Positional sequencing by hybridization
First Claim
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1. A method for determining a nucleotide sequence of a nucleic acid target by hybridization comprising the steps of:
- (a) creating a set of nucleic acid probes wherein each probe is 14-50 nucleotides in length and has a double stranded portion, a single stranded portion, and a variable sequence within the single stranded portion which is determinable;
(b) hybridizing the target which is at least partly single stranded to one or more of the nucleic acid probes; and
(c) determining the nucleotide sequence of the target which is hybridized to the single stranded portion of any probe.
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Abstract
This invention is directed to methods for determining a nucleotide sequence of a nucleic acid using positional sequencing by hybridization, and to the creation of nucleic acids probes which may be used with these methods. This invention is also directed to diagnostic aids for analyzing the nucleic acid composition and content of biological samples, including samples derived from medical and agricultural sources.
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Citations
37 Claims
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1. A method for determining a nucleotide sequence of a nucleic acid target by hybridization comprising the steps of:
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(a) creating a set of nucleic acid probes wherein each probe is 14-50 nucleotides in length and has a double stranded portion, a single stranded portion, and a variable sequence within the single stranded portion which is determinable; (b) hybridizing the target which is at least partly single stranded to one or more of the nucleic acid probes; and (c) determining the nucleotide sequence of the target which is hybridized to the single stranded portion of any probe. - View Dependent Claims (3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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2. A method for determining a nucleotide sequence of a nucleic acid target by hybridization comprising the steps of:
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(a) creating a set of nucleic acid probes wherein each probe is 14-50 nucleotides in length and has a double stranded portion, a single stranded portion, and a variable sequence within the single stranded portion which is determinable; (b) hybridizing the target which is at least partly single stranded to one or more of the nucleic acid probes; (c) ligating the hybridized target to the probe; and (d) determining the nucleotide sequence of the target which is hybridized to the single stranded portion of any probe.
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17. A method for determining a nucleotide sequence of a target nucleic acid by hybridization comprising the steps of:
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(a) creating a set of nucleic acid probes wherein each probe is 14-50 nucleotides in length and has a double stranded portion at a 3'"'"'-terminus, a single stranded portion at a 5'"'"'-terminus, and a variable sequence within the single stranded portion which is determinable; (b) hybridizing the target nucleic acid which is at least partly single stranded to the set; (c) enzymatically extending a strand of the probe using the hybridized target as a template; and (d) determining the nucleotide sequence of the single stranded portion of the target nucleic acid. - View Dependent Claims (19, 20, 21, 22, 23, 24, 25)
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18. A method for determining a nucleotide sequence of a target nucleic acid by hybridization comprising the steps of:
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(a) creating a set of nucleic acid probes wherein each probe is 14-50 nucleotides in length and has a double stranded portion at a 3'"'"'-terminus, a single stranded portion at a 5'"'"'-terminus, and a variable sequence within the single stranded portion which is determinable; (b) hybridizing the target nucleic acid which is at least partly single stranded to the set; (c) ligating the hybridized target to the probe; (d) enzymatically extending a strand of the probe using the hybridized target as a template; and (e) determining the nucleotide sequence of the single stranded portion of the target nucleic acid.
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26. A method for determining a nucleotide sequence of a target by hybridization comprising the steps of:
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(a) creating a set of nucleic acid probes wherein each probe is about 14-50 nucleotides in length and has a double-stranded portion, a single-stranded portion, and a variable nucleotide sequence within the single-stranded portion which is determinable; (b) cleaving a plurality of nucleic acid targets to form fragments of various lengths which are at least partly single-stranded; (c) hybridizing the single-stranded region of the fragments with the single-stranded region of the probes; (d) identifying the nucleotide sequences of the hybridized portions of the fragments; and (e) comparing the identified nucleotide sequences to determine the nucleotide sequence of the target. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34, 35, 36)
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27. A method for determining a nucleotide sequence of a target by hybridization comprising the steps of:
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(a) creating a set of nucleic acid probes wherein each probe is about 14-50 nucleotides in length and has a double-stranded portion, a single-stranded portion, and a variable nucleotide sequence within the single-stranded portion which is determinable; (b) cleaving a plurality of nucleic acid targets to form fragments of various lengths which are at least partly single-stranded; (c) hybridizing the single-stranded region of the fragments with the single-stranded region of the probes; (d) ligating the hybridized fragments to the probes; (e) identifying the nucleotide sequences of the hybridized portions of the fragments; and (f) comparing the identified nucleotide sequences to determine the nucleotide sequence of the target.
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37. A method for determining a nucleotide sequence within a nucleic acid fragment comprising the steps of:
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(a) labeling the nucleic acid fragment with a first detectable label at a terminal site and with a second detectable label in a plurality of internal sites; (b) cleaving the labeled nucleic acid fragment into portions; (c) aligning the relative positions of said portions to the nucleic acid fragment by determining the ratio of the first detectable label to the second detectable label; and (d) determining the nucleotide sequence of said portions to determine the nucleotide sequence within said nucleic acid fragment.
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Specification