Molecular dynamics simulations of end-tethered single-stranded DNA probes on a silica surface

The structure of DNA molecules tethered to surfaces may significantly affect the efficiency of hybridization on the DNA microarray. Understanding the structure of single-stranded DNA (ssDNA) tethered to surfaces is critical for applying the molecular recognition function of DNA microarrays. Although a number of experimental methods have been applied to determine the structure of the DNA probe on surfaces, they can not provide enough information on the dynamical behavior of the ssDNAs on surfaces. Herein, we investigated the dynamics and interaction of seven DNA probes tethered on a silica surface by a molecular dynamics simulation. From the simulation results, we examined the structure and dynamics of the ssDNAs, by calculating the root-mean-square derivations, the tilt angles, the radius of gyration, and the distances of the neighboring ssDNAs. The data obtained from our simulation suggests the packing density has a significant effect on the overall structure and molecular orientation change of surface-tethered ssDNAs, which is complementary to the recent experimental reports. Our simulation provided a structural insight, which is helpful to better understand the behavior of ssDNA on surfaces and optimize the design of DNA microarray.