Hybridization and mismatch discrimination using oligonucleotides conjugated to minor groove binders
First Claim
1. A method for identifying one or more nucleotide polymorphisms in a polynucleotide sample, the method comprising:
- providing an array of support-bound oligonucleotide probes of different sequences;
incubating a polynucleotide sample with said array under hybridization conditions;
incubating a plurality of different minor groove binder-oligonucleotide conjugate probes with said polynucleotide sample with said array under hybridization conditions to form one or more minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids, wherein said minor groove binder is a molecule having a molecular weight of approximately 150 to approximately 2,000 Daltons that binds in a non-intercalating manner into the minor groove of a double-stranded nucleic acid with an association constant of greater than approximately 103M−
; and
detecting the presence of said minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids on said array.
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Accused Products
Abstract
Conjugates between a minor groove binding molecule, such as the trimer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI3), and an oligonucleotide form unusually stable hybrids with complementary target sequences, in which the tethered CDPI3 group resides in the minor groove of the duplex. These conjugates can be used as probes and primers. Due to their unusually high binding affinity, conjugates as short as 8-mers can be used as amplification primers with high specificity and efficiency. MGB conjugation also increases the discriminatory power of short oligonucleotides, providing enhanced detection of nucleotide sequence mismatches by short oligonucleotides. The MGB-conjugated probes and primers described herein facilitate various analytic and diagnostic procedures, such as amplification reactions, PCR, detection of single-nucleotide polymorphisms, gene hunting, differential display, fluorescence energy transfer, hydrolyzable probe assays and others; by allowing the use of shorter oligonucleotides, which have higher specificity and better discriminatory power.
37 Citations
14 Claims
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1. A method for identifying one or more nucleotide polymorphisms in a polynucleotide sample, the method comprising:
-
providing an array of support-bound oligonucleotide probes of different sequences;
incubating a polynucleotide sample with said array under hybridization conditions;
incubating a plurality of different minor groove binder-oligonucleotide conjugate probes with said polynucleotide sample with said array under hybridization conditions to form one or more minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids, wherein said minor groove binder is a molecule having a molecular weight of approximately 150 to approximately 2,000 Daltons that binds in a non-intercalating manner into the minor groove of a double-stranded nucleic acid with an association constant of greater than approximately 103M−
; and
detecting the presence of said minor groove binder-oligonucleotide conjugate probe-target nucleic acid hybrids on said array. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14)
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Specification