Single molecule arrays for genetic and chemical analysis
IPC분류정보
국가/구분
United States(US) Patent
등록
국제특허분류(IPC7판)
C12Q-001/68
C12P-019/34
C12M-001/36
C07H-021/04
출원번호
US-0982467
(2007-10-31)
등록번호
US-8445197
(2013-05-21)
발명자
/ 주소
Drmanac, Radoje
Callow, Matthew J.
Drmanac, Snezana
Hauser, Brian K.
Yeung, George
출원인 / 주소
Callida Genomics, Inc.
대리인 / 주소
Kilpatrick Townsend & Stockton LLP
인용정보
피인용 횟수 :
11인용 특허 :
96
초록▼
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 discre
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. Preferably, such regions have areas substantially less than 1 μm2 and have nearest neighbor distances that permit optical resolution of on the order of 109 single molecules per cm2. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.
대표청구항▼
1. A method of identifying a sequence of a target polynucleotide, said method comprising: (a) providing a substrate comprising a plurality of discrete regions,wherein a majority of said plurality of discrete regions comprises a single concatemer comprising a plurality of monomeric units,wherein each
1. A method of identifying a sequence of a target polynucleotide, said method comprising: (a) providing a substrate comprising a plurality of discrete regions,wherein a majority of said plurality of discrete regions comprises a single concatemer comprising a plurality of monomeric units,wherein each monomeric unit comprises a first target sequence of said target polynucleotide and an adaptor, and said first target sequence is adjacent to said adaptor,and wherein said substrate is prepared by a photolithography method such that said plurality of discrete regions comprise a functional group for non-covalent attachment of said concatemer;(b) applying a first set of probes to said substrate, such that one or more probes from said first set hybridizes to said adaptor;(c) applying a second set of probes to said substrate, such that one or more probes from said second set hybridizes to said first target sequence;(d) ligating probes from said first set and probes from said second set that are hybridized to adjacent sequences of said monomeric unit to form a ligated complex;e) detected said ligated complex, thereby identifying a nucleotide of said target polynucleotide;(f) removing said ligated complex;(g) repeating steps (b) through (f) to determine said sequence of said target polynucleotide. 2. The method of claim 1, wherein said substrate is a planar material that comprises silica. 3. The method of claim 1, wherein said functional group comprises an amine group. 4. The method of claim 3, wherein said amine group is an amino group. 5. The method of claim 1, wherein one or more probes from said first set or from said second set comprise a detectable label and wherein detecting said ligated complex comprises detecting said detectable label. 6. The method of claim 5, wherein said detectable label comprises a fluorophore. 7. The method of claim 1, wherein one or more probes from said first set comprise one or more degenerate nucleotides. 8. The method of claim 1, wherein forming said ligated complex produces a detectable signal, and wherein said detecting step (e) comprises detecting said detectable signal. 9. The method of claim 1, wherein said concatemers are formed by a method comprising: (a) providing fragments of said target polynucleotide;(b) ligating an adaptor to a terminus of a plurality of said fragments;(c) circularizing said fragments ligated to said adaptors to form circular products;(d) generating a concatemer from at least one of said circular products, thereby forming said concatemers. 10. The method of claim 9, wherein said generating is through a rolling circle replication reaction. 11. The method of claim 9, wherein said fragments substantially cover said target polynucleotide. 12. The method of claim 1, wherein at least 70% of said plurality of discrete regions comprise a single concatemer. 13. The method of claim 1, wherein said target polynucleotide is human genomic DNA.
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이 특허에 인용된 특허 (96)
Barany, Francis; Liu, Jianzhao; Kirk, Brian W.; Zirvi, Monib; Gerry, Norman P.; Paty, Philip B., Accelerating identification of single nucleotide polymorphisms and alignment of clones in genomic sequencing.
Birkenmeyer Larry G. (Chicago IL) Carrino John J. (Gurnee IL) Dille Bruce J. (Antioch IL) Hu Hsiang-Yun (Libertyville IL) Kratochvil Jon D. (Kenosha WI) Laffler Thomas G. (Libertyville IL) Marshall R, Amplification of target nucleic acids using gap filling ligase chain reaction.
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Albrecht Glenn ; Brenner Sydney,GBX ; DuBridge Robert B. ; Lloyd David H. ; Pallas Michael C., Massively parallel signature sequencing by ligation of encoded adaptors.
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Rothberg,Jonathan M.; Bader,Joel S.; Dewell,Scott B.; McDade,Keith; Simpson,John W.; Berka,Jan; Colangelo,Christopher M., Method of sequencing a nucleic acid.
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Brennan Thomas M. (2000 Broadway ; No. 705 San Francisco CA 94115) Heyneker Herbert L. (360 Forest Ave. ; No. 506 Palo Alto CA 94301), Methods and compositions for determining the sequence of nucleic acids.
Drmanac Radoje T. ; Drmanac Snezana ; Hou Aaron ; Hauser Brian, Methods for sequencing repetitive sequences and for determining the order of sequence subfragments.
Heller Michael J. (Encinitas CA) Tu Eugene (San Diego CA) Butler William F. (Carlsbad CA), Molecular biological diagnostic systems including electrodes.
Urdea Michael S. (Alamo CA) Warner Brian (Martinez CA) Horn Thomas (Berkeley CA), Nucleic acid multimers and amplified nucleic acid hybridization assays using same.
Newman Peter J. (Shorewood WI) Aster Richard H. (Milwaukee WI), Polymorphism of human platelet membrane glycoprotein IIIa and diagnostic and therapeutic applications thereof.
Neuschafer Dieter,CHX ; Duveneck Gert Ludwig,GBX ; Pawlak Michael,GBX ; Pieles Uwe,GBX ; Budach Wolfgang,CHX, Sensor platform and method for the parallel detection of a plurality of analytes using evanescently excited luminescence.
Rabbani,Elazar; Stavrianopoulos,Jannis G.; Kirtikar,Dollie; Johnston,Kenneth H.; Thalenfeld,Barbara E., System, array and non-porous solid support comprising fixed or immobilized nucleic acids.
Kermani, Bahram Ghaffarzadeh; Drmanac, Radoje, Analyzing genome sequencing information to determine likelihood of co-segregating alleles on haplotypes.
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