title: Simulation Assisted Analysis of the Intrinsic Stiffness for Short DNA Molecules Imaged with Scanning Atomic Force Microscopy.
abstract: Studying the mechanical properties of short segments of dsDNA can provide insight into various biophysical phenomena, from DNA looping to the organization of nucleosomes. Scanning atomic force microscopy (AFM) is able to acquire images of single DNA molecules with near-basepair resolution. From many images, one may use equilibrium statistical mechanics to quantify the intrinsic stiffness (or persistence length) of the DNA. However, this approach is highly dependent upon both the correct microscopic polymer model and a correct image analysis of DNA contours. These complications have led to significant debate over the flexibility of dsDNA at short length scales. We first show how to extract accurate measures of DNA contour lengths by calibrating to DNA traces of simulated AFM data. After this calibration, we show that DNA adsorbed on an aminopropyl-mica surface behaves as a worm-like chain (WLC) for contour lengths as small as ~20 nm. We also show that a DNA binding protein can modify the mechanics of the DNA from that of a WLC.
authors.affiliation: Department of Optics and Optical Engineering, University of Science and Technology of China, Heifei, Anhui, China.|Heifi National Laboratory for Physical Sciences at the Microscale, Heifi, Anhui, China.|Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.
authors.forename: Haowei
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.|Department of Physics, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Milstein
mesh_terms: D004247:DNA / Q000737:chemistry*; D018625:Microscopy, Atomic Force / Q000379:methods*; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA