DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size.

Autor:	Khara DC; Ben-Gurion University of the Negev, Beer-Sheva and the Ilse Katz Institute for Nanoscale Science and Technology, P.O. Box 653, Beer-Sheva, 8410501, Israel., Schreck JS; Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA., Tomov TE; Ben-Gurion University of the Negev, Beer-Sheva and the Ilse Katz Institute for Nanoscale Science and Technology, P.O. Box 653, Beer-Sheva, 8410501, Israel., Berger Y; Ben-Gurion University of the Negev, Beer-Sheva and the Ilse Katz Institute for Nanoscale Science and Technology, P.O. Box 653, Beer-Sheva, 8410501, Israel., Ouldridge TE; Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK., Doye JPK; Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK., Nir E; Ben-Gurion University of the Negev, Beer-Sheva and the Ilse Katz Institute for Nanoscale Science and Technology, P.O. Box 653, Beer-Sheva, 8410501, Israel.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2018 Feb 16; Vol. 46 (3), pp. 1553-1561.
DOI:	10.1093/nar/gkx1282
Abstrakt:	We present a detailed coarse-grained computer simulation and single molecule fluorescence study of the walking dynamics and mechanism of a DNA bipedal motor striding on a DNA origami. In particular, we study the dependency of the walking efficiency and stepping kinetics on step size. The simulations accurately capture and explain three different experimental observations. These include a description of the maximum possible step size, a decrease in the walking efficiency over short distances and a dependency of the efficiency on the walking direction with respect to the origami track. The former two observations were not expected and are non-trivial. Based on this study, we suggest three design modifications to improve future DNA walkers. Our study demonstrates the ability of the oxDNA model to resolve the dynamics of complex DNA machines, and its usefulness as an engineering tool for the design of DNA machines that operate in the three spatial dimensions.
Databáze:	MEDLINE
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