Structure and thermodynamics of ssDNA oligomers near hydrophobic and hydrophilic surfaces

A fundamental understanding of the behavior of single-stranded DNA (ssDNA) on surfaces of varying chemistry is important for DNA-based materials assembly. We use molecular dynamics simulations to study short ssDNA oligomers on model hydrophilic and hydrophobic self-assembled monolayers (SAMs) to elucidate the molecular interactions between the ssDNA, the SAM, and water molecules. These ssDNA oligomers exhibit a favorable binding energy for ssDNA on both hydrophilic and hydrophobic SAMs. When the ssDNA is in the vicinity of the hydrophilic SAM, 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 SAM, 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.