Random array DNA analysis by hybridization
AssigneeCallida Genomics, Inc.
InventorRadoje T. Drmanac
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Abstract
The invention relates to methods and devices for analyzing single molecules, i.e., nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air, and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.
Claims22
A method for determining sequence information for a polynucleotide, comprising:
- (a) providing an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;
- (b) contacting the array with a set of informative oligonucleotide probes, wherein each probe comprises a label and a nucleotide sequence comprising the formula NxByNz, wherein:
- (i) each N is independently a degenerate base;
- (ii) each B is independently an informative base;
- (iii) x and z are each at least one;
- and
- (iv) y is 2 to 20;
- (c) detecting labeled probes once the probes have hybridized to DNA molecules in the array, thereby obtaining data indicating which of the labeled probes are hybridized to each DNA molecule;
- and
- (d) processing the data to obtain said sequence information for the polynucleotide.
A method for determining sequence information for a polynucleotide, comprising:
- (a) providing an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;
- (b) contacting the array with a first set of informative oligonucleotide probes, wherein each probe comprises a label and a nucleotide sequence comprising the formula NxBy or the formula ByNz, wherein:
- (i) each N is independently a degenerate base;
- (ii) each B is independently an informative base;
- (iii) x and z are each at least one;
- and
- (iv) y is 2 to 20;
- (c) detecting labeled probes from said first set once the probes have hybridized to DNA molecules in the array, thereby obtaining data indicating which of the labeled probes are hybridized to each DNA molecule;
- and
- (d) processing the data to obtain said sequence information for the polynucleotide.
A method for determining sequence information for a polynucleotide, comprising:
- (a) providing an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;
- (b) contacting the array with a first set of informative oligonucleotide probes, wherein each probe comprises a label and a nucleotide sequence comprising the formula NxBy or the formula ByNz, wherein:
- (i) each N is independently a degenerate base;
- (ii) each B is independently an informative base;
- and
- (iii) x, y, and z are each at least one;
- (c) contacting the array with a second set of oligonucleotide probes, each configured to bind to a site in a DNA molecule of the array adjacent to a probe from the first set;
- (d) detecting labeled probes from said first set once oligonucleotide probes from both the first and the second set have hybridized to DNA molecules in the array, thereby obtaining data indicating which of the labeled probes are hybridized to each DNA molecule;
- and
- (e) processing the data to obtain said sequence information for the polynucleotide.
Dependencies are inferred from the claim text.