Nucleic acid sequence detection employing probes comprising non-nucleosidic coumarin derivatives as polynucleotide-crosslinking agents
First Claim
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1. A method of detecting a target nucleic acid in a sample, said method comprising the steps of:
- a) hybridizing a target nucleic acid to a capture probe, said capture probe characterized bv having;
i) a polynucleotide having a sequence homologous to that of said target nucleic acid;
ii) a non-nucleosidic coumarin derivative incorporated into the backbone of said polynucleotide such that it replaces one or more nucleotides otherwise complementary to said target nucleic acid, wherein said coumarin derivative acts as a photoactivatable polynucleotide-crosslinking agent; and
iii) optionally at least one label;
b) activating said crosslinking agent, whereby a covalent crosslink occurs between said probe and said target nucleic acid; and
c) detecting the presence of the crosslinked nucleic acid pair as indicative of the presence of said target sequence in said sample.
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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.
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Citations
23 Claims
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1. A method of detecting a target nucleic acid in a sample, said method comprising the steps of:
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a) hybridizing a target nucleic acid to a capture probe, said capture probe characterized bv having;
i) a polynucleotide having a sequence homologous to that of said target nucleic acid;
ii) a non-nucleosidic coumarin derivative incorporated into the backbone of said polynucleotide such that it replaces one or more nucleotides otherwise complementary to said target nucleic acid, wherein said coumarin derivative acts as a photoactivatable polynucleotide-crosslinking agent; and
iii) optionally at least one label;
b) activating said crosslinking agent, whereby a covalent crosslink occurs between said probe and said target nucleic acid; and
c) detecting the presence of the crosslinked nucleic acid pair as indicative of the presence of said target sequence in said sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
hybridizing at least one reporter probe to said target nucleic acid, said reporter probe being characterized by having;
i) a polynucleotide having a sequence that is complementary to that of said target nucleic acid; and
ii) a label, but not iii) a photoactivatable polynucleotide-crosslinking agent.
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10. The method of claim 9 wherein said label of said reporter probe is a fluorophore.
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11. The method of claim 1 further comprising the step of:
d) isolating said crosslinked nucleic acid pair.
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12. The method of claim 1 wherein said target nucleic acid in a sample is genomic DNA in whole blood.
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13. A method according to claim 1, further comprising:
d) simultaneously performing said hybridization and said activation steps for one or more additional target nucleic acids, and/or simultaneously performing said hybridization, activation and detection steps in one or more additional samples in an automated system.
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14. A kit including components for detecting a target nucleic acid in a sample, said kit comprising:
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a) a capture probe characterized by having;
i) a polynucleotide having a sequence homologous to that of said target and capable of hybridizing with said target nucleic acid;
ii) a non-nucleosidic coumarin derivative incorporated into the backbone of said polynucleotide such that it replaces one or more nucleotides otherwise complementary to said target nucleic acid, wherein said coumarin derivative acts as a photoactivatable polynucleotide-crosslinking agent; and
iii) a label. - View Dependent Claims (15, 16, 17, 19, 20, 21)
b) at least one reporter probe, said reporter probe characterized by having;
i) a polynucleotide having a sequence that is complementary to that of said target nucleic acid; and
ii) a label, but not iii) a photoactivatable polvnucleotide-crosslinking agent.
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16. The kit of claim 14 further comprising:
b) a chart of standardized results obtained using said kit with samples that are known to contain and samples that are known not to contain said target nucleic acid.
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17. The kit of claim 14 further comprising:
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a control probe, said control probe having;
i) a polynucleotide having a sequence homologous to that of a target nucleic acid; and
ii) a non-nucleosidic coumarin derivative incorporated into the backbone of said polynucleotide such that it replaces one or more nucleotides otherwise complementary to said target nucleic acid, wherein said coumarin derivative acts as a photoactivatable polynucleotide-crosslinking agent.
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19. The kit of claim 14, wherein said label is selected from the group consisting of an antibody ligand, a lectin-binding sugar and biotin.
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20. The kit of claim 14, wherein said label is selected from the group consisting of a chemiluminescer, a radiolabel and a fluorophore.
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21. The kit of claim 14, further comprising a control sample, wherein said control contains a known amount of said target nucleic acid.
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18. A method of confirming the detection of a target nucleic acid in a sample, said method comprising the steps of:
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a) hybridizing said target nucleic acid in a first aliquot of said sample with a labeled probe, said labeled probe characterized by having;
i) a polynucleotide having a sequence homologous to that of said target nucleic acid;
ii) a non-nucleosidic coumarin derivative incorporated into the backbone of said polynucleotide such that it replaces one or more nucleotides otherwise complementary to said target nucleic acid, wherein said coumarin derivative acts as a photoactivatable polynucleotide-crosslinking agent; and
iii) alabel;
b) hybridizing said target nucleic acid in a second aliquot of said sample with a mixture of said labeled probe and unlabeled probe, said unlabeled probe characterized by having;
i) a polynucleotide having a sequence homologous to that of said target nucleic acid;
ii) a non-nucleosidic coumarin derivative incorporated into the backbone of said polynucleotide such that it replaces one or more nucleotides otherwise complementary to said target nucleic acid, wherein said coumarin derivative acts as a photoactivatable polynucleotide-crosslinking agent;
c) activating said crosslinking agent in each aliquot, whereby a covalent crosslink occurs between each of said probes and said target nucleic acid;
d) detecting the amount of labeled crosslinked nucleic acid pairs in each aliquot; and
e) comparing said amounts with the relative proportions of labeled and unlabeled probe in said first and second aliquots as an indication of the specificity of said detection. - View Dependent Claims (22, 23)
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Specification