Development of An Intermediate-Resolution Model for DNA

DNA microarrays have become a powerful tool for biological research, allowing scientists to track the expression patterns of thousands of genes simultaneously. The molecular level mechanisms that govern hybridization between target and probe sequences on a microarray surface are still not fully understood. We are developing an intermediate resolution model of DNA using a multiscale modeling approach suitable for discontinuous molecular dynamics (DMD) simulations of microarrays. In our multiscale approach, atomistic simulations of single and double stranded DNA molecules with explicit solvent and counterions are performed. The atomistic system is then mapped on to a reduced representation based on discontinuous potentials by matching conformational distributions of both systems. Using the discontinuous potentials obtained, we perform DMD simulations to investigate the hybridization of model DNA single strands of different base sequences and chain lengths at a variety of temperatures.