Allele-specific amplification of nucleic acids

• US 9,238,832 B2
• Filed: 12/08/2010
• Issued: 01/19/2016
• Est. Priority Date: 12/11/2009
• Status: Active Grant

• Current Assignee: Roche Molecular Systems (Roche Holding AG)
• Original Assignee: Roche Molecular Systems (Roche Holding AG)
• Inventors: Will, Stephen, Tsan, Alison, Newton, Nicolas
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Tung, Joyce
• Application Number:
  US12/962,861
• Publication Number:
  US 20110311968A1
• Time in Patent Office: 1,868 Days
• Field of Search: 435/6.12, 435/91.1, 435/91.2
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2525/117 incorporating modified base
• 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 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/166 Oligonucleotides used as internal standards, controls or normalisation probes

Abstract

The present invention includes a method of allele-specific amplification, utilizing an allele-specific oligonucleotide, at least partially complementary to more than one variant of the target sequence, having an internally-placed selective nucleotide complementary to only one variant of the target sequence wherein the allele-specific oligonucleotide is extended by a nucleic acid polymerase predominantly or exclusively when hybridized to the variant of the target sequence for which it has said complementary selective nucleotide.

Claims

1. A method of allele-specific amplification by polymerase chain reaction (PCR) and detection of a desired variant of a target nucleic acid, the target nucleic acid existing in the form of several variant sequences, the method comprising:

(a) providing a reaction mixture in liquid solution that comprises a first oligonucleotide at least partially complementary to one or more variants of the target nucleic acid, and a second oligonucleotide at least partially complementary to one or more variants of the target nucleic acid and has at least one selective nucleotide that is complementary to a corresponding nucleotide in the desired variant of the target nucleic acid but not complementary to the corresponding nucleotide in undesired variants of the target nucleic acid, wherein said selective nucleotide is placed internally of the 3′

terminus, and wherein said second oligonucleotide further comprises at least one nucleotide with a base covalently modified at the exocyclic amino group;

(b) hybridizing said first and second oligonucleotides to at least one variant of the target nucleic acid;

(c) providing conditions for the extension of said first and second oligonucleotides to at least one variant of the target nucleic acid by a nucleic acid polymerase, wherein said polymerase is capable of extending said second oligonucleotide preferentially when said selective nucleotide forms a base pair with the desired variant of the target nucleic acid, and substantially less when said selective nucleotide does not form a base pair with the desired variant of the target nucleic acid; and

(d) detecting the product of primer extension in step (c);

wherein said method of amplification and detection are performed in a homogeneous assay.

2. The method of claim 1, wherein said nucleic acid polymerase in step (c) is capable of extending said second oligonucleotide exclusively when said selective nucleotide forms a base pair with the desired variant of the target nucleic acid.

3. The method of claim 1, wherein said selective nucleotide is at the position between 1 and 5 nucleotides near the 3′

-terminus of the oligonucleotide.

4. The method of claim 1, wherein said nucleic acid polymerase is selected from the group consisting of Taq DNA polymerase, Z05 DNA polymerase, Δ

Z05 DNA polymerase and Δ

Z05-Gold DNA polymerase.

5. The method of claim 1 wherein said nucleic acid polymerase possesses 3′

-5′

nuclease activity.

6. The method of claim 5, wherein said nucleic acid polymerase is selected from the group consisting of Pfu DNA polymerase and Thermatoga Maritima.

7. The method of claim 1, wherein said variant of the sequence in step (a) is a V600E mutation of the human BRAF, EGFR, PIK3CA or KRAS gene.

8. The method of claim 1, wherein said first oligonucleotide is SEQ ID NO:

11.

9. The method of claim 1, wherein said second oligonucleotide is selected from the group consisting of SEQ ID NOS:

2, 3, 4, 5, 7, 8, 9, 10, and 17.

11. The method of claim 1, wherein the structures of the at least one nucleotide with a base covalently modified at the exocyclic amino group is selected from the group consisting of:

12. The method of claim 11, wherein the at least one nucleotide with a base covalently modified at the exocyclic amino group occurs at positions-5, -4, -3, -2 -1 relative to the 3′

-terminus or at the 3′

terminus.

13. The method of claim 12, wherein the base covalently modified at the exocyclic amino group comprises a modifier of the following formula:

14. The method of claim 13, wherein the modifier has the following formula:

15. The method of claim 14, wherein the modifier is selected from the group consisting of:

16. The method of claim 11, wherein the base, covalently modified at the exocyclic amino group is selected from a group consisting of N⁶-benzyl-adenine, N⁶-para-tert-butyl-benzyl adenine, N²-benzyl-guanine and N⁴-benzyl-cytosine.

10. A method of detecting a desired variant of a target nucleic acid, the target nucleic acid existing in the form of several variant sequences, the method comprising:

(a) providing a reaction mixture in liquid solution that comprises a first oligonucleotide at least partially complementary to one or more variants of the target nucleic acid, and a second oligonucleotide at least partially complementary to one or more variants of the target nucleic acid and has at least one selective nucleotide that is complementary to a corresponding nucleotide in the desired variant of the target nucleic acid but not complementary to the corresponding nucleotide in undesired variants of the target nucleic acid, wherein said selective nucleotide is placed internally of the 3′

terminus, and wherein said second oligonucleotide further comprises at least one nucleotide with a base covalently modified at the exocyclic amino group;

(b) hybridizing said first and second oligonucleotides to at least one variant of the target nucleic acid;

(c) providing conditions suitable for the oligonucleotide extension by a nucleic acid polymerase, wherein said polymerase is capable of extending said second oligonucleotide preferentially when said selective nucleotide forms a base pair with the desired variant of the target nucleic acid, and substantially less when said selective nucleotide does not form a base pair with the desired variant of the target nucleic acid;

(d) repeating the sequence of hybridization and extension steps multiple times; and

(e) detecting the products of said oligonucleotide extension, wherein the extension signifies the presence of the desired variant of the target nucleic acid to which the oligonucleotide has a complementary selective nucleotide;

wherein steps (a)-(e) are performed in a homogeneous assay.