AVS 49th International Symposium
    Biomaterials Monday Sessions
       Session BI-MoM

Paper BI-MoM10
Structural Properties of Nucleosomal DNA Characterized by Atomic Force Microscopy

Monday, November 4, 2002, 11:20 am, Room C-201

Session: Theoretical Studies of Biosurfaces/Biotribology and Biorheology
Presenter: M.E. Greene, Northwestern University
Authors: M.E. Greene, Northwestern University
M.A. Ratner, Northwestern University
J. Widom, Northwestern University
M.C. Hersam, Northwestern University
Correspondent: Click to Email
One of the fundamental problems in contemporary molecular biology involves whether a sequence dependence exists in nucleosomal DNA which gives the molecule certain structural properties leading to the formation of nucleosome with histone octamer. A way to approach the solution is to look at the isolated DNA molecules to discern the native structural properties in the absence of histones. Interfacing biological molecules with inorganic substrates and probing them using atomic force microscopy (AFM) allows for such study. AFM has been used to image surfaces with adsorbed biological molecules for over a decade, and in particular DNA has been characterized to an extent that imaging artifacts interfering with proper analysis have been identified. Several technical difficulties have been resolved as well, including substrate selection and a reproducible surface binding protocol, opening the door for AFM to be used as a powerful tool to investigate problems of genuine biological importance. In this investigation, a 342-bp strand of synthetic dsDNA dubbed "601" shown by Lowary and Widom to have a high affinity for binding to histone octamer is examined. This sequence is thought to mimic the behavior of DNA sequences found in chromatin. Preliminary analysis of AFM data of a natual nucleosomal DNA sequence isolated from chicken erythrocyte suggests agreement with the worm-like chain (WLC) model. Attention is given to the quantities of end-to-end distance, contour length, and intrachain bend angles in order to assess the persistence length, bendedness, and bendability of the sequence. AFM data is currently being gathered using Si cantilevers tipped with multiwalled carbon nanotubes as well as high aspect ratio Si tips with a nominal radius of curvature of 2 nm to obtain better lateral resolution and detailed measurements of bends and curvature fluctuations in the chains. An automated analysis methodology to allow the handling of large data sets will be introduced as well.