Single Molecule Arrays for Genetic and Chemical Analysis
First Claim
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 and, wherein each of said discrete regions has an area;
(b) a population of concatemers randomly disposed on said plurality of discrete regions such that at least a majority of said plurality of discrete regions comprises a single concatemer attached thereto and said inter-regional areas are substantially free of concatemers, wherein said concatemers are generated from a circular template and comprise a plurality of monomeric units, and wherein each monomeric unit comprises;
(i) a first target sequence of a target polynucleotide, and(ii) an adaptor,and wherein said concatemers have a diameter that is approximately equal to that of said discrete spaced apart regions,and wherein said population of concatemers comprises a plurality of different target polynucleotides.
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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. 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.
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Citations
15 Claims
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1. A random array of concatemers, wherein said random array comprises:
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(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 and, wherein each of said discrete regions has an area; (b) a population of concatemers randomly disposed on said plurality of discrete regions such that at least a majority of said plurality of discrete regions comprises a single concatemer attached thereto and said inter-regional areas are substantially free of concatemers, wherein said concatemers are generated from a circular template and comprise a plurality of monomeric units, and wherein each monomeric unit comprises; (i) a first target sequence of a target polynucleotide, and (ii) an adaptor, and wherein said concatemers have a diameter that is approximately equal to that of said discrete spaced apart regions, and wherein said population of concatemers comprises a plurality of different target polynucleotides. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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14. A random array of concatemers, wherein said random array comprises:
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(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, wherein each of said discrete regions has an area; (b) a population of concatemers randomly disposed on said plurality of discrete regions such that at least a majority of said plurality of discrete regions comprises a single concatemer attached thereto, wherein said concatemers are generated from a circular template, wherein said inter-regional areas are substantially free of concatemers, and wherein said concatemers comprise a plurality of monomeric units and each monomeric unit comprises; (i) a first target sequence of a target polynucleotide, and (ii) an adaptor, wherein each of said discrete regions comprise a number of reactive functionalities, and wherein said number is such that a single concatemer occupies substantially all of said number of reactive functionalities, and wherein said population of concatemers comprises a plurality of different target polynucleotides.
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15. A random array of concatemers, wherein said random array comprises:
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(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, wherein each of said discrete regions has an area; (b) a population of concatemers randomly disposed on said plurality of discrete regions, wherein each of said discrete regions has an area corresponding in size to that of said concatemers such that at least a majority of said plurality of discrete regions comprises a single concatemer attached thereto, wherein said inter-regional areas are substantially free of concatemers, and wherein said concatemers comprise a plurality of monomeric units and each monomeric unit comprises; (i) a first target sequence of a target polynucleotide, and (ii) an adaptor, wherein said population of concatemers comprises a plurality of different target polynucleotides.
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Specification