458700 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 target’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.
See more of this Group/Topical: Nanoscale Science and Engineering Forum