Abstract: Novel coumarin derivatives comprising a coumarin moiety linked to a non-nucleosidic backbone moiety are disclosed. The resulting molecules are typically used as photoactivate crosslinking groups when incorporated into polynucleotides as replacements for one or more of the complementary nucleoside bases present in probes used in procedures involving nucleic acid hybridization reactions.

Abstract: Methods and compositions are provided for detecting nucleic acid sequences. Probes comprising a crosslinking agent are combined with a sample which may comprise a target sequence which is complementary to the probe. Hybridization is allowed to occur between complementary sequences. The crosslinking agent is activated. Covalent bonds are formed between the probe and the target sequence if they are hybridized to one another. The crosslinked nucleic acids can then be detected to indicate the presence of the target sequence. Also provided are kits comprising reagents.

Abstract: Improved methods for in situ hybridization assays of cellular and subcellular systems and tissue sections, and immobilization-based assay techniques such as Northern blotting, Southern blotting, dot blots, and the like, and assay techniques wherein the probes are bound to substrates are disclosed. The subject invention employs crosslinker-containing hybridization probes capable of forming covalent bonds between the probe and the target nucleic acid. Upon activation, the crosslinker will, if the probe has hybridized with its essentially complementary target, form covalent bonds with the complementary strand to covalently crosslink the probe to the target. Subsequently, stringent wash conditions may be employed to reduce background signals due to non-specific absorption or probes or targets, while retaining all crosslinked probe/target hybrids. Also disclosed are diagnostic kits for use in clinical and diagnostic laboratories.

Abstract: Methods and compositions are provided for detecting nucleic acid sequences. In particular, pairs of probes are employed, where the pair defines a substantially contiguous sequence on a target nucleic acid. Each of the pairs has a side chain which forms a stem of the two side chains which non-covalently binds and is capable of forming a cross-link upon activation, when the probes and sample nucleic acid are base paired. Cross-linking of the stems when unbound to complementary DNA is inhibited. Each of the nucleic acids is initially present as single stranded nucleic acid to allow for base pairing, so that the probes bind to homologous target nucleic acid. The assay mixture is activated to provide cross-linking, the double stranded nucleic acid melted, and the process of base pairing, activation and melting repeated, a sufficient number of cycles, to provide a detectable amount of cross-linked probes.

Abstract: Nucleic acid probes that are susceptible to chemical or enzymatic degradation are described herein. In addition, assays and methods using such probes in the detection of target nucleic acid sequences are disclosed. The target-specific hybridization region or target-complementary region of the degradable probes can be separated via a degradation process from the detectable region. The remaining portion of the degradable probes can be easily detected. The use of the degradable probes described herein improves the signal-to-noise ratio by reducing background specific or non-specific signal generation in assays and methods of nucleic acid detection.

Abstract: Methods and compositions are provided for detecting nucleic acid sequences. In particular, pairs of probes are employed, where the pair defines a substantially contiguous sequence on a target nucleic acid. Each of the pairs has a side chain which forms a stem of the two side chains which non-covalently binds and is capable of forming a cross-link upon activation, when the probes and sample nucleic acid are base paired. Cross-linking of the stems when unbound to complementary DNA is inhibited. Each of the nucleic acids is initially present as single stranded nucleic acid to allow for base pairing, so that the probes bind to homologous target nucleic acid. The assay mixture is activated to provide cross-linking, the double stranded nucleic acid melted, and the process of base pairing, activation and melting repeated, a sufficient number of cycles, to provide a detectable amount of cross-linked probes.

Abstract: Methods and compositions are provided for detecting nucleic acid sequences. Probes comprising a crosslinking agent are combined with a sample which may comprise a target sequence which is complementary to the probe. Hybridization is allowed to occur between complementary sequences. The crosslinking agent is activated. Covalent bonds are formed between the probe and the target sequence if they are hybridized to one another. The crosslinked nucleic acids can then be detected to indicate the presence of the target sequence. Also provided are kits comprising reagents.

Abstract: Novel aryl derivatives comprising an aryl olefin moiety linked to a non-nucleosidic backbone moiety are disclosed. The resulting molecules are typically used as photoactivated crosslinking groups when incorporated into oligonucleotides to crosslink nucleic acid strands.

Abstract: Methods and compositions are provided for detecting nucleic acid sequences. Probes comprising a crosslinking agent are combined with a sample which may comprise a target sequence which is complementary to the probe. Hybridization is allowed to occur between complementary sequences. The crosslinking agent is activated. Covalent bonds are formed between the probe and the target sequence if they are hybridized to one another. The crosslinked nucleic acids can then be detected to indicate the presence of the target sequence. Also provided are kits comprising reagents.

Abstract: Double-stranded conformational polymorphism analysis is performed by combining a probe comprising a cross-linking agent and optionally a label with a sample having a target sequence, which may be complementary or have one or a few mismatches with respect to the probe sequence. After sufficient time for hybridization under mild or lesser stringency conditions, hybridized pairs are irradiated to induce cross-link formation by the cross-linking agent. The sample is then analyzed by denaturing gel electrophoresis where the rate of migration depends upon the degree of complementarity between the probe and the target. For corroboration, in a second experiment, the probe may be combined with the sample under high stringency conditions, where it is found that the formation of cross-linked probe/target is substantially lower for pairs having mismatches than for fully matched pairs. After cross-linking, the sample may be separated by gel electrophoresis, and the amount of cross-linked nucleic acid determined.

