Directed assembly of amplicons to enhance read pairing signature with massively parallel short read sequencers
First Claim
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1. A method of obtaining an informative desired subset of a complex nucleic acid mixture comprising;
- amplifying the desired subset with a plurality of primer pairs to form a plurality of first amplicons, wherein each of the plurality of primer pairs comprises a forward primer and a reverse primer,(a) wherein the forward primer comprises a first asymmetric adapter, and,(b) wherein the reverse primer comprises a second asymmetric adapter;
cleaving the first asymmetric adapter and the second asymmetric adapter of the plurality of first amplicons to form a plurality of sticky fragments comprising a first sticky end and a second sticky end;
ligating the plurality of sticky fragments to form a concatamer comprising a plurality of sticky fragments bearing a determined orientation;
cleaving the concatamer to form a plurality of cleavage products; and
,obtaining an informative desired subset of the complex nucleic acid mixture.
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Abstract
The present teachings relate to improved methods, kits, and compositions for making nucleic acid libraries and sequencing nucleic acids. In some embodiments, directionally defined concatamers are generated, facilitating sequencing efforts.
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Citations
6 Claims
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1. A method of obtaining an informative desired subset of a complex nucleic acid mixture comprising;
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amplifying the desired subset with a plurality of primer pairs to form a plurality of first amplicons, wherein each of the plurality of primer pairs comprises a forward primer and a reverse primer, (a) wherein the forward primer comprises a first asymmetric adapter, and, (b) wherein the reverse primer comprises a second asymmetric adapter; cleaving the first asymmetric adapter and the second asymmetric adapter of the plurality of first amplicons to form a plurality of sticky fragments comprising a first sticky end and a second sticky end; ligating the plurality of sticky fragments to form a concatamer comprising a plurality of sticky fragments bearing a determined orientation; cleaving the concatamer to form a plurality of cleavage products; and
,obtaining an informative desired subset of the complex nucleic acid mixture. - View Dependent Claims (2, 3, 4, 5)
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6. A method of forming a concatamer containing sticky fragments comprising;
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amplifying a complex nucleic acid sample with a plurality of primer pairs to form a plurality of first amplicons, wherein each of the plurality of primer pairs comprises a forward primer and a reverse primer, (a) wherein the forward primer comprises a first asymmetric adapter, and, (b) wherein the reverse primer comprises a second asymmetric adapter; cleaving the first asymmetric adapter and the second asymmetric adapter of the plurality of first amplicons to form a plurality of sticky fragments comprising a first sticky end and a second sticky end; and
,ligating the plurality of sticky fragments to form a concatamer comprising a plurality of sticky fragments bearing a determined orientation, wherein the ligating does not comprise a vector, and wherein the first asymmetric adapter, the second asymmetric adapter, or both the first and the second asymmetric adapter comprise a phosphorothiolate and wherein the cleaving comprises treating with aqueous Silver.
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Specification