Methods of nucleic acid amplification and sequencing

• US 7,115,400 B1
• Filed: 09/30/1999
• Issued: 10/03/2006
• Est. Priority Date: 09/30/1998
• Status: Expired due to Term

• Current Assignee: Illumina Incorporated
• Original Assignee: Solexa Ltd. (Illumina Incorporated)
• Inventors: Mayer, Pascal, Turcatti, Gerardo, Kawashima, Eric, Adessi, Celine, Mermod, Jean-Jacques
• Primary Examiner(s): LU, FRANK WEI MIN
• Application Number:
  US09/806,531
• Time in Patent Office: 2,560 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/183, 435/283.1, 435/287.1, 435/287.2, 436/94, 536/23.1, 536/24.3, 536/24.33, 536/25.3, 536/25.33
• 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) 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 amplification of at least one nucleic acid, comprising the following steps:

(1) forming at least one nucleic acid template comprising the at least one nucleic acid to be amplified, wherein the at least one nucleic acid contains an oligonucleotide sequence Y at the 5′

end and an oligonucleotide sequence Z at the 3′

end, and the at least one nucleic acid carries a means for immobilizing the at least one nucleic acid to a solid support at the 5′

end;

(2) mixing the at least one nucleic acid template, in the presence of the solid support, with one or more colony primers X, each of which can hybridize to the oligonucleotide sequence Z and carries a means for immobilizing the colony primer to the solid support at the 5′

end, whereby the 5′

ends of both the at least one nucleic acid template and the colony primers are immobilized to the solid support;

wherein said 5′

ends of both the at least one nucleic acid template and the colony primers are immobilized to said solid support such that they cannot be removed by washing with water or aqueous buffer under DNA-denaturing conditions; and

(3) performing one or more nucleic acid amplification reactions on the immobilized nucleic acid template, so that nucleic acid colonies are generated.

2. The method of claim 1, wherein the oligonucleotide sequence Z is complementary to oligonucleotide sequence Y and colony primer X is of the same sequence as oligonucleotide sequence Y.

3. The method of claim 1, wherein two different colony primers X are mixed with the at least one nucleic acid template in step (2) of claim 1, and wherein the oligonucleotide sequence Z can hybridise to one of the colony primers X and the oligonucleotide sequence Y is the same as the sequence of one of the colony primers X.

4. The method of claim 1, further comprising an additional step of performing at least one step of sequence determination of nucleic acid templates in one or more of the nucleic acid colonies.

5. The method of claim 4, wherein the sequence determination step involves incorporation and detection of labelled nucleotides.

6. The method of claim 4, wherein the full or partial sequences of nucleic acid templates present in more than one nucleic acid colonies are determined simultaneously.

7. The method of claim 4, further comprising an additional step of visualising the nucleic acid colonies.

8. The method of claim 7, wherein said visualisation step involves the use of a labelled or unlabelled nucleic acid probe.

9. The method of claim 1, wherein the means for immobilizing the at least one nucleic acid template and the colony primers to the solid support comprises means for immobilizing the at least one nucleic acid template and the colony primers covalently to the support.

10. The method of claim 9, wherein said means for immobilizing the at least one nucleic acid template and the colony primers covalently to the solid support is a chemically modifiable functional group.

11. The method of claim 10, wherein said chemically modifiable functional group is a phosphate group, a carboxylic or aldehyde moiety, a thiol, a hydroxyl, a dimethoxytrityl (DMT), or an amino group.

12. The method of claim 11, wherein said chemically modifiable functional group is an amino group.

13. The method of claim 1, wherein said solid support to which said 5′

ends of both the at least one nucleic acid template and the colony primers are immobilized is selected from the group consisting of latex beads, dextran beads, polystyrene and polypropylene surfaces, polyacrylamide gel, gold surfaces, glass surfaces, and silicon wafers.

14. The method of claim 13, wherein the solid support is glass.

15. The method of claim 1, wherein the density of the nucleic acid colonies on the solid support is 10,000/mm² to 100,000/mm².

16. The method of claim 1, wherein the density of the colony primers X attached to the solid support is at least 1 fmol/mm².

17. The method of claim 1, wherein the density of the nucleic acid templates is 10,000/mm² to 100,000/mm².

18. The method of claim 1, wherein said 5′

ends of both the at least one nucleic acid template and the colony primers are immobilized to said solid support via covalent attachment.

19. A method for amplification of at least one nucleic acid, comprising the following steps:

(1) forming at least one nucleic acid template comprising the at least one nucleic acid to be amplified, wherein the at least one nucleic acid contains an oligonucleotide sequence Y at the 5′

end and an oligonucleotide sequence Z at the 3′

end, and the at least one nucleic acid carries a means for immobilizing the at least one nucleic acid to a solid support at the 5′

end;

(2) mixing the at least one nucleic acid template, in the presence of the solid support, with one or more degenerate colony primers X, each of which can hybridize to the oligonucleotide sequence Z and carries a means for immobilizing the colony primer to the solid support at the 5′

end, whereby the 5′

ends of both the at least one nucleic acid template and the colony primers are immobilized to the solid support;

wherein said 5′

ends of both the at least one nucleic acid template and the colony primers are immobilized to said solid support such that they cannot be removed by washing with water or aqueous buffer under DNA-denaturing conditions, and

(3) performing one or more nucleic acid amplification reactions on the immobilized nucleic acid template, so that nucleic acid colonies are generated.

20. The method of claim 19, wherein said 5′

ends of both the at least one nucleic acid template and the colony primers are immobilized to said solid support via covalent attachment.