Patent ID: 6952651

Claim:
A method comprising: (a) obtaining at least four samples comprising a template nucleic acid; (b) individually incubating the samples of (a) under conditions suitable for synthesizing a nucleic acid sequence complementary to the template nucleic acid, wherein the complementary sequence comprises a type of nucleotide precursor specific to a particular sample and structurally suitable for attachment to a bulky group; (c) labeling the nucleotide precursor of (b) by attaching a bulky group to at least a portion of the nucleotide precursors; (d) prior to, simultaneous with, or subsequent to (c), orienting each complementary nucleic acid sequence generated in (b) such that distances between bulky groups can be measured; (e) measuring the distances between the bulky groups associated with each contiguous complementary sequence in each sample and identifying overlapping distances, wherein the distance is measured by scanning probe microscopy; (f) constructing a distance map for each sample based upon the measurements generated in (e); (g) aligning the distance maps of (f); (h) assembling a nucleic acid sequence of the complementary sequence; and (i) determining the sequence of the template nucleic acid based on the sequence of the complementary sequence.