DNA sequencing

• US 10,202,642 B2
• Filed: 05/02/2013
• Issued: 02/12/2019
• Est. Priority Date: 05/02/2012
• Status: Active Grant

• Current Assignee: Ibis Biosciences Incorporated
• Original Assignee: Ibis Biosciences Incorporated
• Inventors: Eshoo, Mark W.
• Primary Examiner(s): Chunduru, Suryaprabha
• Application Number:
  US14/398,267
• Publication Number:
  US 20150184238A1
• Time in Patent Office: 2,112 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/185 incorporating bases where the precise position of the bases in the nucleic acid string is important
• CPC Class Codes: C12Q 2563/107 fluorescence

Abstract

Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, systems, and kits for sequencing a nucleic acid using a degenerate two-base code. Particular embodiments provide: 1) that the two-base degenerate code relates a first element to a base comprising adenine (A) or guanine (G) and a second element to a base comprising cytosine (C) or thymine (T); 2) that the two-base degenerate code relates a first element to a base comprising A or C and a second element to a base comprising G or T; and 3) that the two-base degenerate code relates a first element to a base comprising G or C and a second element to a base comprising A or T.

Claims

1. A method for sequencing a target nucleic acid, the method comprising:

a) choosing a two-base degenerate code; and

b) sequencing a two-base degenerate sequence of the target nucleic acid using the two-base degenerate code and a first nucleotide, a second nucleotide, a third nucleotide and a fourth nucleotide wherein the first nucleotide is labeled with a first label and the second nucleotide is labeled with said first label wherein the third nucleotide is labeled with a second label, and the fourth nucleotide is labeled with said second label wherein the first labeled nucleotide and the second labeled nucleotide base pair with a first nucleotide of the target nucleic acid or a second nucleotide of the target nucleic acid according to a degenerate base pairing rule, wherein the two-base degenerate sequence of the target nucleic acid is determined without determining the four-base sequence of the target nucleic acid.

2. The method of claim 1 wherein the two-base degenerate code consists of a first element representing a purine base and a second element representing a pyrimidine base.

3. The method of claim 1 wherein the two-base degenerate code consists of a first element representing a keto base and a second element representing an amino base.

4. The method of claim 1 wherein the two-base degenerate code consists of a first element representing a strongly hydrogen bonding base and a second element representing a weakly hydrogen bonding base.

5. The method of claim 1 wherein the two-base degenerate code consists of a first element representing a base comprising adenine (A) or guanine (G) and a second element representing a base comprising cytosine (C) or thymine (T).

6. The method of claim 1 wherein the two-base degenerate code consists of a first element representing a base comprising A or C and a second element representing a base comprising G or T.

7. The method of claim 1 wherein the two-base degenerate code consists of a first element representing a base comprising G or C and a second element representing a base comprising A or T.

8. The method of claim 1 further comprising using a first two-base degenerate sequence and a second two-base degenerate sequence to produce a four-base sequence.

9. The method of claim 1 wherein the determining comprises measuring a physical, chemical, and/or electronic characteristic of a base and differentiating between a purine base and a pyrimidine base, between a keto base and an amino base, and/or between a strongly hydrogen bonding base and a weakly hydrogen bonding base.

10. The method of claim 1 further comprising comparing the two-base sequence of the target nucleic acid to a known reference sequence.

11. The method of claim 1 further comprising providing a labeled nucleotide analogue wherein the labeled nucleotide analogue base pairs with a first nucleotide or a second nucleotide according to a degenerate base pairing rule.

12. The method of claim 1 further comprising c) comparing the two-base degenerate sequence of the target nucleic acid to a known sequence of the target nucleic acid using the two base degenerate code.

13. A method for sequencing a target nucleic acid, the method comprising:

a) choosing a two-base degenerate code; and

b) sequencing a two-base degenerate sequence of the target nucleic acid using the two-base degenerate code and a first labeled nucleotide analogue and a second labeled nucleotide analogue wherein the first labeled nucleotide analogue base pairs with a first nucleotide of said target nucleic acid or a second nucleotide of said target nucleic acid and the second labeled nucleotide analogue base pairs with a third nucleotide of said target nucleic acid or a fourth nucleotide of said target nucleic acid according to a degenerate base pairing rule, wherein the two-base degenerate sequence of the target nucleic acid is determined without determining the four-base sequence of the target nucleic acid.