Modelling of the orientational and structural dynamics of single-stranded DNA probe molecules immobilized on fused silica and glass surfaces

Immobilization of single-stranded DNA (ssDNA) onto fused silica and glass surfaces has been widely used for preparation of fiber optic sensors and DNA microarrays. Fundamental investigations of the orientation, motion and hybridization behavior of immobilized ssDNA is important to understand and design sensing devices. Using computational methods to evaluate molecular dynamics we have simulated a solid SiO2-linker-ssDNA system and studied the conformations assumed by such immobilized material under different physical constraints. We have also evaluated the molecular dynamics of fluorescent intercalating dyes that are attached to the ssDNA by tethers of various lengths, with the goal of preparing a label on ssDNA that will transduce hybridization. Periodic boundary conditions were applied to examine packing properties and nearest neighbour interactions of adjacent ssDNA molecules. Molecular dynamics have been performed at room temperature as well as on heated systems. Solvent effects were taken into account and the modelling assumed the presence of an aqueous environment. The results suggest the various conformations and orientations that immobilized ssDNA can assume, and indicate that the orientation is generally far from one that is perpendicular to the interface. Exploration of tether lengths indicates the minimum lengths that are required for a fluorescent label to operate efficiently as an intercalating agent.