DNA extension and analysis with rolling primers

• US 5,780,231 A
• Filed: 03/05/1996
• Issued: 07/14/1998
• Est. Priority Date: 11/17/1995
• Status: Expired due to Term

• Current Assignee: Solexa Incorporated (Illumina Incorporated)
• Original Assignee: Lynx Therapeutics, Inc. (Illumina Incorporated)
• Inventors: Brenner, Sydney
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US08/611,155
• Time in Patent Office: 861 Days
• Field of Search: 435/6, 435/91.1, 435/91.2
• US Class Current: 435/6.11
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target

Abstract

A novel "primer walking" method for DNA sequencing is provided that comprises repeated cycles nucleotide identification by selective extension and primer advancement along a template by template mutation. An important feature of the invention is providing a set of primers, referred to herein as "rolling primers" that contain complexity-reducing nucleotides for reducing the number of primers required for annealing to every possible primer binding site on a sequencing template. Another important feature of the invention is the systematic replacement of at least one of the four nucleotides in the target polynucleotide with its cognate complexity-reducing nucleotide or complement thereof. Sequencing is initiated by annealing rolling primers differing only in their terminal nucleotides to a primer binding site of a sequencing template so that only the rolling primer whose terminal nucleotide forms a perfect complement with the template leads to the formation of an extension product. After amplifying the double stranded extension product to form an amplicon, the terminal nucleotide, and hence its complement in the template, is identified by the identity of the amplicon. The primer binding site of the template of the successfully amplified polynucleotide is then mutated by, for example, oligonucleotide-directed mutagenesis so that a subsequent rolling primer may be selected from the set that forms a perfectly matched duplex with the mutated template at a site which is shifted towards the direction of extension by one nucleotide relative to the binding site of the previous rolling primer. The steps of selective extension, amplification and identification are then repeated. In this manner, the primers "roll" along the polynucleotide during the sequencing process, moving a base at a time along the template with each cycle.

Claims

1. A method for determining the nucleotide sequence of a polynucleotide, the method comprising the steps of:

(a) providing a set of primers, each primer of the set having a terminal nucleotide, a template positioning segment, and an extension region comprising one or more complexity-reducing nucleotides;

(b) forming a template comprising a primer binding site and the polynucleotide, the primer binding site being complementary to at least one primer of the set;

(c) forming an amplicon from the template by amplifying a double stranded DNA selectively formed by extending a primer from the set whose extension region forms a perfectly matched duplex with the primer binding site of the template;

(d) identifying the terminal nucleotide of the extension region of the primer by the identity of the amplicon;

(e) mutating the primer binding site of the template so that the primer binding site is shifted one nucleotide in the direction of extension; and

(f) repeating steps (c) through (e) until the nucleotide sequence of the polynucleotide is determined.

2. The method of claim 1 wherein said amplicon is formed by amplifying said double stranded DNA by a polymerase chain reaction.

3. The method of claim 2 wherein said complexity-reducing nucleotide is deoxyinosine and wherein said polymerase chain reaction and said extending to form said double stranded DNA are carried out in the presence of deoxyadenosine triphosphate, deoxycytidine triphosphate, deoxyinosine triphosphate, and thymidine triphosphate.

4. The method of claim 3 wherein said step of mutating said primer binding site of said template is carried out by extending and amplifying said double stranded DNA with said primer whose said template positioning segment contains a nucleotide mismatched with its adjacent nucleotide in the primer binding site of the double stranded DNA so that the identity of the adjacent nucleotide is changed in said amplicon by oligonucleotide-directed mutagenesis using said primer.