Degenerate Nucleobase Analogs
First Claim
1. A degenerate nucleobase oligomer corresponding to a polynucleotide template having a first polymorphic site characterized by multiple nucleobase variations and a second polymorphic site characterized by multiple nucleobase variations, wherein the oligomer comprises a degenerate nucleobase complementary to multiple nucleobase variations at the first polymorphic site, and a base-specific nucleobase complementary to a single nucleobase variation at the second polymorphic site, wherein the base-specific nucleobase is characteristic of a single allele of the polynucleotide template.
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Abstract
The present invention relates to novel degenerate nucleobase analogs and degenerate nucleobase oligomers derived therefrom, and methods of using such degenerate nucleobase oligomers.
107 Citations
173 Claims
- 1. A degenerate nucleobase oligomer corresponding to a polynucleotide template having a first polymorphic site characterized by multiple nucleobase variations and a second polymorphic site characterized by multiple nucleobase variations, wherein the oligomer comprises a degenerate nucleobase complementary to multiple nucleobase variations at the first polymorphic site, and a base-specific nucleobase complementary to a single nucleobase variation at the second polymorphic site, wherein the base-specific nucleobase is characteristic of a single allele of the polynucleotide template.
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15-26. -26. (canceled)
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28-39. -39. (canceled)
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40-65. -65. (canceled)
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66. A method for determining the genotype of a multi-allelic polynucleotide template, comprising:
- providing a multi-allelic polynucleotide template having a first polymorphic site characterized by multiple nucleobase variations and a second polymorphic site characterized by multiple nucleobase variations;
providing a degenerate nucleobase oligomer comprising a degenerate nucleobase complementary to multiple nucleobase variations at the first polymorphic site, and a base-specific nucleobase complementary to a single nucleobase variation at the second polymorphic site, wherein the base-specific nucleobase is characteristic of a single allele of the polynucleotide template;
hybridizing the degenerate nucleobase oligomer to the polynucleotide template, under conditions wherein each degenerate nucleobase oligomer hybridizes non-selectively to multiple nucleobase variations at the first polymorphic site; and
disassociating the nucleobase oligomer from the polynucleotide template under conditions sufficient to generate a melting curve profile of the duplex characteristic of the allele of the second polymorphic site having the single nucleobase variation corresponding to the base-specific nucleobase. - View Dependent Claims (67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78)
- providing a multi-allelic polynucleotide template having a first polymorphic site characterized by multiple nucleobase variations and a second polymorphic site characterized by multiple nucleobase variations;
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79. A method for quantitating the amount of nucleic acid analyte present in a sample, comprising:
- providing a nucleic acid analyte comprising a multi-allelic polynucleotide template having a first polymorphic site characterized by multiple nucleobase variations and a second polymorphic site characterized by multiple nucleobase variations;
providing a degenerate nucleobase oligomer comprising a degenerate nucleobase complementary to multiple nucleobase variations at the first polymorphic site, and a base-specific nucleobase complementary to a single nucleobase variation at the second polymorphic site, wherein the base-specific nucleobase is characteristic of a single allele of the polynucleotide template;
hybridizing the degenerate nucleobase oligomer to the polynucleotide template, under conditions wherein each degenerate nucleobase oligomer hybridizes non-selectively to multiple nucleobase variations at the first polymorphic site;and quantitatively detecting the amount of nucleic acid analyte present in the sample. - View Dependent Claims (80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91)
- providing a nucleic acid analyte comprising a multi-allelic polynucleotide template having a first polymorphic site characterized by multiple nucleobase variations and a second polymorphic site characterized by multiple nucleobase variations;
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93-104. -104. (canceled)
- 105. A degenerate nucleobase oligomer corresponding to a polynucleotide template having one or more polymorphic site, wherein the oligomer comprises a degenerate nucleobase complementary to multiple nucleobase variations at a polymorphic site and having a hydrogen bonding pattern of pyAAD or puDDA.
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115-167. -167. (canceled)
- 168. A degenerate nucleobase oligomer comprising a degenerate purine nucleobase having an alternate tautomeric hydrogen bonding pattern that is Watson-Crick complementary within an anti-anti purine-purine pair to adenine or guanine.
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172. A degenerate nucleobase oligomer comprising:
- a pyrimidine-like analog bearing hydrogen-bonding functionality arrayed such that the analog can form two hydrogen bonds in a wobble conformation with one purine-like component and two hydrogen bonds in a reverse wobble conformation with the other purine-like component, respectively.
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173. A degenerate nucleobase oligomer comprising:
- a purine-like analog bearing hydrogen-bonding functionality arrayed such that the analog can form two hydrogen bonds in a wobble conformation with one pyrimidine-like component and two hydrogen bonds in a reverse wobble conformation with the other pyrimidine-like component, respectively.
Specification