified oligonucleotides using methods of the invention.
A similar kit may be prepared for providing single guide RNAs (sgRNAs): i) a bead with an initiator sequence attached wherein a T7 promoter is included; ii) customer buys kit with bead, synthesizes its favorite target specific sequence +20-25 nt of the 5′ scaffold domain on the end of the initiator; iii) Upon synthesis completion, (a) Anneal complementary 3′ scaffold domain onto the oligonucleotide still attached to the beads, (b) Allow primer extension to generate a dsDNA, and (c) Allow reverse transcription to generate sgRNA molecules.
KitsThe invention includes kits for carrying out methods of the invention. In some embodiments, “kit” refers to any delivery system for delivering materials or reagents for carrying out a method of the invention. In the context of reaction assays, such delivery systems include systems that allow for the storage, transport, or delivery of reaction reagents (e.g., probes, enzymes, etc. in the appropriate containers) and/or supporting materials (e.g., buffers, written instructions for performing the assay etc.) from one location to another. For example, kits include one or more enclosures (e.g., boxes) containing the relevant reaction reagents and/or supporting materials. Such contents may be delivered to the intended recipient together or separately. For example, a first container may contain an enzyme for use in an assay, while a second container contains probes.
In some embodiments, a kit of the invention includes a template-free polymerase. In some embodiments, a template-free polymerase is a terminal deoxynucleotidyl transferase (TdT) or a variant thereof. In some such kits, a template-free polymerase includes 3′-O-blocked nucleotides. In further embodiments in kits for extending polynucleotides or cDNAs, a kit may include a solid support with an initiator.
In some embodiments, a kit of the invention for synthesizing a random oligonucleotide barcode includes, a TdT or a variant thereof, 3′-O-blocked nucleoside triphosphates, arrays of microwells for carrying out extension and de-blocking reactions for split and mix synthesis of a barcode.
In some embodiments, a kit may include a microfluidic device for processing single cells and for delivering reagents thereto.
In some embodiments, a kit may include one or more solid supports with oligonucleotides attached for carry out methods of synthesizing unique oligonucleotide barcodes on cDNAs. In some embodiments, such one or more solid supports comprise beads; in other embodiments, such one or more solid supports comprise a planar support having a surface coated with capture oligonucleotides.
DefinitionsUnless otherwise specifically defined herein, terms and symbols of nucleic acid chemistry, biochemistry, genetics, and molecular biology used herein follow those of standard treatises and texts in the field, e.g. Kornberg and Baker, DNA Replication, Second Edition (W.H. Freeman, New York, 1992); Lehninger, Biochemistry, Second Edition (Worth Publishers, New York, 1975); Strachan and Read, Human Molecular Genetics, Second Edition (Wiley-Liss, New York, 1999).
