Compositions and methods for enhancing and/or predicting DNA amplification

1. An isolated primer oligonucleotide comprising from 5′ to 3′,

i) a first region comprising a self-complementary sequence comprising from 5′ to 3′ the reverse complement of a nicking enzyme recognition sequence, a palindromic sequence, and said nicking enzyme recognition sequence, and

ii) a second region at least 16 nucleotides long that specifically binds to a complementary region on a target nucleic acid molecule to form a double-stranded primer-target hybrid having a ΔG that is at least 15 kcal/mol lower than the ΔG of a self-dimer comprising the second region, wherein the second region comprises at the 3′ end two or more contiguous 2′ modified nucleotides.

2. The isolated primer oligonucleotide of claim 1 , wherein said palindromic sequence in the first region is 2, 4, or 6 nucleotides long.

3. The isolated primer oligonucleotide of claim 1 , wherein the first region is 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 nucleotides in length.

4. The isolated primer oligonucleotide of claim 1 , in the form of a homodimer formed by hybridization of the self-complementary first region sequences of two primer oligonucleotide molecules.

5. The isolated primer oligonucleotide of claim 1 , wherein the two or more contiguous 2′ modified nucleotides has a 2′ modification selected from the group consisting of 2′-O-methyl, 2′-methoxyethoxy, 2′-fluoro, 2′-hydroxyl, 2′-alkyl, 2′-allyl, 2′-O-[2-(methylamino)-2-oxoethyl], 4′-CH 2 —O-2′-bridge, 4′-(CH 2 ) 2 —O-2′-bridge, 2′-LNA, and 2′-O—(N- methylcarbamate) or those comprising base analogs.

6. The isolated primer oligonucleotide of claim 1 , wherein the two or more contiguous 2′ modified nucleotides at the 3′ end comprises 3, 4, 5, or 6 more contiguous 2′ modified nucleotides.

7. The isolated primer oligonucleotide of claim 1 , wherein the nicking enzyme is one or more of Nt.BspD6I and Nt.BstNBI.

8. The isolated primer oligonucleotide of claim 1 , wherein the recognition sequence of the nicking agent is positioned to cleave the phosphodiester bond between the first and second regions.

9. The isolated primer oligonucleotide of claim 1 , having a first region comprising a nucleic acid sequence selected from the group consisting of:

(SEQ ID NO: 15241)

5′-GACTCN 1 N 1′ GAGTC-3′;

(SEQ ID NO: 15242)

5′-GACTCN 1 N 1′ GAGTCN-3′;

(SEQ ID NO: 15243)

5′-N 2 GACTCN 1 N 1′ GAGTCN 2′ -3′;

(SEQ ID NO: 15244)

5′-N 2 GACTCN 1 N 1′ GAGTCN 2′ N-3′;

(SEQ ID NO: 15245)

5′-N 3 N 2 GACTCN 1 N 1′ GAGTCN 2′ N 3′ -3′;

(SEQ ID NO: 15246)

5′-N 3 N 2 GACTCN 1 N 1′ GAGTCN 2′ N 3′ N-3′;

(SEQ ID NO: 15247)

5′-N 4 N 3 N 2 GACTCN 1 N 1′ GAGTCN 2′ N 3′ N 4′ -3′;

(SEQ ID NO: 15248)

5′-N 4 N 3 N 2 GACTCN 1 N 1′ GAGTCN 2′ N 3′ N 4′ N-3′;

(SEQ ID NO: 15249)

5′-N 5 N 4 N 3 N 2 GACTCN 1 N 1′ GAGTCN 2′ N 3′ N 4′ N 5′ -3′;

(SEQ ID NO: 15250)

5′-GACTCN 2 N 1 N 1′ N 2′ GAGTC-3′;

(SEQ ID NO: 15251)

5′-GACTCN 2 N 1 N 1′ N 2′ GAGTCN-3′;

(SEQ ID NO: 15252)

5′-N 3 GACTCN 2 N 1 N 1′ N 2′ GAGTCN 3′ -3′;

(SEQ ID NO: 15253)

5′-N 3 GACTCN 2 N 1 N 1′ N 2′ GAGTCN 3′ N-3′;

(SEQ ID NO: 15254)

5′-N 4 N 3 GACTCN 2 N 1 N 1′ N 2′ GAGTCN 3′ N 4′ -3′;

(SEQ ID NO: 15255)

5′-N 4 N 3 GACTCN 2 N 1 N 1′ N 2′ GAGTCN 3′ N 4′ N-3′;

(SEQ ID NO: 15256)

5′-N 5 N 4 N 3 GACTCN 2 N 1 N 1′ N 2′ GAGTCN 3′ N 4′ N 5′ -3′;

(SEQ ID NO: 15257)

5′-N 5 N 4 N 3 GACTCN 2 N 1 N 1′ N 2′ GAGTCN 3′ N 4′ N 5′ N-3′; 

(SEQ ID NO: 15258)

5′-N 6 N 5 N 4 N 3 GACTCN 2 N 1 N 1′ N 2′ GAGTCN 3′ N 4′ N 5′ N 6′ -3′,

(SEQ ID NO: 15259)

5′-GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTC-3′;

(SEQ ID NO: 15260)

5′-GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCN-3′;

(SEQ ID NO: 15261)

5′-GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCNN-3′;

(SEQ ID NO: 15262)

5′-GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCNNN-3′;

(SEQ ID NO: 15263)

5′-GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCNNNN-3′;

(SEQ ID NO: 15264)

5′-N 4 GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCN 4′ -3′;

(SEQ ID NO: 15265)

5′-N 4 GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCN 4′ N-3′;

(SEQ ID NO: 15266)

