Methods and systems for nucleic acid amplification

1. A method for nucleic acid processing, comprising:

(a) bringing an invader in contact with a first double-stranded nucleic acid molecule under conditions sufficient to bind said invader to at least a portion of a strand of said first double-stranded nucleic acid molecule and expose a segment of said strand;

(b) coupling an oligonucleotide that is separate from said invader to said segment;

(c) performing an extension reaction along a 5′ to 3′ direction of said oligonucleotide to generate a second double-stranded nucleic acid molecule comprising said strand and an additional strand that is complementary to at least a portion of said strand; and

(d) electronically identifying a sequence of said second double-stranded nucleic acid molecule or derivative thereof.

2. The method of claim 1 , wherein said extension reaction is performed using said oligonucleotide as a primer.

3. The method of claim 1 , wherein said invader comprises a nucleic acid molecule.

4. The method of claim 1 , wherein said invader comprises an enzyme.

5. The method of claim 4 , wherein said enzyme is a recombinase.

6. The method of claim 1 , wherein said first double-stranded nucleic acid molecule is coupled to a support.

7. The method of claim 6 , wherein said support is a particle.

8. The method of claim 6 , wherein said support is planar.

9. The method of claim 1 , wherein (a)-(c) are preformed isothermally.

10. The method of claim 1 , wherein, in (c), said extension reaction is performed with aid of a strand-displacing polymerase.

11. The method of claim 1 , further comprising synthesizing a third double-stranded nucleic acid molecule from a first primer, a second primer and said second double-stranded nucleic acid molecule.

12. The method of claim 11 , wherein said first primer and said second primer are present in unequal amounts during said synthesizing.

13. A method for nucleic acid processing, comprising:

(a) bringing an invader in contact with a first double-stranded nucleic acid molecule under conditions sufficient to bind said invader to at least a portion of a strand of said first double-stranded nucleic acid molecule and expose a segment of said strand, which invader is unextendible during nucleic acid extension;

(b) coupling an oligonucleotide to said segment;

(c) performing an extension reaction along 5′ to 3′ direction of said oligonucleotide to generate a second double-stranded nucleic acid molecule comprising said strand and an additional strand that is complementary to at least a portion of said strand; and

(d) electronically identifying a sequence of said second double-stranded nucleic acid molecule or derivative thereof.

14. The method of claim 13 , wherein said extension reaction is performed using said oligonucleotide as a primer.

15. The method of claim 13 , wherein said invader comprises a nucleic acid molecule.

16. The method of claim 13 , wherein said invader comprises an enzyme.

17. The method of claim 16 , wherein said enzyme is a recombinase.

18. The method of claim 13 , wherein said first double-stranded nucleic acid molecule is coupled to a support.

19. The method of claim 18 , wherein said support is a particle.

20. The method of claim 18 , wherein said support is planar.

21. The method of claim 15 , wherein said invader comprises a 3′-modification that renders said invader unextendible.

22. The method of claim 21 , wherein said modification is selected from the group consisting of: a 3′-dideoxynucleotide, a 3′-biotin, a 3′-amino moiety, a 3′-phosphate, a 3′-dithiol, a 3′-dark quencher, a 3′-fluorophore and a 3′-spacer.

23. The method of claim 13 , wherein (a)-(c) are performed isothermally.

24. The method of claim 13 , wherein (c) is performed with aid of a strand-displacing polymerase.

25. The method of claim 13 , further comprising synthesizing a third double-stranded nucleic acid molecule from a first primer, a second primer and said second double-stranded nucleic acid molecule.

26. The method of claim 25 , wherein said first primer and said second primer are present in unequal amounts during said synthesizing.

27. The method of claim 1 , wherein said electronically identifying in (d) comprises detecting an electronic signal indicative of nucleotide incorporation.

28. The method of claim 1 , wherein said electronically identifying in (d) comprises measuring a change in charge, a change in impedance, or a change in conductivity indicative of nucleotide incorporation.

29. The method of claim 28 , wherein said electronically identifying in (d) comprises measuring said change in impedance.

30. The method of claim 28 , wherein said electronically identifying in (d) comprises measuring said change in charge.

31. The method of claim 28 , wherein said electronically identifying in (d) comprises measuring said change in conductivity.

32. The method of claim 13 , wherein said electronically identifying in (d) comprises detecting an electronic signal indicative of nucleotide incorporation.

33. The method of claim 13 , wherein said electronically identifying in (d) comprises measuring a change in charge, a change in impedance, or a change in conductivity indicative of nucleotide incorporation.

34. The method of claim 33 , wherein said electronically identifying in (d) comprises measuring said change in impedance.

35. The method of claim 33 , wherein said electronically identifying in (d) comprises measuring said change in charge.

36. The method of claim 33 , wherein said electronically identifying in (d) comprises measuring said change in conductivity.