“Amplify,” “amplifies,” “amplified,” “amplification,” as used herein, generally refer to any process by which one or more copies are made of a target polynucleotide or a portion thereof. A variety of methods of amplifying polynucleotides (e.g. DNA and/or RNA) are available, some examples of which are described herein. Amplification may be linear, exponential, or involve both linear and exponential phases in a multi-phase amplification process. Amplification methods may involve changes in temperature, such as a heat denaturation step, or may be isothermal processes that do not require heat denaturation. “Amplicon” means the product of a polynucleotide amplification reaction; that is, a clonal population of polynucleotides, which may be single stranded or double stranded, which are replicated from one or more starting sequences. “Amplifying” means producing an amplicon by carrying out an amplification reaction. The one or more starting sequences may be one or more copies of the same sequence, or they may be a mixture of different sequences. Preferably, amplicons are formed by the amplification of a single starting sequence. Amplicons may be produced by a variety of amplification reactions whose products comprise replicates of the one or more starting, or target, nucleic acids. In one aspect, amplification reactions producing amplicons are “template-driven” in that base pairing of reactants, either nucleotides or oligonucleotides, have complements in a template polynucleotide that are required for the creation of reaction products. In one aspect, template-driven reactions are primer extensions with a nucleic acid polymerase or oligonucleotide ligations with a nucleic acid ligase. Such reactions include, but are not limited to, polymerase chain reactions (PCRs), linear polymerase reactions, nucleic acid sequence-based amplification (NASBAs), rolling circle amplifications, and the like, disclosed in the following references that are incorporated herein by reference: Mullis et al, U.S. Pat. Nos. 4,683,195; 4,965,188; 4,683,202; 4,800,159 (PCR); Gelfand et al, U.S. Pat. No. 5,210,015 (real-time PCR with “taqman” probes); Wittwer et al, U.S. Pat. No. 6,174,670; Kacian et al, U.S. Pat. No. 5,399,491 (“NASBA”); Lizardi, U.S. Pat. No. 5,854,033; Aono et al, Japanese patent publ. JP 4-262799 (rolling circle amplification); and the like. In one aspect, amplicons of the invention are produced by PCRs. An amplification reaction may be a “real-time” amplification if a detection chemistry is available that permits a reaction product to be measured as the amplification reaction progresses, e.g. “real-time PCR” described below, or “real-time NASBA” as described in Leone et al, Nucleic Acids Research, 26: 2150-2155 (1998), and like references. As used herein, the term “amplifying” means performing an amplification reaction. A “reaction mixture” means a solution containing all the necessary reactants for performing a reaction, which may include, but not be limited to, buffering agents to maintain pH at a selected level during a reaction, salts, co-factors, scavengers, and the like.
“Binding compound” means, in some embodiments, any molecule to which oligonucleotide tags can be attached for identification that is capable of specifically binding to a non-nucleic acid ligand. Binding compounds include, but are not limited to, antibodies or compounds derived from antibodies, e.g. Fab fragments. Non-nucleic acid ligands include, but are not limited to, proteins. In some embodiments, binding compounds are attached, e.g. covalently attached, to a surface of a solid support. In some embodiments, oligonucleotide tags are releasably attached to binding compounds; that is, they are attached by a linkage that includes a bond that may be selectively cleaved by predetermined conditions, e.g. light, high pH, low pH, specific redox conditions, specific electrical potential, or the like.
“Functionally equivalent” in reference to amino acid positions in two or more different TdTs means (i) the amino acids at the respective positions play the same functional role in an activity of the TdTs, and (ii) the amino acids occur at homologous amino acid positions in the amino acid sequences of the respective TdTs. It is possible to identify positionally equivalent or homologous amino acid residues in the amino acid sequences of two or more different TdTs on the basis of sequence alignment and/or molecular modelling. In some embodiments, functionally equivalent amino acid positions belong to sequence motifs that are conserved among the amino acid sequences of TdTs of evolutionarily related species, e.g. genus, families, or the like. Examples of such conserved sequence motifs are described in Motea et al, Biochim. Biophys. Acta. 1804(5): 1151-1166 (2010); Delarue et al, EMBO J., 21: 427-439 (2002); and like references.