Abstract: Double-stranded conformational polymorphism analysis is performed by combining a probe comprising a cross-linking agent and optionally a label with a sample having a target sequence, which may be complementary or have one or a few mismatches with respect to the probe sequence. After sufficient time for hybridization under mild or lesser stringency conditions, hybridized pairs are irradiated to induce cross-link formation by the cross-linking agent. The sample is then analyzed by denaturing gel electrophoresis where the rate of migration depends upon the degree of complementarity between the probe and the target. For corroboration, in a second experiment, the probe may be combined with the sample under high stringency conditions, where it is found that the formation of cross-linked probe/target is substantially lower for pairs having mismatches than for fully matched pairs. After cross-linking, the sample may be separated by gel electrophoresis, and the amount of cross-linked nucleic acid determined.

Abstract: Methods and compositions are provided for detecting nucleic acid sequences. In particular, pairs of probes are employed, where the pair defines a substantially contiguous sequence on a target nucleic acid. Each of the pairs has a side chain which forms a stem of the two side chains which non-covalently binds and is capable of forming a cross-link upon activation, when the probes and sample nucleic acid are base paired. Cross-linking of the stems when unbound to complementary DNA is inhibited. Each of the nucleic acids is initially present as single stranded nucleic acid to allow for base pairing, so that the probes bind to homologous target nucleic acid. The assay mixture is activated to provide cross-linking, the double stranded nucleic acid melted, and the process of base pairing, activation and melting repeated, a sufficient number of cycles, to provide a detectable amount of cross-linked probes.

Abstract: Novel coumarin derivatives comprising a coumarin moiety linked to a non-nucleosidic backbone moiety are disclosed. The resulting molecules are typically used as photoactivate cross-linking groups when incorporated into polynucleotides as replacements for one or more of the complementary nucleoside bases present in probes used in procedures involving nucleic acid hybridization reactions.

Abstract: Methods and compositions are provided for detecting nucleic acid sequences. In particular, pairs of probes are employed, where the pair defines a substantially contiguous sequence on a target nucleic acid. Each of the pairs has a side chain which forms a stem of the two side chains which non-covalently binds and is capable of forming a cross-link upon activation, when the probes and sample nucleic acid are base paired. Cross-linking of the stems when unbound to complementary DNA is inhibited. Each of the nucleic acids is initially present as single stranded nucleic acid to allow for base pairing, so that the probes bind to homologous target nucleic acid. The assay mixture is activated to provide cross-linking, the double stranded nucleic acid melted, and the process of base pairing, activation and melting repeated, a sufficient number of cycles, to provide a detectable amount of cross-linked probes.

Abstract: Methods and compositions are provided for detecting nucleic acid sequences. In particular, pairs of probes are employed, where the pair defines a substantially contiguous sequence on a target nucleic acid. Each of the pairs has a side chain which forms a stem of the two side chains which non-covalently binds and is capable of forming a cross-link upon activation, when the probes and sample nucleic acid are base paired. Each of the nucleic acids is initially present as single stranded nucleic acid to allow for base pairing, so that the probes bind to homologous target nucleic acid. The assay mixture is activated to provide cross-linking, the double stranded nucleic acid melted, and the process of base pairing, activation and melting repeated, a sufficient number of cycles, to provide a detectable amount of cross-linked probes. Also provided are kits comprising reagents, as well as automatic devices, for carrying out the subject method.

Abstract: Methods and compositions are provided for detecting nucleic acid sequences. In particular, pairs of probes are employed, where the pair defines a substantially contiguous sequence on a target nucleic acid. Each of the pairs has a side chain which forms a stem of the two side chains which non-covalently bind to is capable of forming a cross-link upon activation, when the probes and sample nucleic acid are base paired. Each of the nucleic acids is initially present as single stranded to allow for base pairing, so that the probes bind to homologous target nucleic acid. The assay mixture is activated to provide cross-linking, the double stranded nucleic acid melted, and the process of base pairing, activation and melting repeated, a sufficient number of cycles, to provide a detectable amount of cross-linked probes. Kits are provided with the appropriate reagents for carrying out the subject method.

Abstract: A photoactivatible nucleoside analogue is disclosed, comprising a coumarin moiety linked through its phenyl ring to the 1-position of a ribose or deoxyribose sugar moiety. The resulting nucleoside analogue is typically used as a photocrosslinking group when inserted into a polynucleotide as a replacement for one or more of the complementary nucleoside bases present in a probe used in a hybridization assay.

Abstract: Hematopoietic cells are selectively eliminated by cytotoxic agents which rely upon light activation. The cytotoxic agents are joined to ligands, particularly sugars, specific for myeloid monocyte and lymphocytic lineages. Further specificity can be achieved by limiting the light target. The method and compositions find particular use in organ transplants and arthritis.

Abstract: A method for the stereoselective snythesis of a cis-syn, furan-side mono-adducted linear furocoumarin:nucleoside adduct, which comprises reacting a linear furocoumarin with a nucleophilic acid to form a 3,4-dihydro-4-substituted linear furocoumarin intermediate, and contacting the intermediate with a nucleoside under photoactivating conditions. The reaction produces a cis-syn, furan-side, mono-adducted 3,4-dihydro-4-substituted linear furocoumarin:nucleoside adduct which can then be deblocked to give the final product under mild conditions.