Method of amplifying a nucleic acid

1. A method of identifying the presence of a target sequence in a nucleic acid sample, the method comprising:

a. mixing in a reaction mixture ingredients comprising:

i. a nucleic acid sample;

ii. a first primer binding at a first binding site of a first strand of a nucleic acid target sequence having a 5′ end and a 3′ end;

iii. a second primer binding at a second binding site to a complementary strand to the target sequence 5′ to the first binding site with respect to the first strand;

iv. an internal primer pair comprising a third primer binding to the first strand at a third binding site between the first binding site and the second binding site and a fourth primer binding to the complementary strand at a fourth binding site between the first binding site and the third binding site; and

v. one or more spiral primers binding the target sequence between the third binding site and the fourth binding site, selected from:

(i) a reverse internal spiral primer having a 5′ portion and a 3′ portion in which the 5′ portion binds to the first strand and the 3′ portion binds to the complementary strand;

(ii) a forward internal spiral primer having a 5′ portion and a 3′ portion in which the 5′ portion binds to the complementary strand and the 3′ portion binds to the first strand;

(iii) a reverse internal triplex spiral primer having a 5′ portion, a 3′ portion and a middle portion in which the 5′ portion and the 3′ portion binds the first strand and the middle portion binds the complementary strand; and

(iv) a forward internal triplex spiral primer having a 5′ portion, a 3′ portion and a middle portion in which the 5′ portion and the 3′ portion binds the complementary strand and the middle portion binds the first strand;

vi. a DNA polymerase; and

b. incubating the reaction mixture at a temperature or combination of temperatures effective to produce one or more amplification products in a reaction mixture containing a nucleic acid comprising the target sequence.

2. The method of claim 1 in which the nucleic acid sample comprises the target sequence.

3. The method of claim 1 in which the one or more spiral primers of the reaction mixture comprises:

a. a reverse internal spiral primer having a 5′ portion and a 3′ portion in which the 5′ portion binds to the first strand and the 3′ portion binds to the complementary strand; and

b. a forward internal spiral primer having a 5′ portion and a 3′ portion in which the 5′ portion binds to the complementary strand and the 3′ portion binds to the first strand;

in which the reverse internal spiral primer, and the forward internal spiral primer bind the target sequence between the third and fourth binding sites.

4. The method of claim 1 in which the one or more spiral primers of the reaction mixture comprises:

a. a reverse internal triplex spiral primer having a 5′ portion, a 3′ portion and a middle portion in which the 5′ portion and the 3′ portion binds the first strand and the middle portion binds the complementary strand; and

b. a forward internal triplex spiral primer having a 5′ portion, a 3′ portion and a middle portion in which the 5′ portion and the 3′ portion binds the complementary strand and the middle portion binds the first strand;

in which the reverse internal triplex spiral primer and a forward internal triplex spiral primer bind the target sequence between the third and fourth binding sites.

5. The method of claim 4 in which the reverse internal triplex spiral primer binds the target sequence at a binding site 5′ to a binding site of the forward triplex internal spiral primer.

6. A method of identifying the presence of a target sequence in a nucleic acid sample, the method comprising:

a. mixing in a reaction mixture ingredients comprising:

i. a nucleic acid sample;

ii. a first primer binding at a first binding site of a first strand of a nucleic acid target sequence having a 5′ end and a 3′ end;

iii. a second primer binding at a second binding site to a complementary strand to the target sequence 5′ to the first binding site with respect to the first strand;

iv. a reverse internal spiral primer having a 5′ portion and a 3′ portion in which the 5′ portion binds to the first strand and the 3′ portion binds to the complementary strand;

v. a second reverse internal spiral primer having a 5′ portion and a 3′ portion in which the 5′ portion binds to the first strand and the 3′ portion binds to the complementary strand;

vi. a forward internal spiral primer having a 5′ portion and a 3′ portion in which the 5′ portion binds to the complementary strand and the 3′ portion binds to the first strand;

in which the reverse internal spiral primer, the second reverse internal spiral primer, and the forward internal spiral primer, bind the target sequence between the first and second binding sites; and

vii. a DNA polymerase; and

b. incubating the reaction mixture at a temperature or combination of temperatures effective to produce one or more amplification products in a reaction mixture containing a nucleic acid comprising the target sequence.

7. The method of claim 6 in which the forward internal spiral primer binds the target sequence at a binding site between binding sites of the reverse internal spiral primer and the second reverse internal spiral primer.

8. The method of claim 6 in which the 3′ portion of one or more of the reverse internal spiral primer, the second reverse internal spiral primer and the forward internal spiral primer bind to the target sequence 3′ to and immediately adjacent to the binding site of the 5′ portion of the same primer.

9. A method of identifying the presence of a target sequence in a nucleic acid sample, the method comprising:

a. mixing in a reaction mixture ingredients comprising:

i. a nucleic acid sample;

ii. a first primer binding at a first binding site of a first strand of a nucleic acid target sequence having a 5′ end and a 3′ end;

iii. a second primer binding at a second binding site to a complementary strand to the target sequence 5′ to the first binding site with respect to the first strand;

iv. a reverse internal triplex spiral primer having a 5′ portion, a 3′ portion, and a middle portion in which the 5′ portion and the 3′ portion binds the first strand and the middle portion binds the complementary strand;

v. a forward internal triplex spiral primer having a 5′ portion, a 3′ portion, and a middle portion in which the 5′ portion and the 3′ portion binds the complementary strand and the middle portion binds the first strand;

in which the reverse internal triplex spiral primer and a forward internal triplex spiral primer bind the target sequence between the first and second binding sites;

vi. a DNA polymerase; and

b. incubating the reaction mixture at a temperature or combination of temperatures effective to produce one or more amplification products in a reaction mixture containing a nucleic acid comprising the target sequence.

10. The method of claim 9 in which the reverse internal triplex spiral primer binds the target sequence at a binding site 5′ to a binding site of the forward triplex internal spiral primer.

11. The method of claim 1 in which the nucleic acid sample comprises RNA and either the DNA polymerase has reverse transcriptase activity or the reaction mixture further comprises a reverse transcriptase.

12. The method of claim 1 in which the 3′ portion of the third primer binds to the target strand 3′ to and immediately adjacent to the binding site of the 5′ portion of the third primer.

13. The method of claim 1 in which the amplification is isothermic, using a strand-displacing polymerase.

14. The method of claim 1 in which the method is multiplexed such that a second nucleic acid is amplified in the reaction mixture.

15. The method of claim 1 in which the target sequence is a sequence of a pathogen.

16. The method of claim 15 in which the pathogen is selected from the group consisting of influenza A virus, influenza B virus, West Nile virus, HIV virus, Dengue virus, Klebsiella, E. coli and Chlamydia.

17. The method of claim 1 , in which one or more inner primer comprises a detectable tag.