Simulation of Semiflexible Cyclic and Linear Chains Moderately and Strongly Confined in Nanochannels

Citations Over TimeTop 10% of 2012 papers

Abstract

The constraints due to the chain closure in combination with the geometrical constraints of a DNA molecule are inevitable for many biological processes. In this work, structural properties of flexible and semiflexible cyclic chains and their linear analogues confined in cylindrical channels were studied using the coarse-grained Metropolis Monte Carlo simulations. The radius of gyration satisfactorily represents the longitudinal stretching of both chain topologies. Transition between the moderate and strong confinement regime of semiflexible cyclic chains is described for the first time. Qualitatively similar response of the chain elongation to the confinement strength variation Rg(D) is obtained in the case of cyclic chains. However, the relative chain extension is stronger, the Odijk strong confinement regime is extended to larger channel diameters D, and under moderate confinement the chain extension declines less steeply for cyclic chains. All three findings are explained in terms of the strong self-avoidance of confined chains relative to their linear analogues and the last finding is consistent with the reported experimental measurements. In the Odijk regime, the relative chain extension is governed by the same analytical functions provided half of the contour length for a cyclic chain is considered at the full extension. The orientation correlations for a cyclic chain in narrow channels are characterized by a typical sharp central minimum. Upon increasing the channel cross-sectional area, the minimum is broadened, turns into a negative maximum and, ultimately, the orientation correlations merge with those for a free cycle. Confined flexible and less stiff chains resemble their linear analogues more readily. The static structure factor for tightly confined chains provides better differentiation between the chain architecture than for free chains.

Related Papers

• → Radius of gyration as an indicator of protein structure compactness(2008)1,587 cited
• → How Large is an α-Helix? Studies of the Radii of Gyration of Helical Peptides by Small-angle X-ray Scattering and Molecular Dynamics(2005)72 cited
• → Ultrasonic wave spectroscopy study of sugar oligomers and polysaccharides in aqueous solutions: The hydration length concept(2005)22 cited
• [Radius of gyration is indicator of compactness of protein structure].(2008)
• → Radius of Gyration of a Sphere and a Barrel(2006)