5′-N 4 GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCN 4′ NN-3′;

(SEQ ID NO: 15267)

5′-N 4 GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCN 4′ NNN-3′;

(SEQ ID NO: 15268)

5′-N 5 N 4 GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCN 4′ N 5′ -3′;

(SEQ ID NO: 15269)

5′-N 5 N 4 GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCN 4′ N 5′ N-3′;

(SEQ ID NO: 15270)

5′-N 6 N 5 N4GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCN 4′ N 5′ N 6′ -3′;

(SEQ ID NO: 15271)

5′-N 6 N 5 N4GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCN 4′ N 5′ N 6′ N-3′; 

and

(SEQ ID NO: 15272)

5′-N 7 N 6 N 5 N 4 GACTCN 3 N 2 N 1 N 1′ N 2′ N 3′ GAGTCN 4′ N 5′ N 6′ N 7′ -3′,

where N is an adenine (A), thymine (T), cytosine (C), or guanine (G) nucleobase, and Ni is complementary to N 1 ′, N 2 to N 2 ′, N 3 to N 3 ′, N 4 to N 4 ′, N 5 to N 5 ′, N 6 to N 6 ′, and N 7 to N 7 ′.

10. A method of amplifying a specific product in a nicking and extension amplification reaction, the method comprising:

(a) contacting a target nucleic acid molecule with a polymerase, two or more primers, each of which specifically binds to a complementary sequence on the target nucleic acid molecule, a nicking enzyme, and a detectable polynucleotide probe, wherein at least one primer comprises from 5′ to 3′,

i) a first region comprising a self-complementary sequence comprising from 5′ to 3′ the reverse complement of a nicking enzyme recognition sequence, a palindromic sequence, and said nicking enzyme recognition sequence, and

ii) a second region at least 16 nucleotides long that specifically binds to a complementary region on a target nucleic acid molecule to form a double-stranded primer-target hybrid having a ΔG that is at least 15 kcal/mol lower than the ΔG of a self-dimer comprising the second region of the primer, wherein the second region comprises at the 3′ end two or more contiguous 2′ modified nucleotides; and

(b) generating amplicons comprising at least a portion of said target nucleic acid molecule.

11. A method of claim 10 , further comprising: (c) detecting a signal specific for oligonucleotide probe hybridization to the target nucleic acid molecule or amplicon thereof, wherein the signal indicates the presence of the target nucleic acid molecule present in the sample or an amplicon thereof.

12. The method of claim 11 , wherein the oligonucleotide probe comprises:

i) an oligonucleotide;

ii) a fluorescent reporter; and

iii) a quenching molecule capable of absorbing the excitation energy from the fluorescent reporter;

wherein the fluorescent reporter and quenching molecule are covalently attached to opposite 5′ and 3′ ends of the oligonucleotide,

wherein the oligonucleotide comprises a first region having a nucleic acid sequence that is substantially complementary to a target nucleic acid sequence and

a) a second region 5′ upstream of the first region, and

b) a third region 3′ downstream of the first region that has a nucleic acid sequence complementary to the second region,

wherein the oligonucleotide is capable of forming a stem-loop hairpin structure by hybridization of the second and third regions when the oligonucleotide is not bound to the target nucleic acid molecule.

13. The method of claim 10 , wherein the polymerase is a Geobacillus spp. or Bacillus stearothermophilus DNA polymerase I, or active fragments and derivatives thereof.

14. The method of claim 10 , wherein the two or more contiguous 2′ modified nucleotides has a 2′ modification selected from the group consisting of 2′-O-methyl, 2′-methoxyethoxy, 2′-fluoro, 2′-hydroxyl, 2′-alkyl, 2′-allyl, 2′-O-[2-(methylamino)-2-oxoethyl], 4′-thio, 4′-CH 2 —O-2′-bridge, 4′-(CH 2 ) 2 —O-2′-bridge, 2′-LNA, and 2′-O—(N-methylcarbamate) or those comprising base analogs.

15. The method of claim 10 , wherein the two or more contiguous 2′ modified nucleotides at the 3′ end comprises 3, 4, 5, 6 or more contiguous 2′ modified nucleotides.

16. A kit for amplifying a target sequence in a nicking amplification reaction, the kit comprising one or more primer oligonucleotides comprising from 5′ to 3′,

i) a first region comprising a self-complementary sequence comprising from 5′ to 3′ the reverse complement of a nicking enzyme recognition sequence, a palindromic sequence, and said nicking enzyme recognition sequence, and

ii) a second region at least 16 nucleotides long that specifically binds to a complementary region on a target nucleic acid molecule to form a double-stranded primer-target hybrid having a ΔG that is at least 15 kcal/mol lower than the ΔG of a self-dimer comprising the second region of the primer, wherein the second region comprises at the 3′ end two or more contiguous 2′ modified nucleotides;

and directions for use of the primer.

17. The kit of claim 16 , further comprising an oligonucleotide probe comprising:

i) an oligonucleotide;

ii) a fluorescent reporter; and

iii) a quenching molecule capable of absorbing the excitation energy from the fluorescent reporter;

wherein the fluorescent reporter and quenching molecule are covalently attached to opposite 5′ and 3′ ends of the oligonucleotide,

wherein the oligonucleotide comprises a first region having a nucleic acid sequence that is substantially complementary to a target nucleic acid sequence and

a) a second region 5′ upstream of the first region, and

b) a third region 3′ downstream of the first region that has a nucleic acid sequence complementary to the second region,

wherein the oligonucleotide is capable of forming a stem-loop hairpin structure by hybridization of the second and third regions when the oligonucleotide is not bound to the target nucleic acid molecule.