title: Effect of Hydrophobic and Hydrophilic Surfaces on the Stability of Double-Stranded DNA.
abstract: DNA hybridization is the foundation for numerous technologies like DNA origami and DNA sensing/microarrays. Using molecular simulations, enhanced-sampling methods, and free-energy calculations, we show the effects of hydrophilic and hydrophobic surfaces on DNA hybridization. Hydrophilic surfaces compete with terminal bases' H-bonds but stabilize central base stacking. Hydrophobic surfaces strengthen terminal H-bonds but destabilize central base stacking. Regardless of surface chemistry, for terminal bases, melting proceeds through breaking H-bonds, followed by unstacking from the neighboring base. For central bases in bulk or near hydrophobic surfaces, melting proceeds by disruption of H-bonds, followed by unstacking, whereas on hydrophilic surfaces, unstacking from one neighboring base precedes complete disruption of the H-bonds, followed by unstacking from the second neighboring base. Kinetic barriers to melting and hybridization show that the central bases melt rapidly near hydrophobic surfaces, which can accelerate conformational searching and thereby accelerate folding into the desired conformation.
authors.affiliation: †U.S. Army Research Laboratory, Aberdeen Proving Ground, MD 21005, United States.|‡Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Elder
authors.affiliation: §Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.
authors.forename: Jim
authors.initials: J
authors.lastname: Pfaendtner
authors.affiliation: ‡Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States.|∥Departments of Chemical and Biomolecular Engineering and Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.
authors.forename: Arthi
authors.initials: A
authors.lastname: Jayaraman
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation
chemical_list: D004247:DNA