Methods of nucleic acid amplification and sequencing

• US 8,652,810 B2
• Filed: 08/17/2006
• Issued: 02/18/2014
• Est. Priority Date: 09/30/1998
• Status: Expired due to Term

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Adessi, Celine, Kawashima, Eric, Mayer, Pascal, Mermod, Jean-Jacques, Turcatti, Gerardo
• Primary Examiner(s): Lu, Frank
• Application Number:
  US11/506,146
• Publication Number:
  US 20080160580A1
• Time in Patent Office: 2,742 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/183, 436/94, 436/501, 536/23.1, 536/24.3, 536/24.33
• US Class Current: 435/91.2
• CPC Class Codes: C12N 15/1068 Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• 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 2565/543 characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification

Abstract

Methods for amplification and sequencing of at least one nucleic acid comprising the following steps: (1) forming at least one nucleic acid template comprising the nucleic acid(s) to be amplified or sequenced, wherein said nucleic acid(s) contains at the 5′ end an oligonucleotide sequence Y and at the 3′ end an oligonucleotide sequence Z and, in addition, the nucleic acid(s) carry at the 5′ end a means for attaching the nucleic acid(s) to a solid support; (2) mixing said nucleic acid template(s) with one or more colony primers X, which can hybridize to the oligonucleotide sequence Z and carries at the 5′ end a means for attaching the colony primers to a solid support, in the presence of a solid support so that the 5′ ends of both the nucleic acid template and the colony primers bind to the solid support; (3) performing one or more nucleic acid amplification reactions on the bound template(s), so that nucleic acid colonies are generated and optionally, performing at least one step of sequence determination of one or more of the nucleic acid colonies generated. Solid supports, kits and apparatus for use in these methods.

Claims

1. A method for parallel amplification of a whole of a collection of single nucleic acid molecules having different sequences comprising:

a) providing a vessel comprising the collection of single nucleic acid molecules,

b) treating all of the single nucleic acid molecules in the vessel by attaching a known, common sequence at the 5′ and

3′

ends of each nucleic acid molecule of the collection, thereby generating a collection of treated nucleic acid molecules wherein each of the collection of treated nucleic acid molecules contains a different sequence and the known, common sequence at its 5′ and

3′

ends,

c) separating the collection of treated nucleic molecules such that individual molecules from the collection of treated nucleic acid molecules are separated from each other, and

d) performing a single amplification reaction using forward colony primers and reverse colony primers complementary to and/or identical to the known common sequence, wherein at least one of the colony primers is immobilized on a solid support, thereby simultaneously amplifying the different sequence of each of the treated nucleic acid molecules separated in step c) under conditions such that a plurality of nucleic acid colonies is formed on the solid support and the whole of the collection of single nucleic acid molecules having different sequences is amplified.

2. The method according to claim 1, wherein said solid support is a planar surface.

3. The method according to claim 1, wherein said solid support is a bead or microparticle.

6. The method according to claim 1 or claim 5, wherein the collection of single nucleic acid molecules comprises genomic DNA sequences from an organism.

7. The method according to claim 1 or claim 5, wherein the collection of single nucleic acid molecules comprises mRNA sequences from an organism.

8. The method according to any one of claim 1, 4 or 5, wherein the forward colony primers and the reverse colony primers have an identical sequence.

4. A method for parallel amplification of a whole of a collection of single nucleic acid molecules having different sequences comprising:

a) treating the collection of nucleic acid molecules thereby generating a collection of treated nucleic acid molecules wherein each of the collection of treated nucleic acid molecules contains a different sequence and a known, common sequence at its 5′ and

3′

ends,

b) immobilizing the treated nucleic acid molecules on a solid support, thereby separating the collection of treated nucleic acid molecules such that individual treated nucleic acid molecules from the collection of treated nucleic acid molecules are separated from each other, and

c) performing an amplification reaction using forward colony primers and reverse colony primers complementary to and/or identical to the known common sequence, wherein at least one of the colony primers is immobilized directly to the solid support, thereby simultaneously amplifying the different sequence of each of the treated nucleic acid molecules separated in step b) under conditions such that a plurality of nucleic acid colonies is formed on the solid support and the whole of the collection of single nucleic acid molecules having different sequences is amplified.

5. A method for parallel amplification of a whole of a collection of single nucleic acid molecules having different sequences comprising:

a) providing a vessel comprising the collection of single nucleic acid molecules, wherein the collection comprises genomic DNA sequences or mRNA sequences from an organism,

b) treating all of the single nucleic acid molecules in the vessel by attaching a known, common sequence at the 5′ and

3′

ends of each nucleic acid molecule of the collection, thereby generating a collection of treated nucleic acid molecules wherein each of the collection of treated nucleic acid molecules contains a different sequence and the known, common sequence at its 5′ and

3′

ends,

c) separating the collection of treated nucleic acid molecules such that individual treated nucleic acid molecules from the collection of treated nucleic acid molecules are separated from each other, and

d) performing a single amplification reaction using forward colony primers and reverse colony primers complementary to and/or identical to the known common sequence, wherein at least one of the colony primers is immobilized on a solid support, thereby simultaneously amplifying the different sequence of each of the treated nucleic acid molecules separated in step c) under conditions such that a plurality of nucleic acid colonies is formed on the solid support and the whole of the collection of single nucleic acid molecules having different sequences is amplified.

9. A method for parallel amplification of a collection of single nucleic acid molecules having different sequences comprising:

a) treating the collection of nucleic acid molecules thereby generating a collection of treated nucleic acid molecules wherein each of the collection of treated nucleic acid molecules contains a different sequence and a known, common sequence at its 5′ and

3′

ends,

b) immobilizing the treated nucleic acid molecules on a solid support, the solid support comprising a lawn of immobilized colony primers comprising forward colony primers and/or reverse colony primers, the colony primers being complementary to and/or identical to the known common sequence, thereby separating the collection of treated nucleic acid molecules such that individual treated nucleic acid molecules from the collection of treated nucleic acid molecules are immobilized at intervals within the lawn of immobilized colony primers, and

c) performing an amplification reaction using the forward colony primers and/or the reverse colony primers thereby simultaneously amplifying the different sequence of each of the treated nucleic acid molecules separated in step b) under conditions such that a plurality of nucleic acid colonies is formed on the solid support and the collection of single nucleic acid molecules having different sequences is amplified.

10. The method of claim 9, wherein the lawn of immobilized colony primers comprises forward colony primers and reverse colony primers.

11. The method of claim 9, further comprising an additional step of performing at least one step of sequence determination of nucleic acids in one or more of the nucleic acid colonies.

12. The method of claim 9, wherein the density of the nucleic acid colonies on the solid support is 10,000/mm² to 100,000/mm².