Atomistic Simulations of Biomolecules at the Water‐Amorphous Silica Interface: Application to Peptides and DNA Oligomers

B. Shi, Y.K. Shin, A. Hassanali, S.J. Singer
Ohio State University, US

Keywords: amorphous silica, nanofluidics, microfluidics, DNA, protein, biomolecule


Realistic modeling of biomolecules near amorphous silica (“glass”), a material commonly used for biomedical device fabrication, is required for device design and evaluation. Our potential model, based on ab initio quantum chemical calculations, is designed to provide sufficient accuracy yet be tractable for the large spatial and time scale simulations needed to treat realistic device applications. We provide a microscopic interpretation of recent fluorescence depolarization data for lys-trp-lys and glu-trp-glu tripeptides bound to hydroxylated silica. Both peptides readily bind to the surface, as judged by multiple trajectories initiated with the peptides far from the surface. This is not surprising when positively charged lys-trp-lys binds to the negative silica surface. However, the fact that negatively charged glu-trp-glu rapidly binds to silica illustrates the rich interplay among site charges of both sign present in the adsorbate and surface, and explains how negatively charged biomolecules like DNA or albumin bind to silica. In addition, hydrophobic attractions between the indole group of the trp residue, and hydrophobic patches on the silica surface, often are important for both lys-trp-lys and glu-trp-glu binding. Finally, we report binding studies of both single- and double-stranded DNA oligomers to the silica surface, which are in progress.