(700a) Investigations of the Effect of Overhang and Strand Length on DNA Hybridization at the Solid-Liquid Interface
This study looks specifically at the effect of strand length and the appearance of overhang on hybridization mechanisms and two-dimensional surface diffusion. DNA targets in solution at 100 pM were flown across a solid interface with covalently attached complementary strands. Experiments were performed with systems designed to create short (15bp) duplexes, long (30bp) duplexes, or a partially complementary system where a 30-base target hybridizes with a 15-base probe, introducing a 15-base overhang. Analyses of association lifetimes show that a majority of short associations with long-lived distribution tails, indicative of different melting modes. The longest duplexes maintain longer lifetimes, as expected due to higher stability and more Watson-Crick base pair bonding. The presence of a toehold, or overhang, on the duplex decreases association lifetimes. This suggests exposed and unhybridized DNA nucleobases increase the targetâ??s attraction to the surface, stabilizing the transition from the hybridized to a surface state. The long-lived events appear to have 1st-order dissociation behavior, indicating that melting is initiated by a nucleation event before undergoing complex unzipping behavior. This gives further insight into the mechanisms within surface-mediated DNA hybridization systems, so that devices relying on these interactions in the future can be designed to give stronger signals and more stable hybridizations to provide their desired functions.