Determining protein-induced DNA bending in force-extension experiments: theoretical analysis.
Computer simulations were used to investigate the possibility of determining protein-induced DNA bend angles by measuring the extension of a single DNA molecule. Analysis of the equilibrium sets of DNA conformations showed that shortening of DNA extension by a single protein-induced DNA bend can be as large as 35 nm. The shortening has a maximum value at the extending force of approximately 0.1 pN. At this force, the DNA extension experiences very large fluctuations that dramatically complicate the measurement. Using Brownian dynamics simulation of a DNA molecule extended by force, we were able to estimate the observation time needed to obtain the desired accuracy of the extension measurement. Also, the simulation revealed large fluctuations of the force, acting on the attached magnetic bead from the stretched DNA molecule.
Vologodskii
Alexander
A
Department of Chemistry, New York University, New York, NY 10003, USA. alex.vologodskii@nyu.edu
D000465:Algorithms; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008958:Models, Molecular; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D013997:Time Factors
D004268:DNA-Binding Proteins; D004247:DNA