“Microfluidics” device or “nanofluidics” device, used interchangeably herein, each means an integrated system for capturing, moving, mixing, dispensing or analyzing small volumes of fluid, including samples (which, in turn, may contain or comprise cellular or molecular analytes of interest), reagents, dilutants, buffers, or the like. Generally, reference to “microfluidics” and “nanofluidics” denotes different scales in the size of devices and volumes of fluids handled. In some embodiments, features of a microfluidic device have cross-sectional dimensions of less than a few hundred square micrometers and have passages, or channels, with capillary dimensions, e.g. having maximal cross-sectional dimensions of from about 500 gm to about 0.1 μm. In some embodiments, microfluidics devices have volume capacities in the range of from 1μL to a few nL, e.g. 10-100 nL. Dimensions of corresponding features, or structures, in nanofluidics devices are typically from 1 to 3 orders of magnitude less than those for microfluidics devices. One skilled in the art would know from the circumstances of a particular application which dimensionality would be pertinent. In some embodiments, microfluidic or nanofluidic devices have one or more chambers, ports, and channels that are interconnected and in fluid communication and that are designed for carrying out one or more analytical reactions or processes, either alone or in cooperation with an appliance or instrument that provides support functions, such as sample introduction, fluid and/or reagent driving means, such as positive or negative pressure, acoustical energy, or the like, temperature control, detection systems, data collection and/or integration systems, and the like. In some embodiments, microfluidics and nanofluidics devices may further include valves, pumps, filters and specialized functional coatings on interior walls, e.g. to prevent adsorption of sample components or reactants, facilitate reagent movement by electroosmosis, or the like. Such devices may be fabricated as an integrated device in a solid substrate, which may be glass, plastic, or other solid polymeric materials, and may have a planar format for ease of detecting and monitoring sample and reagent movement, especially via optical or electrochemical methods. In some embodiments, such devices are disposable after a single use. In some embodiments, microfluidic and nanofluidic devices include devices that form and control the movement, mixing, dispensing and analysis of droplets, such as, aqueous droplets immersed in an immiscible fluid, such as a light oil. The fabrication and operation of microfluidics and nanofluidics devices are well-known in the art as exemplified by the following references that are incorporated by reference: Ramsey, U.S. Pat. Nos. 6,001,229; 5,858,195; 6,010,607; and 6,033,546; Soane et al, U.S. Pat. Nos. 5,126,022 and 6,054,034; Nelson et al, U.S. Pat. No. 6,613,525; Maher et al, U.S. Pat. No. 6,399,952; Ricco et al, International patent publication WO 02/24322; Bjornson et al, International patent publication WO 99/19717; Wilding et al, U.S. Pat. Nos. 5,587,128; 5,498,392; Sia et al, Electrophoresis, 24: 3563-3576 (2003); Unger et al, Science, 288: 113-116 (2000); Enzelberger et al, U.S. Pat. No. 6,960,437; Cao, “Nanostructures & Nanomaterials: Synthesis, Properties & Applications,” (Imperial College Press, London, 2004); Haeberle et al, LabChip, 7: 1094-1110 (2007); Cheng et al, Biochip Technology (CRC Press, 2001); and the like.
“Mutant” or “variant,” which are used interchangeably, refer to polypeptides derived from a natural or reference TdT polypeptide described herein, and comprising a modification or an alteration, i.e., a substitution, insertion, and/or deletion, at one or more positions. Variants may be obtained by various techniques well known in the art. In particular, examples of techniques for altering the DNA sequence encoding the wild-type protein, include, but are not limited to, site-directed mutagenesis, random mutagenesis, sequence shuffling and synthetic oligonucleotide construction. Mutagenesis activities consist in deleting, inserting or substituting one or several amino-acids in the sequence of a protein or in the case of the invention of a polymerase. The following terminology is used to designate a substitution: L238A denotes that amino acid residue (Leucine, L) at position 238 of a reference, or wild type, sequence is changed to an Alanine (A). A132V/I/M denotes that amino acid residue (Alanine, A) at position 132 of the parent sequence is substituted by one of the following amino acids: Valine (V), Isoleucine (I), or Methionine (M). The substitution can be a conservative or non-conservative substitution. Examples of conservative substitutions are within the groups of basic amino acids (arginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), polar amino acids (glutamine, asparagine and threonine), hydrophobic amino acids (methionine, leucine, isoleucine, cysteine and valine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and small amino acids (glycine, alanine and serine).
