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Nanoscale gymnastics: Dynamics of protein-DNA complexes with high speed AFM



By: Yuri L Lyubchenko
Professor of Pharmaceutical Sciences
From: University of Nebraska Medical Center
When: Wednesday, March 22, 2017
4:00 PM - 5:00 PM
Where: Dell Butcher Hall
Abstract: A low data acquisition rate of AFM is a serious deficiency if AFM is applied to imaging of the majority of biological processes. For example, the translocation of RNA polymerase along DNA occurs on the second time scale, therefore the observation on the minute time scale reveals only few percent of the events. The high-speed AFM (HS-AFM) instrument developed by T. Ando operates with the sub-second image acquisition speed 1. Key issues for high-speed AFM realized in the Ando design are as follows (1) small cantilevers with a resonant frequency above several hundred kHz and a small spring constant, (2) a high-speed scanner with a resonant frequency that matched the cantilever characteristics, (3) active damping techniques to suppress mechanical vibrations of the scanner, (4) fast feedback control and (5) gentle touch of the sample –the current HS-AFM instrument can capture images with the video rate without significant disturbance of weak biomolecular interactions 1 2. In this talk, I review results of HS-AFM applications to a number protein-DNA complexes. They included direct visualization of interaction with DNA SSB protein that binds to single-stranded segments of DNA only 3; visualization of dynamics of APOBEC3G protein in its interaction with the cognate site within DNA 4; discovery of spontaneous unwrapping of nucleosomes 2; observation of the long-range sliding of synaptosome along DNA5 and visualization and analysis of concerted cleavage by type IIF restriction enzyme SfiI 6. Prospects for the future applications of HS-AFM to biological systems will be discussed.