Eur. Phys. J. E (2016) 39: 50
https://doi.org/10.1140/epje/i2016-16050-5

Regular Article

Numerical investigation of molecular nano-array in potential-energy profile for a single dsDNA

School of Mechanical Engineering, Shiraz University, Shiraz, Iran

^* e-mail: rkamali@shirazu.ac.ir

Received: 3 November 2015
Revised: 20 January 2016
Accepted: 5 April 2016
Published online: 29 April 2016

Abstract

A Rigorous numerical investigation on dsDNA translocation in quasi-2-dimensional nano-array filter is performed using Molecular Dynamics (MD) method. Various dsDNA molecules with different sizes are chosen in order to model Ogston sieving in a nano-array filter. The radius of gyration of dsDNA molecule is less than the characteristic length of the shallow region in nano-array. The dsDNA molecule is assumed to be in the 0.05M NaCl electrolyte. MD shows acceptable results for potential-energy profile for nano-array filter. According to the MD outcomes, the dsDNA electrophoretic mobility decreases almost linearly with dsDNA size and show the same trend as Ogston sieving for gel electrophoresis. In addition, different shapes for nano-array filter are studied for a unique dsDNA molecule. It is concluded that steeping the nano-array wall can cause the retardation of dsDNA translocation and decreases dsDNA electrophoretic mobility.