Nucleic acid accessible hybridization sites

A method for identifying accessible sites on a target nucleic acid 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 that is complementary to said target nucleic acid adjacent to said accessible site;
• c) determining at least a portion of the sequence of an extension product;
• and
• d) identifying said accessible site by locating a region of said target nucleic acid adjacent to sequence that is complementary to said extension product.

A method of locating accessible sites on a target nucleic acid 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 first region and second regions, wherein said first regions of said plurality of primers differ in sequence from each other, wherein said plurality of primers comprise first regions that are complementary to different portions of said target nucleic acid, and wherein said second region is located 5′ of said first region;
• iii) a template-dependent nucleic acid extension agent;
• iv) an amplification agent;
• and
• v) first and second amplification primers, said first amplification primer complementary to at least a portion of said second regions of said plurality of extension primers and said second amplification primer capable of hybridizing to a sequence complementary to a first domain of said target nucleic acid;
• 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) treating said extension products with said amplification agent and said first and second amplification primers to generate one or more amplification products, said amplification products having a length, wherein said length of said amplification products provides a distance of an accessible site on said target nucleic acid from said first domain of said target nucleic acid;
• and
• d) determining a location of one or more accessible sites on said target nucleic acid using said distance.

A method for detecting the presence of an HIV target sequence comprising:

• a. providing:
• i. a sample suspected of containing an HIV target sequence;
• and
• ii. an oligonucleotide selected from the group consisting of SEQ ID NOs:160-229;
• b. exposing said sample to said oligonucleotide;
• and
• c. detecting the presence or absence of said HIV target sequence in said sample.