Methods for long-range sequence analysis of nucleic acids
First Claim
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1. A method for sequencing a target nucleic acid, comprising:
- a) generating overlapping fragments of a target nucleic acid;
b) contacting the fragments with an array of capture oligonucleotides under conditions that do not eliminate mismatched hybridization of the fragments to the capture oligonucleotides;
c) measuring the mass of hybridized fragments at each array locus by mass spectrometry; and
d) constructing the nucleotide sequence of the target nucleic acid from the mass measurements.
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Abstract
Provided are methods for sequencing a target nucleic acid by fragmenting a target nucleic acid, hybridizing fragments to an array of capture oligonucleotides, determining the mass of the hybridized fragments, and constructing a nucleotide sequence of the target nucleic acid from the mass measurements.
202 Citations
31 Claims
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1. A method for sequencing a target nucleic acid, comprising:
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a) generating overlapping fragments of a target nucleic acid;
b) contacting the fragments with an array of capture oligonucleotides under conditions that do not eliminate mismatched hybridization of the fragments to the capture oligonucleotides;
c) measuring the mass of hybridized fragments at each array locus by mass spectrometry; and
d) constructing the nucleotide sequence of the target nucleic acid from the mass measurements. - View Dependent Claims (3, 4, 5, 6, 7, 8, 9, 10, 15)
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2. A method for sequencing a target nucleic acid, comprising
a) generating overlapping fragments of a target nucleic acid; -
b) contacting the fragments with an array of capture oligonucleotides, wherein one or more of the capture oligonucleotides are partially degenerate;
c) measuring the mass of fragments hybridized to the capture oligonucleotides at each array position by mass spectrometry; and
d) constructing a nucleotide sequence of the target nucleic acid the mass measurements. - View Dependent Claims (11, 12, 13, 14)
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16. A method for controlling the complexity of a mass spectrum of target nucleic acid fragments, comprising:
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(a) modulating the number of different nucleotide sequences in a first region of target nucleic acid fragments that hybridize to the capture oligonucleotide probe, whereby two or more target nucleic acid fragments containing different nucleotide sequences in the respective first regions hybridize to the capture oligonucleotide probe; and
(b) measuring the mass of the target nucleic acid fragments hybridized to the capture oligonucleotide probe by mass spectrometry, whereby the complexity of the mass spectrum is controlled. - View Dependent Claims (17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29)
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30. A composition for identifying a portion of a target nucleic acid, comprising:
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(a) an array of two or more capture oligonucleotides on a solid support, wherein at least one capture oligonucleotide is partially degenerate; and
(b) a mass spectrometer operably coupled to the array. - View Dependent Claims (31)
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Specification