Dna array
AssigneeComplete Genomics, Inc.
InventorsRadoje Drmanac, Matthew J. Callow, Snezana Drmanac, Brian K. Hauser, George Yeung
Life of this patent
Estimating the term…
Abstract
Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer.
Claims22
An array of polymer molecules comprising:
- a support having a surface;
- and a plurality of polymer molecules attached to the surface, wherein each polymer molecule has a random coil state and comprises a branched or linear structure of multiple copies of one or more linear polymeric units, such that the polymer molecule is attached to the surface within a region substantially equivalent to a projection of the random coil on the surface and randomly disposed at a density such that at least thirty percent of the polymer molecules are separately detectable.
An array of polynucleotide molecules comprising:
- a support having a surface;
- and a plurality of polynucleotide molecules attached to the surface, wherein each polynucleotide molecule has a random coil state and comprises a concatemer of multiple copies of a target sequence such that the polynucleotide molecule is attached to the surface within a region substantially equivalent to a projection of the random coil on the surface and randomly disposed at a density such that at least thirty percent of the polynucleotide molecules have a nearest neighbor distance of at least fifty nm.
20-69. (canceled)
A method of determining a nucleotide sequence of a target polynucleotide, the method comprising the steps of:
- (a) generating a plurality of target concatemers from the target polynucleotide, each target concatemer comprising multiple copies of a fragment of the target polynucleotide and the plurality of target concatemers including a number of fragments that substantially covers the target polynucleotide;
- (b) forming a random array of target concatemers fixed to a surface at a density such that at least a majority of the target concatemers are optically resolvable;
- (c) hybridizing one or more probes from a first set of probes to the random array under conditions that permit the formation of perfectly matched duplexes between the one or more probes and complementary sequences on target concatemers;
- (d) hybridizing one or more probes from a second set of probes to the random array under conditions that permit the formation of perfectly matched duplexes between the one or more probes and complementary sequences on target concatemers;
- (e) ligating probes from the first and second sets hybridized to a target concatemer at contiguous sites;
- (f) identifying the sequences of the ligated first and second probes;
- and (g) repeating steps (c) through (f) until the sequence of the target polynucleotide can be determined from the identities of the sequences of the ligated probes.
71-73. (canceled)
Dependencies are inferred from the claim text.