“Polymerase chain reaction” or “PCR” means a reaction for the in vitro amplification of specific DNA sequences by the simultaneous primer extension of complementary strands of DNA. In other words, PCR is a reaction for making multiple copies or replicates of a target nucleic acid flanked by primer binding sites, such reaction comprising one or more repetitions of the following steps: (i) denaturing the target nucleic acid, (ii) annealing primers to the primer binding sites, and (iii) extending the primers by a nucleic acid polymerase in the presence of nucleoside triphosphates. Usually, the reaction is cycled through different temperatures optimized for each step in a thermal cycler instrument. Particular temperatures, durations at each step, and rates of change between steps depend on many factors well-known to those of ordinary skill in the art, e.g. exemplified by the references: McPherson et al, editors, PCR: A Practical Approach and PCR2: A Practical Approach (IRL Press, Oxford, 1991 and 1995, respectively). For example, in a conventional PCR using Taq DNA polymerase, a double stranded target nucleic acid may be denatured at a temperature >90° C., primers annealed at a temperature in the range 50-75° C., and primers extended at a temperature in the range 72-78° C. Reaction volumes typically range from a few hundred nanoliters, e.g. 200 nL, to a few hundred μL, e.g. 200 μL.
“Primer” means an oligonucleotide, either natural or synthetic, that is capable, upon forming a duplex with a polynucleotide template, of acting as a point of initiation of nucleic acid synthesis and being extended from its 3′ end along the template so that an extended duplex is formed. The sequence of nucleotides added during the extension process are determined by the sequence of the template polynucleotide. Usually primers are extended by a DNA polymerase. Primers usually have a length in the range of from 14 to 36 nucleotides.
“Polynucleotide” and “oligonucleotide” are used interchangeably and each mean a linear polymer of nucleotide monomers. Monomers making up polynucleotides and oligonucleotides are capable of specifically binding to a natural polynucleotide by way of a regular pattern of monomer-to-monomer interactions, such as Watson-Crick type of base pairing. Such monomers and their internucleosidic linkages may be naturally occurring or may be analogs thereof, e.g. naturally occurring or non-naturally occurring analogs. Non-naturally occurring analogs may include phosphorothioate internucleosidic linkages, locked nucleic acids, bases containing linking groups permitting the attachment of labels, such as fluorophores, or haptens, or other oligonucleotides, and the like. Whenever the use of an oligonucleotide or polynucleotide requires enzymatic processing, such as extension by a polymerase, ligation by a ligase, or the like, one of ordinary skill in the art would understand that oligonucleotides or polynucleotides in those instances would not contain certain analogs of intemucleosidic linkages, sugar moities, or bases at any or some positions. Polynucleotides typically range in size from a few monomeric units, e.g. 5-40, when they are usually referred to as “oligonucleotides,” to several thousand monomeric units. Whenever a polynucleotide or oligonucleotide is represented by a sequence of letters (upper or lower case), such as “ATGCCTG,” it will be understood that the nucleotides are in 5′→3′ order from left to right and that “A” denotes deoxyadenosine, “C” denotes deoxycytidine, “G” denotes deoxyguanosine, and “T” denotes thymidine, “I” denotes deoxyinosine, “U” denotes uridine, unless otherwise indicated or obvious from context. Unless otherwise noted the terminology and atom numbering conventions will follow those disclosed in Strachan and Read, Human Molecular Genetics 2 (Wiley-Liss, New York, 1999). Usually polynucleotides comprise the four natural nucleosides (e.g. deoxyadenosine, deoxycytidine, deoxyguanosine, deoxythymidine for DNA or their ribose counterparts for RNA) linked by phosphodiester linkages; however, they may also comprise non-natural nucleotide analogs, e.g. including modified bases, sugars, or intemucleosidic linkages. Those skilled in the art would recognize when an enzyme has specific oligonucleotide or polynucleotide substrate requirements for activity, e.g. single stranded DNA, RNA/DNA duplex, or the like, and would be capable of selecting the appropriate compositions, especially with guidance from treatises, such as Sambrook et al, Molecular Cloning, Second Edition (Cold Spring Harbor Laboratory, New York, 1989), and like references. As used herein, “native polynucleotide” means a polymer of ribonucleotides or deoxyribonucleotides, without non-natural phosphate linkages, sugars, or bases. In some embodiments, native polynucleotides excludes polynucleotides having protection groups (such as exocyclic amine protection groups), linkers (including groups for attaching labels to bases), or labels, capture moieties, or the like. In some embodiments, a native polynucleotide may be a polynucleotide extracted from nature, a chemically or enzymatically synthesized polynucleotide without protection groups, or either of the foregoing attached to a support or with a label, linker or reactive moiety attached.
