Single molecule arrays for genetic and chemical analysis
원문보기
IPC분류정보
국가/구분
United States(US) Patent
등록
국제특허분류(IPC7판)
C12Q-001/68
C07H-021/04
C12M-001/36
출원번호
US-0981767
(2007-10-31)
등록번호
US-8445196
(2013-05-21)
발명자
/ 주소
Drmanac, Radoje T.
Callow, Matthew J.
Drmanac, Snezana
Hauser, Brian K.
Yeung, George
출원인 / 주소
Callida Genomics, Inc.
대리인 / 주소
Kilpatrick Townsend & Stockton LLP
인용정보
피인용 횟수 :
6인용 특허 :
94
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 random array of concatemers, wherein said random array comprises: (a) a solid substrate comprising a surface, wherein said surface comprises a plurality of discrete spaced apart regions defined on said surface, wherein said discrete spaced apart regions are separated by inter-regional areas;(b)
1. A random array of concatemers, wherein said random array comprises: (a) a solid substrate comprising a surface, wherein said surface comprises a plurality of discrete spaced apart regions defined on said surface, wherein said discrete spaced apart regions are separated by inter-regional areas;(b) concatemers randomly disposed on said plurality of discrete spaced apart regions such that at least a majority of said plurality of discrete spaced apart regions comprises a single concatemer immobilized thereon and said concatemers do not bind to said inter-regional areas,wherein said concatemers comprise a plurality of monomeric units and each monomeric unit comprises:(i) a first target sequence of a target polynucleotide of unknown sequence;(ii) an adaptor comprising a Type Ils endonuclease restriction site, wherein said first target sequence is adjacent to said adaptor; andwherein each said single concatemer is immobilized on a discrete spaced apart region by attractive noncovalent interactions between said discrete spaced apart region and multiple monomeric units of said single concatemer. 2. The random array of claim 1, wherein said plurality of concatemers are immobilized on said discrete spaced apart regions through attractive noncovalent interactions. 3. The random array of claim 2, wherein said attractive noncovalent interactions are a member selected from Van der Waal forces, hydrogen bonding, ionic and hydrophobic interactions. 4. The random array of claim 1, wherein said surface comprises silica. 5. The random array of claim 4, wherein said discrete spaced apart regions comprise functional moieties. 6. The random array of claim 5, wherein said functional moieties comprise amines. 7. The random array of claim 1, wherein said adaptor further comprises a palindrome. 8. The random array of claim 1, wherein a majority of said concatemers disposed on said discrete spaced apart regions have a nearest neighbor distance of about 50 nanometers or greater. 9. The random array of claim 8, wherein said majority of said concatemers have a nearest neighbor distance of about 200 nanometers or greater. 10. The random array of claim 1, wherein said majority of said concatemers are disposed on said discrete spaced apart regions at a density of at least 1000 per μm2. 11. A random array of concatemers, wherein said random array comprises: (a) a solid substrate comprising a surface, wherein said surface comprises a plurality of discrete spaced apart regions defined on said surface, wherein said discrete spaced apart regions are separated by inter-regional areas;(b) concatemers randomly disposed on said plurality of discrete spaced apart regions such that at least a majority of said discrete spaced apart regions comprises a single concatemer immobilized thereon and said concatemers do not bind to said inter-regional areas, wherein said concatemers are immobilized on said discrete spaced apart regions through attractive noncovalent interactions, andwherein said concatemers comprise a plurality of monomeric units and each monomeric unit comprises:(i) a first target sequence of a target polynucleotide of unknown sequence;(ii) an adaptor, wherein said first target sequence is adjacent to said adaptor; andwherein each said single concatemer is immobilized on a discrete spaced apart region by attractive noncovalent interactions between said discrete spaced apart region and multiple monomeric units of said single concatemer. 12. The random array of claim 11, wherein said attractive noncovalent interactions are a member selected from Van der Waal forces, hydrogen bonding, ionic and hydrophobic interactions. 13. The random array of claim 11, wherein said discrete spaced apart regions comprise functional moieties. 14. The random array of claim 13, wherein said functional moieties comprise amines. 15. A random array of concatemers, wherein said random array comprises: (a) a solid substrate comprising a surface, wherein said surface comprises a plurality of discrete spaced apart regions defined on said surface, wherein said discrete spaced apart regions are separated by inter-regional area;(b) concatemers randomly disposed on said plurality of discrete spaced apart regions such that at least a-majority of said plurality of discrete spaced apart regions comprises a single concatemer immobilized thereon and said concatemers do not bind to said interregional areas, wherein said concatemers are immobilized on said discrete spaced apart regions through attractive noncovalent interactions, andwherein said concatemers comprise a plurality of monomeric units and each monomeric unit comprises:(i) a first target sequence of a target polynucleotide of unknown sequence;(ii) an adaptor comprising a Type IIs endonuclease restriction site, wherein said first target sequence is adjacent to said adaptor; andwherein each said single concatemer is immobilized on a discrete spaced apart region by attractive noncovalent interactions between said discrete spaced apart region and multiple monomeric units of said single concatemer. 16. The random array of claim 15, wherein said concatemers are generated from a circular template, wherein said circular template comprises said adaptor and said first target sequence. 17. The random array of claim 15, wherein said target polynucleotide is a genomic sequence. 18. The random array of claim 15, wherein substantially all of said plurality of discrete spaced apart regions have at most a single concatemer attached. 19. The random array of claim 1, 11, or 15, wherein said discrete spaced apart regions are prepared by photolithography. 20. The random array of claim 1, 11, or 15, wherein said inert interregional areas comprise hydrophobic barriers. 21. The random array of claim 11, wherein said discrete spaced apart regions are arranged on said surface in a rectilinear pattern.
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이 특허에 인용된 특허 (94)
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.
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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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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.
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