METHODS FOR MAKING NUCLEOTIDE PROBES FOR SEQUENCING AND SYNTHESIS
First Claim
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1. A method of making a plurality of probes for analyzing a plurality of nucleic acid samples comprising the steps of:
- providing linear, single stranded DNA encoding a plurality of probes, wherein a probe includes two regions of homology to target genomic DNA at the ends of the probe and two PCR primer regions common to all probes;
converting the linear, single stranded DNA to circular DNA;
amplifying the circular DNA; and
releasing the plurality of probes from the amplified DNA.
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Abstract
Compositions and methods for making a plurality of probes for analyzing a plurality of nucleic acid samples are provided. Compositions and methods for analyzing a plurality of nucleic acid samples to obtain sequence information in each nucleic acid sample are also provided.
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Citations
88 Claims
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1. A method of making a plurality of probes for analyzing a plurality of nucleic acid samples comprising the steps of:
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providing linear, single stranded DNA encoding a plurality of probes, wherein a probe includes two regions of homology to target genomic DNA at the ends of the probe and two PCR primer regions common to all probes; converting the linear, single stranded DNA to circular DNA; amplifying the circular DNA; and releasing the plurality of probes from the amplified DNA. - View Dependent Claims (2, 5, 6, 7, 8, 9, 10, 12, 13, 82, 86)
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3-4. -4. (canceled)
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11. (canceled)
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14. A method of making a plurality of probes comprising the steps of:
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providing linear, single stranded DNA encoding a plurality of probes, wherein a probe includes two regions of homology to target genomic DNA at the ends of the probe and two PCR primer regions common to all probes; converting the linear, single stranded DNA to circular DNA; amplifying the circular DNA to form amplified double stranded, circular DNA; converting the amplified double stranded, circular DNA to single stranded, circular DNA; and releasing the plurality of probes from the single stranded, circular DNA. - View Dependent Claims (15, 18, 21, 22, 23, 24, 25, 26, 83, 84, 85)
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16-17. -17. (canceled)
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19-20. -20. (canceled)
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27. A method of making a renewable pool of probes for analyzing a plurality of nucleic acid samples comprising the steps of:
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providing a plurality of linear, single stranded DNA probes, wherein a probe includes two regions of homology to target genomic DNA at its ends, two PCR primer regions common to all probes; converting the linear, single stranded DNA to circular DNA; amplifying the circular DNA by rolling circle amplification to form linear concatemers; digesting the linear concatemers to form monomers; and ligating the monomers to form a plurality of circular molecules complementary to either the plus strand or the minus strand of the circular DNA. - View Dependent Claims (28, 87)
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29-81. -81. (canceled)
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88. A method of making a plurality of probes comprising the steps of:
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providing linear, single stranded DNA encoding a plurality of probes, wherein a probe includes two regions of homology to target genomic DNA at the ends of the probe and two PCR primer regions common to all probes; amplifying the linear, single stranded DNA to form amplified, linear, double stranded DNA; converting the amplified, linear, double stranded DNA to linear, single stranded DNA; and releasing the plurality of probes from the linear, single stranded DNA.
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Specification