Highly selective nucleic acid amplification primers

• US 9,909,159 B2
• Filed: 02/07/2014
• Issued: 03/06/2018
• Est. Priority Date: 02/07/2013
• Status: Active Grant

• Current Assignee: Rutgers University
• Original Assignee: Rutgers University
• Inventors: Marras, Salvatore, Vargas-Gold, Diana, Tyagi, Sanjay, Kramer, Fred R.
• Primary Examiner(s): Strzelecka, Teresa E
• Application Number:
  US14/766,139
• Publication Number:
  US 20150361475A1
• Time in Patent Office: 1,488 Days
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2535/131 Allele specific probes

Abstract

This invention discloses multi-part primers for primer-dependent nucleic acid amplification methods. Also disclosed are primer-dependent nucleic acid amplification reactions, particularly DNA amplification reactions, reaction mixtures and reagent kits for such reactions. This invention relates to primer-dependent nucleic acid amplification reactions, particularly DNA amplification reactions such as PCR, and primers, reaction mixtures and reagent kits for such reactions and assays employing same.

Claims

1. An amplification and detection method that is capable of detecting as few as ten copies of at least one rare mutant DNA target sequence in a mixture containing, for each mutant target sequence, 100,000 copies of a closely related wild-type DNA target sequence, comprising:

(a) repeatedly cycling a reaction mixture in a primer-dependent amplification reaction having a primer-annealing temperature, said reaction mixture including said at least one mutant target sequence or its closely related wild-type target sequence or both, a DNA polymerase, other reagents needed for amplification, and for each mutant target sequence a primer pair that includes a multi-part primer comprising, in the 5′

to 3′

direction the following three contiguous DNA sequences;

an anchor sequence that hybridizes with the mutant target sequence and with its closely related wild-type target sequence during primer annealing;

a bridge sequence at least six nucleotides long that does not hybridize to either the mutant target sequence or its closely related wild-type target sequence during primer annealing; and

a foot sequence that is 5-8 nucleotides long, perfectly complementary to the mutant sequence and mismatched to its wild-type sequence by one or two nucleotides, wherein;

(i) if the anchor sequence and the foot sequence of the primer are hybridized either to the mutant target sequence or to its closely related wild-type target sequence, there is in the target sequence an intervening sequence at least eight nucleotides long that does not hybridize to the primer'"'"'s bridge sequence during primer-annealing, and the bridge sequence and the intervening sequence, together create a bubble in the hybrid having a circumference of 28-52 nucleotides,

(ii) the circumference of the bubble and the length of the foot sequence in combination result in a weak foot/mutant-target-sequence hybrid that makes copying the intended target sequence unlikely as evidenced by a delay of at least five cycles in the threshold cycle (C_T) of amplification of said at least one mutant target sequence using said multi-part primer as compared to using a conventional primer,

(iii) the bridge sequence and the foot sequence do not together prime non-target sequences in the mixture, and

(iv) the probability that during said cycling a multi-part primer/wild-type-target-sequence hybrid will be extended is at least 10,000 times lower than the probability that during said cycling a multi-part primer/mutant-target-sequence hybrid will be extended, as evidenced by a Δ

C_T of at least 13.3 cycles; and

(b) detecting amplified product or products with a dsDNA binding dye, or for each multi-part primer a fluorescent hybridization probe that signals upon hybridization to the amplification product of the primer, or for each multi-part primer a quenched, fluorescently labeled oligonucleotide hairpin at the primer'"'"'s 5′

end that fluoresces only when incorporated in or hybridized to the primer'"'"'s amplified product.

2. The method of claim 1, wherein the foot sequence of each multi-part primer is mismatched to its wild-type target at either or both of the primer'"'"'s 3′

nucleotide and 3′

penultimate nucleotide.

3. The method of claim 2, wherein the at least one mutant target sequence is cDNA.

4. The method of claim 2, wherein the amplification reaction is a polymerase chain reaction (PCR), and wherein detection is real-time detection.

5. The method of claim 3, wherein for each of the at least one multi-part primers, the C_T delay is at least 10 cycles.

6. The method of claim 3, wherein the PCR reaction is non-symmetric with each multi-part primer being an excess primer.

7. The method of claim 3, wherein for each of the at least one multi-part primers the threshold cycle (C_T) of an assay begun with 10⁶ copies of its mutant target sequence is at least 18 cycles earlier than the C_T of an assay begun with 10⁶ copies of its closely related wild-type target sequence.

8. The method of claim 3, wherein the at least one mutant target sequence is one mutant target sequence.

9. The method of claim 8, wherein the multi-part primer for the mutant target sequence has a foot sequence that is 6-7 nucleotides long, wherein the bubble circumference is 28-44 nucleotides long, and wherein detection of amplified product is by SYBR Green or another dsDNA binding dye.

10. The method of claim 9, wherein the amplification reaction is a symmetric PCR reaction.

11. The method of claim 9, wherein the threshold cycle (C_T) of an assay begun with 10⁶ copies of the mutant target sequence is at least 18 cycles earlier than the C_T of an assay begun with 10⁶ copies of its closely related wild-type target sequence.

12. The method of claim 8, wherein the multi-part primer contains a functional moiety located 5′

to the anchor sequence, said functional moiety not hybridizing either to the mutant target sequence or to the wild-type target sequence.

13. The method of claim 4, wherein the at least one rare mutant target sequence comprises at least two mutant target sequences that do not share sequence homology and are located at different positions in a genome, wherein there is a multi-part primer and a reverse primer for each mutant target sequence, and wherein amplified product from each multi-part primer is separately detected by a uniquely colored dual-labeled fluorescent probe that signals upon hybridizing to that amplified product.

14. The method of claim 13, wherein the PCR reaction is a non-symmetric PCR reaction.

15. The method of claim 13, wherein the threshold cycle (C_T) of an assay begun with 10⁶ copies of each mutant target sequence is at least 18 cycles earlier than the C_T of an assay begun with 10⁶ copies of its closely related wild-type target sequence.

16. The method of claim 13, wherein each multi-part primer contains a unique functional moiety located 5′

to the anchor sequence, said functional group not hybridizing either to the mutant target sequence or to the wild-type target sequence.

17. The method of claim 4, wherein the at least one mutant target sequence comprises at least two mutant target sequences that are close to each other in an intended target and differ by one or two single-nucleotide polymorphisms, wherein there is a multi-part forward primer for each of said at least two mutant sequences and a common reverse primer, wherein each multi-part primer has a different bridge sequence, and wherein amplified products from each multi-part primer are separately detected.

18. The method of claim 17, wherein each multi-part primer contains a different quenched, fluorescently labeled hairpin located 5′

to the anchor sequence.