Abstract: Disclosed are oligonucleotides probes which are useful for determining a sequence of nucleotides in a target ploynucleotide. In one embodiment, the probe is of the formula: HO-(3')(B)j(5')-OP(.dbd.O-)NH-(B)k-Bt*, wherein B is a nucleotide or an analog thereof; j is in range of from 1 to 12; is in the range of from 0 to 12, such that the sum of j and k is less than or equal to 12; and Bt* is a labeled chain-terminating moiety. In s second embodiment, the probe has a formula selected from the group consisting of (1) OP(.dbd.O)(O--)O--(5.dbd.)(B)sRRRR(B)wBt*, and (2) OP(.dbd.O)(O--)(5')(B)sRRRR(B)w(3')OP(.dbd.O)(O--)O, wherein: is a deoxyribonucleotide or an analog thereof; R is a ribonucleotide; s is in the range of from 1 to 8; w is in the range of from 0 to 8, such that the sum of j and k is less than or equal to 8; and Bt* is a labeled chain-terminating moiety.

Abstract: Modified oligonucleotides 3'-NHP(O)(O.sup.-)O-5' phosphoramidates were synthesized on a solid phase support. The phosphoramidate analogs were found to have significantly increased resistance toward phosphodiesterase digestion. Thermal dissociation experiments demonstrated that these compounds form more stable duplexes than phosphodiesters with complementary DNA and particularly RNA strands. Further, the phosphoramidate analogs can also form stable triplexes with double-stranded DNA target, where under similar conditions parent phosphodiester compounds failed to do so.

Abstract: Compounds and methods for use in immunosuppressive and anti-inflammatory treatment, and for inhibiting male fertility, are described. The compounds are triptolide analogs with improved water solubility and low toxicity.

Abstract: An improvement in adaptor-based sequence analysis is provided that addresses the problems created by self-ligation of target polynucleotides that have complementary ends. The improvement includes preparation of target polynucleotides with dephosphorylated 5' strands and the use of adaptors having a 3' blocking group. In a preferred embodiment, adaptors are ligated to target polynucleotides by a single strand, 3' blocking groups are removed, the adjacent 5' hydroxyl of the target polynucleotide is phosphorylated, and the ligation of the adaptor is completed by treatment with a ligase.

Abstract: Long wavelength, narrow emission bandwidth fluorecein dyes are provided for detecting spacially overlapping target substances. The dyes comprise 4,7-dichlorofluoresceins, and particularly 2',4',5',7'-tetrachloro-4,7-dichloro-5- (and 6-) carboxyfluoresceins. Methods and kits for using the dyes in DNA analysis are provided.

Abstract: The invention provides a method of synthesizing oligonucleotide N3'.fwdarw.P5' phosphoramidates using an amine-exchange reaction of phosphoramidites in which a -deprotected 3'-amino group of a solid phase supported oligonucleotide chain is exhanged for the amino portion of a 5'-phosphoramidite of an incoming monomer which has a protected 3'-amino group. The resulting internucleotide phosphoramidite linkage is then oxidized to form a stable protected phosphoramidate linkage. The method of the invention greatly improves product yields and reduces reagent usage over currently available methods for synthesizing the above class of compound.

Abstract: A composition for use in immunosuppression therapy is disclosed. The composition includes an immunosuppressant drug, such as cyclosporin A, and an ethanol extract of the root xylem of Tripterygium wilfordii. The extract is effective alone, or in combination with such an immunosuppressant, in the treatment of transplantation rejection. Also disclosed is a method of immunosuppression that includes administering to a subject a pharmaceutically effective amount of an immunosuppressant drug and an extract of the type above, in an amount effective to potentiate the action of the drug.

Abstract: A method of identifying the presence of activated T-cells in a sample containing a plurality of different cell types is disclosed. The method includes the detection of polynucleotide sequences selectively expressed in activated T-cells.

Abstract: Compounds referred to herein as oligonucleotide clamps are provided that stably bind to target polynucleotides in a sequence-specific manner. The oligonucleotide clamps comprise one or more oligonucleotide moieties capable of specifically binding to a target polynucleotide and one or more pairs of binding moieties covalently linked to the oligonucleotide moieties. In accordance with the invention, upon annealing of the oligonucleotide moieties to the target polynucleotide, the binding moieties of a pair are brought into juxtaposition so that they form a stable covalent or non-covalent linkage or complex. The interaction of the binding moieties of the one or more pairs effectively clamps the specifically annealed oligonucleotide moieties to the target polynucleotide.

Abstract: Method and composition for detecting one or more selected polynucleotide regions in a target polynucleotide. In the method, a mixture of sequence-specific probes are reacted with the target polynucleotide under hybridization conditions, and the hybridized probes are treated to selectively modify those probes which are bound to the target polynucleotide in a base-specific manner. The resulting labeled probes include a polymer chain which imparts to each different-sequence probe, a distinctive ratio of charge/translational frictional drag, and a detectable label. The labeled probes are fractionated by electrophoresis in a non-sieving matrix, and the presence of one or more selected sequences in the target polynucleotide are detected according to the observed electrophoretic migration rates of the labeled probes in a non-sieving medium.

