Nucleic acid amplification using nicking agents

• US 7,112,423 B2
• Filed: 07/15/2002
• Issued: 09/26/2006
• Est. Priority Date: 07/15/2001
• Status: Expired due to Fees

• Current Assignee: Keck Graduate Institute
• Original Assignee: Keck Graduate Institute
• Inventors: Van Ness, Lori K, Van Ness, Jeffrey, Galas, David J
• Primary Examiner(s): STRZELECKA, TERESA E
• Application Number:
  US10/197,239
• Publication Number:
  US 20030104431A1
• Time in Patent Office: 1,534 Days
• Field of Search: 435/91.2, 435/6, 435/91.1, 536/23.1, 536/24.3
• US Class Current: 435/91.2
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2521/301 Endonuclease
• CPC Class Codes: C12Q 2521/307 Single strand endonuclease
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2521/513 Winding/unwinding enzyme, e.g. helicase
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2527/107 Temperature of melting, i.e. Tm
• CPC Class Codes: C12Q 2531/119 Strand displacement amplification [SDA]
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

The present invention provides methods and kits for amplifying target nucleic acids (including whole genomes) using nicking agents. In certain aspects, the amplification does not require the use of any external oligonucleotide primers that are capable of annealing to a portion of the target nucleic acid. This invention is useful in many areas such as genetic disease diagnoses, forensic analyses and palcoarcheological studies.

Claims

1. A method for nucleic acid amplification comprising forming a mixture of

(a) a double-stranded target nucleic acid of which at least one strand has two or more nicking sites;

(b) a nicking agent capable of nicking at the two or more nicking sites; and

(c) a DNA polymerase;

under a condition allowing for the making of two or more copies of at least a portion of the target nucleic acid, wherein the amplification does not require the presence of an external oligonucleotide primer (ODNP) that is capable of specifically annealing to a portion of the target nucleic acid, and is performed by multiple cycles of nicking by the nicking agent and extension by the DNA polymerase.

8. The method of claim 1 wherein the DNA polymerase is selected from the group consisting of exo⁻

Vent, exo⁻

Deep Vent, exo⁻

Bst, exo⁻

Pfu, exo⁻

Bca, the Klenow fragment of DNA polymerase I, T5 DNA polymerase, Phi29 DNA polymerase, phage M2 DNA polymerase, phage PhiPRD1 DNA polymerase, Sequenase, PRD1 DNA polymerase, 9°

Nm™

DNA polymerase, and T4 DNA polymerase homoenzyme.

9. The method of claim 1 wherein the amplification is performed under an isothermal condition.

10. The method of claim 1 wherein the target nucleic acid is isolated from a single cell.

11. The method of claim 1 wherein the target nucleic acid comprises a whole genome of an organism.

12. The method of claim 1 wherein the nicking agent is a nicking endonuclease.

14. The method of claim 1 wherein the amplification is performed at 50°

C.–

70°

C.

2. A method for nucleic acid amplification comprising

(a) multiply nicking at least one strand of a double-stranded target nucleic acid with a nicking agent to provide at least two new 3′

termini in that strand;

(b) extending one or more of the at least two new 3′

termini with a DNA polymerase;

(c) nicking the extension product of step (b) with the nicking agent; and

(d) extending the nicking product of step (c) to thereby amplify at least a portion of one strand of the target nucleic acid.

3. The method of claim 2 wherein the target nucleic acid is isolated from a single cell.

4. The method of claim 2 wherein the target nucleic acid comprises a whole genome of an organism.

5. The method of claim 4 wherein the organism is a human.

6. The method of claim 2 wherein the nicking agent is a nicking endonuclease.

7. The method of claim 6 wherein the nicking endonuclease is any one selected from the group consisting of N.BstNB I, N.Alv I, N.BbvC I-a and N.BbvC I-b.

13. The method of claim 2 wherein the DNA polymerase is selected from the group consisting of exo⁻

Vent, exo⁻

Deep Vent, exo⁻

Bst, exo⁻

Pfu, exo⁻

Bca, the Klenow fragment of DNA polymerase I, T5 DNA polymerase, Phi29 DNA polymerase, phage M2 DNA polymerase, phage PhiPRD1 DNA polymerase, Sequenase, PRD1 DNA polymerase, 9°

Nm™

DNA polymerase, and T4 DNA polymerase homoenzyme.

15. The method of claim 2 wherein steps (a)–

(d) are performed at 50°

C.–

70°

C.

16. The method of claim 2 wherein steps (a)–

(d) are performed under an isothermal condition.