Single molecule arrays for genetic and chemical analysis
원문보기
IPC분류정보
국가/구분
United States(US) Patent
등록
국제특허분류(IPC7판)
C12Q-001/68
C12M-001/36
C07H-021/04
출원번호
US-0451691
(2006-06-13)
등록번호
US-8445194
(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 :
60인용 특허 :
95
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 plurality of concatemers are randomly disposed on said plurality of said discrete regions, wherein at least a majority of said disc
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 plurality of concatemers are randomly disposed on said plurality of said discrete regions, wherein at least a majority of said discrete regions comprises a single concatemer, wherein at least a majority of said concatemers at said plurality of discrete regions are optically resolvable, andwherein each concatemer comprises a plurality of monomeric units and each monomeric unit comprises: i) a first target sequence of said target polynucleotide;ii) an adaptor comprising a Type IIs endonuclease restriction site, wherein said first target sequence is adjacent to said adaptor;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) detecting said ligated complex thereby identifying a nucleotide of said target polynucleotide;f) stripping off said ligated complex;g) repeating steps (b) through (f) in order to determine said sequence of said target polynucleotide. 2. 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. 3. The method of claim 2, wherein said detectable label comprises a fluorophore. 4. The method of claim 1, wherein said one or more probes from said first set comprise one or more degenerate nucleotides. 5. 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. 6. The method of claim 1, wherein one or more probes of said second set of probes comprise one or more degenerate nucleotides. 7. 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. 8. The method of claim 7, wherein said generating is accomplished using rolling circle replication. 9. The method of claim 7, wherein said fragments substantially cover said target polynucleotide. 10. The method of claim 1, wherein said Type IIs endonuclease is Mmel or Eco P15l. 11. 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 plurality of concatemers are randomly disposed on said plurality of discrete regions, wherein at least a majority of said discrete regions comprises a single concatemer disposed thereon, wherein at least a majority of said concatemers at said plurality of discrete regions are optically resolvable, andwherein each concatemer comprises a plurality of monomeric units and each monomeric unit comprises: i) a first target sequence of said target polynucleotide;ii) an adaptor, wherein said first target sequence is adjacent to said adaptor;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) detecting said ligated complex;thereby identifying said sequence of said target polynucleotide. 12. The method of claim 11, wherein said substrate is formed by a method comprising: a) providing a support comprising a surface, wherein said surface comprises said plurality of discrete regions;b) providing a composition comprising a plurality of DNA concatemers, wherein each concatemer comprises a plurality of monomeric units;c) depositing said composition on said surface, thereby randomly disposing said concatemers on said surface such that a majority of said plurality of discrete regions comprises a concatemer;d) immobilizing said concatemers on said discrete regions. 13. The method of claim 12, wherein said plurality of discrete regions comprise reactive functionalities and said concatemers comprise functionalities complementary to said reactive functionalities, and wherein said immobilizing step (d) occurs by covalent linkages formed between said reactive functionalities and said complementary functionalities. 14. The method of claim 11 wherein said substrate further comprises inter-regional areas between said discrete regions, and said concatemers do not bind to said inter-regional areas. 15. The method of claim 11 wherein said majority of said concatemers are immobilized on said plurality of discrete regions through a noncovalent interaction. 16. The method of claim 15 wherein said concatemers have a diameter that is approximately equal to that of the discrete regions. 17. The method of claim 12 wherein said majority of said concatemers are immobilized on said plurality of discrete regions through a noncovalent interaction. 18. 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 plurality of concatemers are randomly disposed on said plurality of said discrete regions, wherein a at least majority of said discrete regions comprises a single concatemer, wherein said substrate further comprises inter-regional areas between said discrete regions, wherein said concatemers do not bind to said inter-regional areas, wherein at least a majority of said concatemers at said plurality of discrete regions are optically resolvable, andwherein each concatemer comprises a plurality of monomeric units and each monomeric unit comprises:(i) a first target sequence of said target polynucleotide;(ii) an adaptor, wherein said first target sequence is adjacent to said adaptor;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) detecting said ligated complex, thereby identifying a nucleotide of said target polynucleotide;f) stripping off said ligated complex;g) repeating steps (b) through (f) in order to determine said sequence of said target polynucleotide. 19. The method of claim 18, wherein said majority of said concatemers are immobilized on said plurality of discrete regions through a noncovalent interaction. 20. The method of claim 19 wherein said wherein said inter-regional areas are hydrophobic.
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이 특허에 인용된 특허 (95)
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.
Chee Mark ; Cronin Maureen T. ; Fodor Stephen P. A. ; Huang Xiaohua X. ; Hubbell Earl A. ; Lipshutz Robert J. ; Lobban Peter E. ; Morris MacDonald S. ; Sheldon Edward L., Arrays of nucleic acid probes on biological chips.
Whiteley Norman M. (San Carlos CA) Hunkapiller Michael W. (San Carlos CA) Glazer Alexander N. (Orinda CA), Detection of specific sequences in nucleic acids.
Pirrung Michael C. (Durham NC) Read J. Leighton (Palo Alto CA) Fodor Stephen P. A. (Palo Alto CA) Stryer Lubert (Stanford CA), Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof.
Albrecht Glenn ; Brenner Sydney,GBX ; DuBridge Robert B. ; Lloyd David H. ; Pallas Michael C., Massively parallel signature sequencing by ligation of encoded adaptors.
Adams Christopher P. (Winter Hill MA) Kron Stephen Joseph (Boston MA), Method for performing amplification of nucleic acid with two primers bound to a single solid support.
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.
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.
Drmanac Radoje T. (Zvecanska 46 Beograd 11000) Crkvenjakov Radomir B. (Bulevar JNA 118 Beograd YUX 11000), Method of sequencing of genomes by hybridization of oligonucleotide probes.
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.
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