Methods and compositions for isolating asymmetric nucleic acid complexes

A method for isolating nucleic acid synthesis-competent nucleic acid templates comprising:

• obtaining a sample comprising asymmetrically tagged nucleic acid templates each comprising a double-stranded insert region, a first hairpin adapter at one end, and a second hairpin adapter at the opposite end, wherein the first hairpin adapter comprises a synthesis primer binding site and a capture primer binding site positioned 3′ of the synthesis primer binding site;
• contacting the nucleic acid sample with a capture primer specific for the capture primer binding site under nucleic acid hybridization conditions;
• immobilizing capture primer-hybridized nucleic acid templates to a solid support via a capture region on the capture primer;
• contacting the nucleic acid templates immobilized to the solid support with a nucleic acid polymerase having strand displacement activity under conditions that promote nucleic acid synthesis from a synthesis primer hybridized to the synthesis primer binding site;
• and
• collecting nucleic acid templates eluted from the solid support by the strand displacement activity of the nucleic acid polymerase, thereby isolating nucleic acid synthesis-competent nucleic acid templates.