WOBBLE SEQUENCING

• US 20070207482A1
• Filed: 02/02/2007
• Published: 09/06/2007
• Est. Priority Date: 08/04/2004
• Status: Abandoned Application

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Church, George, Shendure, Jay, Porreca, Gregory
• Application Number:
  US11/670,588
• Publication Number:
  US 20070207482A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/15 incorporating a consensus or conserved sequence
• 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 2533/101 Primer extension
• CPC Class Codes: C12Q 2537/125 Sandwich assay format

Abstract

Novel methods and compositions for DNA sequencing are provided. The methods described herein are useful for sequencing homopolymeric regions of DNA. The methods also prevent the accumulation of mistakes and inefficiencies in the sequencing reaction.

Claims

1. A method described above for DNA sequencing, useful for sequencing homopolymeric regions of DNA.

2. A method of sequencing a target nucleic acid comprising:

a. providing a sequencing primer, wherein the sequencing primer has at least one anchor sequence and a universal base;

b. hybridizing the sequencing primer to a target nucleic acid; and

c. extending the sequencing primer.

3. A method of sequencing a target nucleic acid comprising:

a. providing a sequencing primer, wherein the sequencing primer has at least one anchor sequence and a degenerate base;

b. hybridizing the sequencing primer to a target nucleic acid; and

c. extending the sequencing primer.

4. A method of sequencing a target nucleic acid comprising:

a. providing a sequencing primer, wherein the sequencing primer has at least one anchor sequence and a natural base;

b. hybridizing the sequencing primer to a target nucleic acid; and

c. extending the sequencing primer.

5. A method for sequencing a target nucleic acid comprising:

(a) hybridization of one of several anchor primers to a common sequence adjacent to an unknown sequence,

(b) ligation of fluorescently labeled, degenerate oligonucleotides to the anchor primer, such that identity of the fluorophore is informative of the identity of one or more positions within the degenerate oligonucleotide,

(c) imaging to determine primer ligation,

(d) stripping of the anchor primer;

degenerate oligonucleotide complexes, and

(e) repeating steps (a)-(d) one or more times.