“Sequence identity” refers to the number (or fraction, usually expressed as a percentage) of matches (e.g., identical amino acid residues) between two sequences, such as two polypeptide sequences or two polynucleotide sequences. The sequence identity is determined by comparing the sequences when aligned so as to maximize overlap and identity while minimizing sequence gaps. In particular, sequence identity may be determined using any of a number of mathematical global or local alignment algorithms, depending on the length of the two sequences. Sequences of similar lengths are preferably aligned using a global alignment algorithm (e.g. Needleman and Wunsch algorithm; Needleman and Wunsch, 1970) which aligns the sequences optimally over the entire length, while sequences of substantially different lengths are preferably aligned using a local alignment algorithm (e.g. Smith and Waterman algorithm (Smith and Waterman, 1981) or Altschul algorithm (Altschul et al., 1997; Altschul et al., 2005)). Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software available on internet web sites such as http://blast.ncbi.nlm.nih.gov/ or ttp://www.ebi.ac.uk/Tools/emboss/. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithm needed to achieve maximal alignment over the full length of the sequences being compared. For purposes herein, % amino acid sequence identity values refer to values generated using the pair wise sequence alignment program EMBOSS Needle, that creates an optimal global alignment of two sequences using the Needleman-Wunsch algorithm, wherein all search parameters are set to default values, i.e. Scoring matrix=BLOSUM62, Gap open=10, Gap extend=0.5, End gap penalty=false, End gap open=10 and End gap extend=0.5.
“Sequence tag” (or “tag”) or “barcode” means an oligonucleotide that is attached to Qa polynucleotide or template molecule and is used to identify and/or track the polynucleotide or template in a reaction or a series of reactions. A sequence tag may be attached to the 3′- or 5′-end of a polynucleotide or template or it may be inserted into the interior of such polynucleotide or template to form a linear conjugate, sometime referred to herein as a “tagged polynucleotide,” or “tagged template,” or “tag-polynucleotide conjugate,” “tag-molecule conjugate,” or the like. Sequence tags may vary widely in size and compositions; the following references, which are incorporated herein by reference, provide guidance for selecting sets of sequence tags appropriate for particular embodiments: Brenner, U.S. Pat. No. 5,635,400; Brenner and Macevicz, U.S. Pat. No. 7,537,897; Brenner et al, Proc. Natl. Acad., Sci., 97: 1665-1670 (2000); Church et al, European patent publication 0 303 459; Shoemaker et al, Nature Genetics, 14: 450456 (1996); Morris et al, European patent publication 0799897A1; Lorinez et al., U.S. Pat, No. 5,981,179; and the like, Lengths and compositions of sequence tags can vary widely, and the selection of particular lengths and/or compositions depends on several factors including, without limitation, how tags are used to generate a readout, e.g, via a hybridization reaction or via an enmatic reaction, such as sequencing; whether they are labeled, e.g. with a fluorescent dye or the like; the number of distinguishable oligonucleotide tags required to unambiguously identify a set of polynucleotides, and the like, and how different must tags of a set be in order to ensure reliable identification, e.g. freedom from cross hybridization or misidentification from sequencing errors. in one aspect, sequence tags can each have a length within a range of from 2 to 36 nucleotides, or from 4 to 30 nucleotides, or from 8 to 20 nucleotides, or from 6 to 10 nucleotides, respectively. In one aspect, sets of sequence tags are used wherein each sequence tag of a set has a unique nucleotide sequence that differs from that of every other tag of the same set by at least two bases; in another aspect, sets of sequence tags are used wherein the sequence of each tag of a set differs from that of every other tag of the same set by at least three bases.
