Patent ID: 8841075
Filing Date: 2014-09-23
Classification: C12Q

Abstract:
1. A method for detecting pairing between homologous nucleic acid (DNA) sequences comprising: providing a system containing DNA species; forming inverted repeats from homologous pairing partners in a portion of the DNA species that include a homologous sequence that is spatially juxtaposed with another homologous sequence wherein forming inverted repeats from homologous pairing partners is performed by generating head-to-head ligation products, whereby the DNA species not including juxtaposed homologous sequences are not converted into inverted repeats; forming hairpin DNA molecules from the inverted repeats by rapid intrastrand annealing; forming single stranded DNA molecules from another portion of the DNA species that do not contain inverted repeats; separating the single stranded DNA molecules from the hairpin DNA molecules, thereby enabling detection of pairing between homologous DNA sequences; wherein rapid intrastrand annealing is performed by denaturation followed by renaturation, and denaturation and renaturation are carried out under conditions that (i) promote intramolecular annealing over intermolecular annealing, and that (ii) allow annealing between homologous sequences but discourage annealing between non-homologous sequences.