(634f) Structure and Thermodynamics of Single- and Double-Stranded DNA Oligomers Near Hydrophilic and Hydrophobic Functionalized Surfaces

Understanding the influence of functionalized surfaces on the behavior of DNA will accelerate the development of emerging biotechnologies that rely on the self-assembly of single-stranded DNA (ssDNA) molecules into double-stranded DNA (dsDNA) duplexes. Using atomistic molecular dynamics simulations and enhanced sampling techniques, we study the effects of model hydrophobic and hydrophilic surfaces, and the effects of temperature, on the conformations and stability of ssDNA and dsDNA oligomers. These simulations capture the expected interactions between ssDNA and the two surfaces (e.g. hydrogen bonds, hydrophobic interactions), and we quantify the thermodynamics governing the conformations of ssDNA oligomers, including contributions from counterions and water molecules. Then, we study the interactions of dsDNA oligomers with the hydrophilic and hydrophobic surfaces to examine how DNA-surface interactions may influence the stability of nanostructures constructed from hybridized DNA strands.