(520f) Nanoscale Behavior of DNA Oligomers Near Hydrophobic and Hydrophilic Functionalized Surfaces

A fundamental understanding of the interactions of DNA with surfaces, and the behavior of DNA near surfaces, is important for emerging biomaterials technologies, such as DNA origami and the self-assembly of DNA-grafted nanoparticles. We use atomistic molecular dynamics and biased sampling techniques to study single-stranded DNA (ssDNA) oligomers on model hydrophilic and hydrophobic functionalized surfaces to elucidate the molecular interactions between the DNA, the surface, and water molecules. ssDNA oligomers are amphiphilic and adsorb strongly to both hydrophilic and hydrophobic surfaces, but different forces govern adsorption to the two surfaces. When the ssDNA is in the vicinity of the hydrophilic surface, it forms attractive hydrogen bonds with the surface species, while facing a repulsive force from the dense, strongly adsorbed water molecules at the surface. When the ssDNA is in the vicinity of the hydrophobic surface, it experiences weak hydrophobic attraction to the surface and a surprising repulsive force associated with a low-density region of water near the hydrophobic surface.