A “substitution” means that an amino acid residue is replaced by another amino acid residue. Preferably, the term “substitution” refers to the replacement of an amino acid residue by another selected from the naturally-occurring standard 20 amino acid residues, rare naturally occurring amino acid residues (e.g. hydroxyproline, hydroxylysine, allohydroxylysine, 6-N-methylysine, N-ethylglycine, N-methylglycine, N-ethylasparagine, allo-isoleucine, N-methylisoleucine, N-methylvaline, pyroglutamine, aminobutyric acid, ornithine, norleucine, norvaline), and non-naturally occurring amino acid residue, often made synthetically, (e.g. cyclohexyl-alanine). Preferably, the term “substitution” refers to the replacement of an amino acid residue by another selected from the naturally-occurring standard 20 amino acid residues. The sign “+” indicates a combination of substitutions. The amino acids are herein represented by their one-letter or three-letters code according to the following nomenclature: A: alanine (Ala); C: cysteine (Cys); D: aspartic acid (Asp); E: glutamic acid (Glu); F: phenylalanine (Phe); G: glycine (Gly); H: histidine (His); I: isoleucine (Ile); K: lysine (Lys); L: leucine (Leu); M: methionine (Met); N: asparagine (Asn); P: proline (Pro); Q: glutamine (Gin); R: arginine (Arg); S: serine (Ser); T: threonine (Thr); V: valine (Val); W: tryptophan (Trp) and Y: tyrosine (Tyr). In the present document, the following terminology is used to designate a substitution: L238A denotes that amino acid residue (Leucine, L) at position 238 of the parent sequence is changed to an Alanine (A). A132V/I/M denotes that amino acid residue (Alanine, A) at position 132 of the parent sequence is substituted by one of the following amino acids: Valine (V), Isoleucine (I), or Methionine (M). The substitution can be a conservative or non-conservative substitution. Examples of conservative substitutions are within the groups of basic amino acids (arginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), polar amino acids (glutamine, asparagine and threonine), hydrophobic amino acids (methionine, leucine, isoleucine, cysteine and valine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and small amino acids (glycine, alanine and serine).
“Transcriptome” means a collection of all (or nearly all) gene transcripts produced in a particular cell, collection of cells, sample or tissue type. In some embodiments, a transcriptiomne comprises all or nearly all of the polyA messenger RNA (mRNA) of a cell, collection of cells, sample or tissue type.
“Viable” in reference to cells, tissues or organisms, in some embodiments, means that the cells, tissues or organisms are capable of being grown, cultured, or further propagated. In some embodiments, viable cells are alive and capable of mitotic or meiotic division and further growth after being subjected to at least one cycle of template-free enzymatic elongation of an attached initiator oligonucleotide. The term “viable cell” may include viable eurkaryotic cells, prokaryotic cells, or viruses. In some embodiments, “viable cell” means viable eurkaryotic cell; and in other embodiments, “viable cell” means viable mammalian cell. “Viable conditions” as the term is used herein are physiochemical reaction conditions (e.g.
temperature, salt concentration, solvent, and the like) that have no substantial deleterious effect on cell viability. In some embodiments, it is understood that additional reaction mixture components would be required for particular cell types, e.g. vitamins, amino acids, or the like, for viability; that is, as used herein, ‘viable conditions” refers to necessary conditions for cell viability but not sufficient conditions for viability of every cell type. In some embodiments, viable conditions comprise an aqueous reaction mixture with physiological salts, especially, sodium, calcium and/or potassium, at a concentration in the range of 0.8 to 1.0 percent (w/v), pH in the range of 6.8-7.8, and temperature in the range of 15°-41° C.
