Methods for generating target specific probes for solution based capture
First Claim
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1. A method for generating a population of single-stranded nucleic acid probes, each probe comprising a predetermined nucleotide sequence, the method comprising:
- a) providing a starting population of linear double-stranded nucleic acid precursor molecules each precursor molecule having (i) a probe region having the predetermined sequence which is flanked at a 5′ and
a 3′
end by a first and a second restriction enzyme recognition sequence for generating ligation substrates and for ligating a plurality of the double-stranded nucleic acid precursor molecules into head-to-tail concatemers (ii) the 5′
flanking region including the first restriction enzyme recognition sequence and (iii) the 3′
flanking region including the second restriction enzyme recognition sequence;
b) contacting the 5′ and
3′
flanking regions of the linear double-stranded nucleic acid precursor molecules with a first and a second restriction enzyme to cleave the first and second restriction enzyme recognition sequences so as to generate ligation substrates;
c) ligating the ligation substrates together so as to generate a plurality of random head-to-tail concatemers;
d) amplifying the plurality of head-to-tail concatemers;
e) contacting the amplified head-to-tail concatemers with the first and second restriction enzymes so as to release a plurality of double-stranded monomer linear precursor molecules; and
f) selectively removing one strand of the double-stranded monomer linear precursor molecules so as to generate a population of single-stranded nucleic acid probes, each probe comprising the predetermined nucleotide sequence.
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Abstract
Provided herein are compositions and kits for single-stranded nucleic acid probes, and methods for making the single-stranded nucleic acid probes, where the single-stranded nucleic acid probes comprise a probe region having a predetermined sequence which is flanked by a 5′ region having a first restriction enzyme recognition sequence and flanked by a 3′ region having a second restriction enzyme recognition sequence, and a region which hybridizes to a capture nucleic acid molecule. The single-stranded nucleic acid probes are useful for solution-based capture methods.
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Citations
28 Claims
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1. A method for generating a population of single-stranded nucleic acid probes, each probe comprising a predetermined nucleotide sequence, the method comprising:
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a) providing a starting population of linear double-stranded nucleic acid precursor molecules each precursor molecule having (i) a probe region having the predetermined sequence which is flanked at a 5′ and
a 3′
end by a first and a second restriction enzyme recognition sequence for generating ligation substrates and for ligating a plurality of the double-stranded nucleic acid precursor molecules into head-to-tail concatemers (ii) the 5′
flanking region including the first restriction enzyme recognition sequence and (iii) the 3′
flanking region including the second restriction enzyme recognition sequence;b) contacting the 5′ and
3′
flanking regions of the linear double-stranded nucleic acid precursor molecules with a first and a second restriction enzyme to cleave the first and second restriction enzyme recognition sequences so as to generate ligation substrates;c) ligating the ligation substrates together so as to generate a plurality of random head-to-tail concatemers; d) amplifying the plurality of head-to-tail concatemers; e) contacting the amplified head-to-tail concatemers with the first and second restriction enzymes so as to release a plurality of double-stranded monomer linear precursor molecules; and f) selectively removing one strand of the double-stranded monomer linear precursor molecules so as to generate a population of single-stranded nucleic acid probes, each probe comprising the predetermined nucleotide sequence. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
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Specification