Methods and compositions for isolating template nucleic acids
First Claim
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1. A method for isolating circular template nucleic acids containing one or more target sequences from a mixture of nucleic acids, said method comprising:
- (a) providing a population of nucleic acid constructs, said constructs comprising circular template nucleic acids, wherein a plurality of said circular template nucleic acids comprises said one or more target sequences;
(b) amplifying said population of nucleic acid constructs with a strand displacing polymerase to produce amplified template nucleic acids, wherein said amplified template nucleic acids each comprise one of said circular template nucleic acids hybridized to a linear nascent strand comprising at least one copy of a sequence complementary to said one or more target sequences;
(c) associating one or more affinity handles with said amplified template nucleic acids, wherein said one or more affinity handles comprises an affinity oligonucleotide moiety and a retrieval moiety, wherein said affinity oligonucleotide moiety hybridizes to said at least one copy of a sequence complementary to said one or more target sequences;
(d) separating amplified template nucleic acids associated with said affinity handles from amplified template nucleic acids not associated with said affinity handles using said retrieval moieties;
(e) after said separating, treating said amplified template nucleic acids such that said circular template nucleic acids are separated from said linear nascent strands; and
(f) isolating said circular template nucleic acids containing one or more target sequences from the mixture of nucleic acids.
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Abstract
The present invention is directed to methods and compositions for isolating template nucleic acids containing target sequences of interest, wherein those isolated template nucleic acids can be further assessed for information related to sequence and nucleic acid modifications.
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13 Claims
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1. A method for isolating circular template nucleic acids containing one or more target sequences from a mixture of nucleic acids, said method comprising:
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(a) providing a population of nucleic acid constructs, said constructs comprising circular template nucleic acids, wherein a plurality of said circular template nucleic acids comprises said one or more target sequences; (b) amplifying said population of nucleic acid constructs with a strand displacing polymerase to produce amplified template nucleic acids, wherein said amplified template nucleic acids each comprise one of said circular template nucleic acids hybridized to a linear nascent strand comprising at least one copy of a sequence complementary to said one or more target sequences; (c) associating one or more affinity handles with said amplified template nucleic acids, wherein said one or more affinity handles comprises an affinity oligonucleotide moiety and a retrieval moiety, wherein said affinity oligonucleotide moiety hybridizes to said at least one copy of a sequence complementary to said one or more target sequences; (d) separating amplified template nucleic acids associated with said affinity handles from amplified template nucleic acids not associated with said affinity handles using said retrieval moieties; (e) after said separating, treating said amplified template nucleic acids such that said circular template nucleic acids are separated from said linear nascent strands; and (f) isolating said circular template nucleic acids containing one or more target sequences from the mixture of nucleic acids. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
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Specification