Claims
1. A method of synthesizing on a viable cell an oligonucleotide with a predetermined sequence, the method comprising the steps of:
- a) providing an initiator with a free 3′-hydroxyl attached to a cell surface molecule of the cell or anchored in the cell surface membrane of the cell; and
- b) repeating under biological conditions for a plurality of cycles the steps of (i) contacting the initiator or elongated fragments having free 3′-O-hydroxyls with a 3′-O-blocked nucleoside triphosphate and a template-independent DNA polymerase so that the initiator or elongated fragments are elongated by incorporation of a 3′-O-blocked nucleoside triphosphate to form 3′-O-blocked elongated fragments, and (ii) deblocking the elongated fragments to form elongated fragments having free 3′-hydroxyls, thereby synthesizing the oligonucleotide of predetermined sequence.
2. The method of claim 1, wherein said 3′-O-blocked nucleoside triphosphate is a 3′-phosphate-nucleoside triphosphate and said step of deblocking is carried out by treating said 3′-O-blocked elongated fragments with a 3′-phosphatase activity.
3. The method of claim 2, wherein said 3′-phophatase activity is provided by T4 polynucleotide kinase, recombinant shrimp alkaline phosphatase, or a calf intestinal alkaline phosphatase.
4. The method of claim 1. wherein said 3′-O-blocked nucleoside triphosphate is a 3′-ester-blocked nucleoside triphosphat; and said step of deblocking is carried out by treating said 3′-O-ester-blocked elongated fragments with an esterase activity.
5. The method of claim 1, wherein said biological conditions comprise buffered physiological salts at a pH in the range of from 6.8 to 7.8 and a temperature in the range of from 15° C. to 41° C.
6. The method of claim 1, wherein said viable cells are mammalian cells.
7. The method of claim 1, wherein said initiator comprises an oligonucleotide having a lipophilic anchor covalently attached to a 5′ end, wherein the lipophilic anchor inserts stably into a cell surface membrane of said viable cell.
8. A method of generating a cDNA library with cell-specific oligonucleotide barcodes, the method comprising the steps of:
- (a) synthesizing under biological conditions a unique oligonucleotide barcode on the cell surface membrane of each cell in a population of cells to form a population of barcoded cells;
- (b) isolating each barcoded cell in a reactor;
- (c) lysing barcoded cells in each reactor; and
- (d) performing reverse-transcriptase polymerase chain reaction (RT-PCR) in each reactor to produce a cDNA library with cell-specific oligonucleotide barcodes.
9. The method of claim 8, wherein said step of synthesizing comprises (a) attaching initiators to said cell surface membrane of each of said cells of said population, and (b) repeating cycles of
- (i) contacting under biological conditions the initiators or elongated fragments having free 3′-O-hydroxyls with a 3′-O-blocked nucleoside triphosphate and a template-independent DNA polymerase so that the initiators or elongated fragments are elongated by incorporation of a 3′-O-blocked nucleoside triphosphate to form 3′-O-blocked elongated fragments, and
- (ii) deblocking the elongated fragments to form elongated fragments having free 3′-hydroxyls.
10. The method of claim 9, wherein each of said cycles further comprises splitting said population of said cells among separate reaction mixtures in which said initiators or elongated fragments are elongated by a different kind of nucleoside triphosphate to form said elongated fragments after which said cells of the separate reaction mixtures are combined.
11. The method of claim 8, wherein said reactors are micelles of a water-in-oil emulsion.
12. The method of claim 11, wherein said micelles are generated by a microfluidics device.
13. The method of claim 9, wherein said cDNAs from said reactors are combined and analyzed by high throughput DNA sequencing.
