METHODS AND RELATED DEVICES FOR SINGLE MOLECULE WHOLE GENOME ANALYSIS
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Abstract
Provided are methods of labeling and analyzing features along at least one macromolecule such as a linear biopolymer, including methods of mapping the distribution and frequency of specific sequence motifs or the chemical or proteomic modification state of such sequence motifs along individual unfolded nucleic acid molecules. The present invention also provides methods of identifying signature patterns of sequence or epigenetic variations along such labeled macromolecules for direct massive parallel single molecule level analysis. The present invention also provides systems suitable for high throughput analysis of such labeled macromolecules.
13 Citations
59 Claims
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1-39. -39. (canceled)
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40. A method for generating a pattern of sequence-related structural features of a double stranded DNA, comprising:
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nicking one strand of a double stranded DNA at a nick site by an agent capable of introducing a single stranded break; labeling the nicked DNA at or about the nick site; ligating the labeled DNA with a ligase; and detecting the label on the labeled DNA to generate a pattern of sequence-related structural features of the double stranded DNA. - View Dependent Claims (41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 58, 59)
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51. A method for generating a pattern of sequence-related structural features of a double-stranded DNA, comprising:
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nicking the double-stranded DNA with a site-specific nicking enzyme without breaking the other strand; incorporating one or more bases into the nicking site of the nicked DNA, wherein incorporating the bases comprises contacting the nicked DNA with; a. a polymerase; b. one or more nucleotides; and c. a ligase. wherein at least one said nucleotide is labeled, thus labeling the DNA; and detecting the label on the labeled DNA to generate a pattern of sequence-related structural features of the DNA. - View Dependent Claims (52, 53, 54, 55, 56, 57)
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Specification