First Passage Time Study of DNA Strand Displacement

DNA strand displacement is a process by which duplex invaded single-stranded nucleic acid, annealing to one and displacing the other. Strand has many applications in nanoengineering fundamental biological processes such as homologous recombination repair of double breaks. previously been studied bulk; however, slow, bimolecular toehold formation step obscures kinetics bulk studies. Here, we describe single-molecule FRET assay dubbed “fission” allows us study first passage time directly. We report an average recorded 35ms for short (14bp) invasion domains. show that times depend on sequence invader, differing up factor 13, complimentary invaders can yield different mean times. demonstrate extending length invading slows down invasion. Substituting with RNA, identical except T->U substitution, also affects The salt concentration buffer, does not appear have effect. Finally, fit one-dimensional random walk model our data, providing rates each four bases.