METHODS FOR SINGLE-MOLECULE ANALYSIS

1 - 36 . (canceled)

37 . A method of characterizing a DNA, the method comprising:

nicking a first DNA at a first sequence motif, wherein the first DNA is double stranded, and wherein the first DNA remains double-stranded adjacent to the nicks;

labeling the nicks on the first DNA with a first label;

marking the labeled first DNA with a third label, wherein the third label is non-sequence-specific, and wherein the third label is different from the first label;

linearizing the first DNA following labeling with the first and third labels; and

detecting the pattern of the first label on the linearized first DNA.

38 . The method of claim 37 , further comprising repairing the nicks on the first DNA.

39 . The method of claim 37 , further comprising:

nicking a second DNA at the first sequence motif;

labeling the nicks on the second DNA with the first label;

repairing the nicks on the second DNA;

marking the repaired second DNA with the third label;

linearizing the second DNA following labeling with the first and third labels; and

detecting the pattern of the first label on the linearized second DNA.

40 . The method of claim 37 , further comprising:

nicking the repaired first DNA at a second sequence motif, wherein the repaired first DNA remains double-stranded adjacent to the nicks;

labeling the nicks at the second sequence motif on the first DNA with a second label, wherein the third label is different from the second label; and

repairing the nicks on the first DNA following labeling with the second label.

41 . The method of claim 40 , wherein the first label and second label comprise the same label.

42 . The method of claim 37 , wherein the first DNA and the second DNA are each from the same source.

43 . The method of claim 37 , wherein the linearizing comprises transporting the DNA into a nanochannel.

44 . The method of claim 37 , further comprising comparing the pattern of the first labels to a pattern of labels on a reference DNA.

45 . The method of claim 37 , wherein nicking the first DNA comprises nicking with Nt.BpsQI.

46 . The method of claim 37 , wherein the first label is selected from the group consisting of a fluorophore, a quantum dot, a dendrimer, a nanowire, a bead, a hapten, a streptavidin, an avidin, a neutravidin, a biotin, and a reactive group.

47 . The method of claim 37 , wherein the first label does not comprise a fluorophore, and wherein the first label does not comprise a quantum dot.

48 . A method of characterizing DNA, the method comprising:

nicking one strand of a first DNA at a recognition sequence with a first nicking endonuclease, wherein the first DNA is double stranded, and wherein the first DNA remains double-stranded adjacent to the nicks;

labeling the first DNA at the nicking sites with a first label;

repairing the nicks on the first DNA;

nicking a complementary strand of a second DNA at the recognition sequence with a second nicking endonuclease, wherein the complementary strand of the second DNA is complementary to the one strand of the first DNA, wherein the second DNA is double stranded, and wherein the second DNA remains double-stranded adjacent to the nicks;

labeling the second DNA at the nicking sites with a second label;

repairing the nicks on the second DNA;

marking the repaired first and second DNA with a third label, wherein the third label is non-sequence specific;

linearizing the marked first DNA and marked second DNA; and

detecting a pattern of the first and second label on the linearized first DNA and linearized second DNA.

49 . The method of claim 48 , further comprising:

nicking one strand of a third DNA at a recognition sequence with the first nicking endonuclease, wherein the third DNA is double stranded, and wherein the third DNA remains double-stranded adjacent to the nicks;

labeling the third DNA at the nicking sites;

repairing the nicks on the third DNA;

nicking a complementary strand of a fourth DNA at the recognition sequence with the second nicking endonuclease, wherein the complementary strand of the fourth DNA is complementary to the one strand of the third DNA;

labeling the fourth DNA at the nicking sites;

repairing the nicks on the fourth DNA; and

marking the repaired third and fourth DNAs with a third label, wherein the third label comprises a non-sequence-specific label.

50 . The method of claim 48 , wherein the first DNA and second DNA are each from the same source.

51 . The method of claim 48 , wherein the first DNA and second DNA are each from a first source, and wherein the second and third DNA are each from a second source.

52 . The method of claim 48 , wherein the first label and second label comprise the same label.

53 . The method of claim 48 , wherein the first label is selected from the group consisting of a fluorophore, a quantum dot, a dendrimer, a nanowire, a bead, a hapten, a streptavidin, an avidin, a neutravidin, a biotin, and a reactive group.

54 . The method of claim 48 , wherein the first label does not comprise a fluorophore, and wherein the first label does not comprise a quantum dot.

55 . The method of claim 48 , wherein the linearizing includes transporting the DNA into a nanochannel.

56 . A method of characterizing a DNA comprising a double-stranded DNA comprising at least one base flap on either strand of the DNA, the method comprising: treating the double-stranded DNA with a 5′ to 3′ exonuclease activity of a polymerase under conditions wherein at least one species of dNTP is present in limited concentration or omitted compared to other dNTPs that are present;

ligating the nicks to restore strand integrity at flap regions; and

characterizing the DNA.