Compositions and Methods for Intramolecular Nucleic Acid Rearrangement

A method of sample analysis, comprising:

• a) annealing a reflex sequence in a polynucleotide strand in a sample with a complement of the reflex sequence present in the polynucleotide strand, wherein the polynucleotide strand comprises the following in a 5′ to 3′ orientation:
• a first domain;
• the reflex sequence;
• a polynucleotide of interest having a desired site that is distal to the first domain;
• and
• the complement of the reflex sequence, wherein the complement of the reflex sequence is present at the 3′ end of the polynucleotide strand;
• b) extending from the 3′ end of the complement of the reflex sequence through the first domain to produce a double stranded region comprising a complement of the first domain at the 3′ end of the extended polynucleotide strand, thereby moving the first domain into proximity with the desired site;
• and
• c) amplifying the desired site from the polynucleotide strand of step b) using a first nucleic acid synthesis primer that anneals at the 3′ end of the complement of the first domain and a second nucleic acid synthesis primer that comprises a 3′ priming domain that is complementary to a site within the polynucleotide of interest.