Orientation of DNA on a surface from simulation

Abstract

DNA orientation near surfaces determines many properties related to hybridization efficiency. We performed a 40‐ns molecular dynamics simulation to study the structure and orientation of a 12‐base‐pair DNA duplex tethered to a neutral, epoxide‐coated silica surface. Starting with a canonical B‐form tethered in an up‐right position, normal to the surface, the DNA tilted to over 55° and back. The time scale was a few nanoseconds for tilting events. The linker between the DNA and the surface went from standing upright to tilted, and finally collapsed on the surface. Although the DNA conformation fluctuated, it remained closed to B‐form for the entire 40 ns. Calculations of helical parameters of the DNA show that the tethered end of the DNA changed its conformation noticeably when attracted to the surface. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004