14. A method of extending one or more native polynucleotides with a predetermined nucleotide sequence, comprising:
- providing the one or more native polynucleotides in a reaction mixture under TdT reaction conditions, the one or more native polynucleotides having free 3′-O-hydroxyls; and
- extending the one or more native polynucleotides with the predetermined nucleotide sequence by repeated cycles of the steps (i) contacting the one or more native polynucleotides or elongated native polynucleotides having the free 3′-O-hydroxyls with a 3′-O-blocked nucleoside triphosphate and a TdT variant so that the one or more native polynucleotides or elongated native polynucleotides are elongated by incorporation of the 3′-O-blocked nucleoside triphosphate to form 3′-O-blocked elongated native polynucleotides, and (ii) deblocking the elongated native polynucleotides to form elongated native polynucleotides having free 3′-O-hydroxyls, thereby synthesizing on the one or more native polynucleotides an oligonucleotide of the predetermined nucleotide sequence.
15. The method of claim 14, wherein said predetermined nucleotide sequence comprises at least a plurality of different kinds of nucleotides.
16. The method of claim 15, wherein said predetermined nucleotide sequence is unique for each native polynucleotide of the one or more native polynucleotides.
17. The method of claim 14, wherein each of said cycles further comprises:
- prior to step (i), splitting said one or more native polynucleotides or said elongated native polynucleotides among two or more separate reaction mixtures, wherein
- contacting with the 3′-O-blocked nucleoside triphosphate in step (i) comprises contacting said native polynucleotides or said elongated native polynucleotides with two or more different kinds of nucleoside triphosphate to form said elongated native polynucleotides: and
- after step (i), combining said elongated native polynucleotides of the separate reaction mixtures.
18. A method of generating cDNA libraries each with an oligonucleotide label, the method comprising the steps of:
- (a) capturing an mRNA by hybridizing the mRNA to capture oligonucleotides attached to one or more solid supports, wherein the capture oligonucleotides are complementary to segments of the mRNA, and the capture oligonucleotides are attached to the one or more solid supports by 5′-ends and have 3′-ends with free 3′-hydroxyls;
- (b) extending the 3′-ends of the capture oligonucleotides with a reverse transcriptase using the captured mRNAs as templates to form the cDNA libraries on the one or more solid supports; and
- (c) synthesizing oligonucleotide labels on cDNAs of the one or more solid supports by template-free enzymatic synthesis.
19. The method of claim 18, wherein:
- said step of capturing includes capturing the mRNA of a single cell on a bead to form said cDNA libraries that are cell-specific cDNA libraries; and
- said oligonucleotide labels are unique cell-specific oligonucleotide barcodes.
20. The method of claim 18, wherein said step of synthesizing comprises synthesizing said unique cell-specific oligonucleotide barcodes is by a split and mix synthesis method.
21. The method of claim 18, wherein:
- said one or more solid supports is a solid surface with said capture oligonucleotides attached thereto; and
- said step of capturing includes capturing mRNA of a permeabilized tissue slice disposed on the solid surface to form a spatial cDNA library array that preserves a spatial distribution of the cDNAs of the permeabilized tissue slice.
22. The method of claim 21, wherein said step of synthesizing includes synthesizing at each of a plurality of different predetermined positions on said spatial cDNA library array a unique position tag to form position tag-cDNA conjugates.
23. The method of claim 22, further comprising:
- steps of releasing and sequencing said position tag-cDNA conjugates to determine the spatial distribution of said mRNAs in said permeabilized tissue slice.
24. The method of claim 21, wherein said solid surface includes binding compounds attached thereto for capturing predetermined non-nucleic acid ligands.
25. The method of claim 24, wherein said binding compounds comprise one or more kinds of antibodies each with a predetermined specificity for one of said predetermined non-nucleic acid ligands, each different kind of antibody having attached a releasable oligonucleotide barcode from which the antibody can be identified.
Type: Application
Filed: Mar 4, 2022
Publication Date: Jun 16, 2022
Applicant: DNA Script SAS (Le Kremlin-Bicêtre)
Inventors: Xavier Godron (Paris), Adrian Horgan (Paris), Sylvain Gariel (Paris), Jeffrey Jeddeloh (Verona, WI), Robert Nicol (Cambridge, MA), Thomas Ybert (Paris)
Application Number: 17/687,128
