DNA hybridization mechanism on silicon nanowires: A molecular dynamics approach

We report on a computational study of DNA detection systems, based on the hybridization between a DNA target, present in solution, and its complementary probe tethered to a solid support. Classical all-atom molecular dynamics were used to simulate the association process and to fully characterize the motion of the formed duplex. The hybridization event starts with a random collision, controlled by diffusion. Subsequently, the resulting complex evolves in a few nanoseconds towards the final duplex, the latter being stable for the rest of the simulation time (70 ns). The complex adopted upright and tilted orientations, with respect to the functionalized layer, sometimes reaching it at hydrogen bonding distance. Although the duplex conformation fluctuated for the entire run, it remained close to a B-like structure.