Surface-tethered single-strand DNA (ssDNA) impacts a number of technologies. ssDNA provide a highly size-reproducible oligomer model for fundamental studies of tethered molecules. The behavior of ssDNA also dictates the behavior of biosensors such as DNA microarrays or gene chips. While DNA array technology is well established, much less is known about the dynamic atomic-scale behavior of the surface-tethered DNA probe, in particularly how probe-probe and probe-surface interactions affect hybridization rate and specificity.

In this study we use molecular dynamics (MD) simulations to examine the interaction of two 25-mer ssDNA oligomers tethered to silica or gold surfaces and immersed in an aqueous buffer. We use a simulation box sufficiently large that the two strands do not interact with their periodic neighbors. We find that the interaction between strands is rapid and a number of non-Watson-Crick base-pairing motifs are evident.

The figure below shows the MD evolution of identical 25mer hydrated ssDNA strands linked to a silica surface by a thio terminated silane. Simulations depict initial configuration (left), 1 ns (center) and 2.4 ns (right). For clarity, water and Na+ counter ions are not shown.