Simulation study of the effects of surface chemistry and temperature on the conformations of ssDNA oligomers near hydrophilic and hydrophobic surfaces

Abstract

We study the effects of the presence of a hydrophilic and a hydrophobic surface on the conformations and interactions of a single-stranded DNA (ssDNA) oligomer using atomistic molecular dynamics, umbrella sampling, and temperature-replica exchange. Our simulations capture the expected interactions between the ssDNA and the two surfaces (e.g., hydrogen bonds, hydrophobic interactions), but we find that the surface chemistry does not strongly affect the exposure of the relatively hydrophobic nucleobases or the hydrophilic phosphate backbone in a 16-base ssDNA. Likewise, the surfaces do not strongly affect the preferred size of the ssDNA compared to bulk solution, although the hydrophilic surface does favor slightly more compact ssDNA conformations than the hydrophobic surface. In more compact conformations, the negative charge of the ssDNA is more concentrated, and the energetic interactions of the DNA and DNA-bound counterions with the hydrophilic surface are more favorable, which consequently favors smaller ssDNA sizes. Increasing temperature, regardless of the presence or chemistry of a surface, makes it less unfavorable for the ssDNA to assume both compact and extended conformations. With increasing temperature the free energy cost of assuming a compact conformation is reduced to a greater extent than the cost of assuming an extended conformation. The reason for this difference is the entropically favorable release of DNA-bound water molecules upon assuming a compact conformation. Increasing temperature decreases water-DNA interactions while surprisingly increasing counterion-DNA interactions, changes which are attributed to the relative balance of entropic and energetic contributions for water molecules and counterions bound to the ssDNA.