Separating and/or identifying polymorphic nucleic acids using universal bases
First Claim
1. A method for identifying a nucleic acid molecule, comprising:
- (a) hybridizing a first nucleic acid whose sequence matches, or is complementary to, a nucleic acid having a plurality of polymorphic positions with a reference nucleic acid whose sequence is substantially complementary to the first nucleic acid to form a test duplex, wherein one or more of the polymorphic positions, or the positions complementary thereto, of the first nucleic acid are replaced with a universal base; and
(b) separating the test duplex.
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Abstract
The present invention provides methods for analyzing polymorphic nucleic acids using duplex separation and/or identification techniques. In the present methods one of the nucleic acids has a sequence which includes universal bases that correspond in position to one or more of the polymorphic positions of the polymorphic nucleic acid. The nucleic acid including the universal bases can either represent the polymorphic nucleic acid and hybridize with a reference strand, or act as a reference strand and hybridize with the polymorphic nucleic acid directly, to form a duplex. Separation and/or identification of the duplex from other duplexes and materials can then be performed.
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Citations
21 Claims
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1. A method for identifying a nucleic acid molecule, comprising:
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(a) hybridizing a first nucleic acid whose sequence matches, or is complementary to, a nucleic acid having a plurality of polymorphic positions with a reference nucleic acid whose sequence is substantially complementary to the first nucleic acid to form a test duplex, wherein one or more of the polymorphic positions, or the positions complementary thereto, of the first nucleic acid are replaced with a universal base; and
(b) separating the test duplex. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 19, 20)
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9. A method for identifying a nucleic acid molecule, comprising:
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(a) hybridizing a polymorphic nucleic acid having one or more polymorphic positions with a reference nucleic acid that is substantially complementary to a reference nucleic acid to form a test duplex, wherein one or more positions of the reference nucleic acid complementary to the one or more polymorphic position are replaced with a universal base; and
(b) separating the test duplex. - View Dependent Claims (10, 11, 12, 13, 14, 15, 16, 17, 21)
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18. A modified nucleic acid comprising the sequence set forth in SEQ ID NO:
- 1 (TTGNNGCAGGTTAANNNTGAG), SEQ ID NO;
2 (GNCCCCNCAGCACGTTTCCTGNN GCAGGTTAANNNTGAGTGTCATTTC), SEQ ID NO;
3 (GNCCCCNCAGCACGTTTCN TGNNGNANNNTANNNNNNANTGTNANTTCTTCAAT), SEQ ID NO;
4 (GNCCC CNCAGCACGTTTCNTGNNGNANNNTANNNNTNAGTGTNATTTCTTCAAT) or a nucleic acid having a sequence complementary to SEQ ID NO;
1, SEQ ID NO;
2, SEQ ID NO;
3 or SEQ ID NO;
4, wherein N denotes a universal base that is capable of hybridizing to any other nucleic acid residue.
- 1 (TTGNNGCAGGTTAANNNTGAG), SEQ ID NO;
Specification