Abstract: The invention provides 1,4-naphthoquinone compounds and a method for inhibiting tumor cell growth in a subject by administering such compounds. The compounds are represented by the structures: ##STR1## where R.sub.1 is lower alkyl, halogenated lower alkyl, phenyl, benzyl, phenethyl, or --(CH.sub.2).sub.m COOX where m is 2 or 3 and X is H, methyl, or ethyl; R.sub.2 is halo or NHY, where Y is hydrogen, lower alkyl, halogenated lower alkyl, hydroxylated lower alkyl, lower dialkylaminoalkyl, phenyl, benzyl, or phenethyl; R.sub.3 is lower alkyl, halogenated lower alkyl, phenyl, benzyl, phenethyl, or --(CH.sub.2).sub.m COOX, where m and X are as defined for R.sub.1 above; and R.sub.4 is hydrogen, lower alkyl, lower aminoalkyl, halogenated lower alkyl, phenyl, benzyl, or phenethyl.

Abstract: Method and composition for detecting one or more selected polynucleotide regions in a target polynucleotide. In one embodiment of the invention, a plurality of different-sequence probe pairs are added to a target polynucleotide, where each probe pair includes two polynucleotide probe elements which are complementary in sequence to adjacent portions of a selected one of the target sequences in the target polynucleotide. In each probe pair, one of the probe elements contains a non-polynucleotide polymer chain which imparts a distinctive mobility to the associated probe pair, when the elements in the pair are ligated. The other element in the pair contains a detectable reporter label. After the probe pairs have been allowed to hybridize with the target polynucleotide, the hybridized polynucleotides are treated under conditions effective to ligate the end subunits of target-bound probe elements when their end subunits are base-paired with adjacent target bases.

Abstract: An improved method for suppressing xenograft rejection in a host subject is disclosed. The method includes administering an immunosuppressant drug, where the drug or the amount of drug administered is, by itself, ineffective to suppress xenograft rejection. Effective xenograft suppression is achieved by also administering an ethanolic extract of Triterygium wilfordii or a purified triptolide component thereof.

Abstract: A method is provided for determining a genotype by comparing the nucleotide sequence of members of a gene system which flank the polymorphous sections of a locus or loci of interest. In a general embodiment of the method, the nucleotide sequences chosen for comparison (i) contain one or two sequences that are completely conserved between the members of the gene family, where two or more members are selected from different sources, and (ii) the completely conserved sequences flank strongly conserved sections of genetic material. The completely conserved sequences are typically used to amplify, from different sources, the strongly conserved sections of genetic material. The resulting amplified nucleic acid sequences from the different sources are then compared to establish genotypes.

Abstract: An electrophoresis separation medium is disclosed comprising a matrix of a copolymer composed of a linear hydrophilic polymer segment having a selected substantially uniform segment length and hydrophobic polymer segments carried on each end. Also disclosed is an electrophoresis method employing the separation medium which permits high resolution separation of polynucleotides, especially in DNA sequencing operations.

Abstract: A pyridinoline composition in which pyridinoline is derivatized specifically at its aliphatic hydroxyl group by a selected chemical group is disclosed. In various embodiments, the composition may be used as a standard for HPLC or immunoassay of pyridinoline, a pyridinoline immunogen for producing anti-pyridinoline antibodies, and a solid-phase reagent for use in an immunoassay kit. Also disclosed are methods for making and using the composition.

Abstract: A method for detecting a target polynucleotide is provided which relies on the exponential amplification of oligonucleotide fragments. Separated populations of oligonucleotides are provided that contain complementary sequences to one another and that contain at least one scissile linkage which is cleaved whenever a perfectly matched duplex is formed containing the linkage. When a target polynucleotide contacts a first oligonucleotide cleavage occurs and a first fragment is produced which can hybridize with a second oligonucleotide. Upon such hybridization, the second oligonucleotide is cleaved releasing a second fragment that can, in turn, hybridize with a first oligonucleotide in a manner similar to that of the target polynucleotide.

Abstract: Compounds referred to herein as oligonucleotide clamps are provided that stably bind to target polynucleotides in a sequence-specific manner. The oligonucleotide clamps comprise one or more oligonucleotide moieties capable of specifically binding to a target polynucleotide and one or more pairs of binding moieties covalently linked to the oligonucleotide moieties. In accordance with the invention, upon annealing of the oligonucleotide moieties to the target polynucleotide, the binding moieties of a pair are brought into juxtaposition so that they form a stable covalent or non-covalent linkage or complex. The interaction of the binding moieties of the one or more pairs effectively clamps the specifically annealed oligonucleotide moieties to the target polynucleotide.

Abstract: A method of assaying bone collagen breakdown levels in a human subject useful to screen for the presence of bone resorption disorders. Also disclosed is a method for monitoring the progression and/or treatment response of a cancer condition which involves or has the potential to progress to a metastatic condition which involves abnormalities in bone resorption rates.

Abstract: A solid support having surface-attached carboxylic acid groups is reacted with an isoxazolium salt to form an activated support having enol ester and sulfonate groups. After washing to remove residual isoxazolium salt and base, the activated support is dried. A polypeptide is covalently or non-covalently bound to the support. The resultant immobilized polypeptide can be conveniently sequenced by N- and C-terminal sequencing methods. The support can be a polyvinylidene difluoride membrane or a glass fiber membrane having surface attached carboxylic acid groups, and the enol and sulfonate groups are provided by reacting the support with 2-ethyl-5'-phenylisoxazolium sulfonate. The dry support can be stored for at least about 3 months to achieve a peptide immobilization yield that is substantially the same as the yield obtained in the absence of drying.