Patent ID: 7060436

Claim:
A method for selecting a primer, comprising: a) providing: i) a target nucleic acid having at least one accessible site and at least one inaccessible site; ii) a plurality of extension primers, each of said primers comprising a first region, wherein said first regions of said plurality of primers differ in sequence from each other, and wherein said plurality of primers comprise first regions that are complementary to different portions of said target nucleic acid; and iii) a template-dependent nucleic acid extension agent; b) exposing said plurality of extension primers and said extension agent to said target nucleic acid under conditions wherein primers comprising first regions that are complementary only to an inaccessible site in said target nucleic acid are not extended by said extension agent, and wherein primers comprising first regions that are complementary to at least one accessible site of said target nucleic acid form an extension product; c) selecting a primer complementary to at least one accessible site by identifying a member of said plurality of primers that forms an extension product.