Method and sequences for determinate nucleic acid hybridization

• US 7,537,892 B2
• Filed: 08/16/2005
• Issued: 05/26/2009
• Est. Priority Date: 03/28/2001
• Status: Expired due to Fees

• Current Assignee: Searete LLC (Intellectual Ventures LLC)
• Original Assignee: Searete LLC (Intellectual Ventures LLC)
• Inventors: Hillis, William Daniel
• Primary Examiner(s): Myers; Carla
• Assistant Examiner(s): HANEY, AMANDA MARIE
• Application Number:
  US11/205,583
• Publication Number:
  US 20070042389A1
• Time in Patent Office: 1,379 Days
• Field of Search: None
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/117 incorporating modified base

Abstract

Provided are methods for using nucleic acid sequences having two or more degenerately pairing nucleotides, each degenerate nucleotide having a partially overlapping set of complementarity, to reduce the number of hybridizing nucleotide sequences or probes used in biochemical and molecular biological operations having sequence specific hybridization. The method may be employed for various hybridization procedures with sequence specific hybridization, including sequencing methods measuring hybridization directly, and tagging by hybridization methods in which the sequence is determined by analyzing the pattern of tags that hybridize thereto, and hybridization dependent amplification methods. The method involves hybridizing to the nucleic acid sequence of interest a first hybridizing nucleotide sequence and a second hybridizing nucleotide sequence, each comprising a sequence complementary, or complementary except at a position of interest or variable position, to a nucleic acid sequence of interest, and analyzing the whether some, all or none of the probes or tags hybridize.

Claims

1. A method of determining the identity of an unknown nucleotide at a position of interest on a target nucleic acid analyte comprising:

contacting the target nucleic acid analyte under hybridizing conditions with at least two non-identical oligonucleotide probes having a variable position nucleotide, wherein the variable position nucleotide of at least one of the at least two oligonucleotide probes is a nucleotide that will base pair with at least two nucleotides, the variable position nucleotide of at least one other of the at least two oligonucleotide probes is either a nucleotide that will base pair with at least two nucleotides or a nucleotide incapable of degenerate base pairing, wherein the nucleotides in the variable positions of the at least two oligonucleotide probes collectively base pair with all but one nucleotide;

wherein the hybridizing conditions are sufficient to permit the at least two oligonucleotide probes to hybridize to the target nucleic acid analyte when the nucleotide occupying the variable position base pairs with the nucleotide occupying the position of interest, and do not permit the at least two oligonucleotide probes to hybridize to the target nucleic acid analyte when the nucleotide occupying the variable position does not base pair with the nucleotide occupying the position of interest; and

wherein the identity of the position of interest is determined by comparing the variable positions of any hybridized oligonucleotide probes for complementarity and the variable positions of any nonhybridized oligonucleotide probes for lack of complementarity.

2. The method of claim 1, wherein four nucleotides are possible at the position of interest.

3. The method of claim 2, wherein the nucleotides for the position of interest are G, T, A and C if the target nucleic acid analyte is DNA;

or G, U, A or C if the target nucleic acid analyte is RNA.

4. The method of claim 3, comprising contacting the target nucleic acid analyte under hybridizing conditions with two oligonucleotide probes.

5. The method of claim 4, wherein the nucleotides occupying the variable positions of the two oligonucleotide probes are doubly degenerate.

6. The method of claim 5, wherein the variable position nucleotide of one of the two oligonucleotide probes is dP.

7. The method of claim 5, wherein the variable position nucleotide of one of the two oligonucleotide probes is 8-oxo-dG.

8. The method of claim 5, wherein the variable position nucleotide of one oligonucleotide probe is 8-oxo-dG and the variable position nucleotide of the other oligonucleotide probe is dP.

9. The method of claim 8, wherein dP hybridizes to either A or G, and 8-oxo-dG hybridizes to either A or C.

10. The method of claim of claim 9, wherein hybridization of neither probe indicates a T or U at the position of interest in the target nucleic acid analyte.

11. A method of determining the identity of an unknown nucleotide at a position of interest on a target nucleic acid analyte wherein four nucleotide identities are possible at the position of interest, comprising:

contacting the target nucleic acid analyte under hybridizing conditions with two non-identical oligonucleotide probes each having a variable position nucleotide, wherein the variable position of each oligonucleotide probe is a nucleotide that will base pair with two of the four possible nucleotides, wherein the nucleotides in each variable position overlap in base pair degeneracy with one of the four possible nucleotides;

wherein the hybridizing conditions are sufficient to permit an oligonucleotide probe to hybridize to the target nucleic acid analyte when the nucleotide occupying the variable position base pairs with the nucleotide occupying the position of interest, and does not permit an oligonucleotide probe to hybridize to the target nucleic acid analyte when the nucleotide occupying the variable position does not base pair with the nucleotide occupying the position of interest; and

wherein the identity of the position of interest is determined by comparing the variable positions of any hybridized oligonucleotide probe for complementarity and the variable positions of any nonhybridized oligonucleotide probe for lack of complementarity.

12. The method of claim 11, wherein the nucleotide occupying the variable position of one oligonucleotide probe is dP, and the wherein the nucleotide occupying the variable position of the other oligonucleotide probe is 8-oxo-dG.

13. The method of claim 12, wherein dP hybridizes to either A or G, and 8-oxo-dG hybridizes to either A or C.

14. The method of claim of claim 13, wherein hybridization of neither probe indicates a T or U at the position of interest in the target nucleic acid analyte.