Simulations of cyclic and linear DNA chains moderately and strongly confined in nanochannels
Seminar Room 1, Newton Institute
Structural properties of flexible and semiflexible cyclic and linear chains confined in nanochannels were studied by molecular simulations mimicking single molecule experiments in microfuidic channels used to analyze genomic macromolecules. Experiments (1) with linear and ring macromolecules showed differences in the response to confinement. Simulations of rings (comprising few persistence lengths per chain, as in plasmid rings (2)) and their linear analogs confirmed these trends (3). The radius of gyration Rg of chains satisfactorily represents the stretching of both chain topologies along the channel. Apart from focus on moderate confinement we show that strong confinement applies also for semiflexible rings, though unanticipated for rings in contrast to linear chains where it is known as Odijk regime. Similar response of chain elongation to the confinement Rg(D) is obtained in the case of rings compared to linear chains. However, the relative chain extension in channel is larger for rings, the strong confinement regime extends to larger channel diameters D and under moderate confinement the extension declines less steeply for rings. These findings are explained (3) in terms of a strong self-avoidance of confined rings relative to their linear analogs, stemming from the increased local density in channel due to looping of cycle. The extension of rings is governed by the same analytical function as for linear chain provided half of the contour length for a cyclic chain is considered at full extension. Orientation correlation function and static structure factor for both topologies point out features responsible for recognition of ring architecture.
(1) F. Persson, P. Utko,W. Reisner, N.B. Larsen, A. Kristensen, Nano Lett. 9, 1382-1385, 2009, (2) P. Cifra, Z. Benková, Macrom. Theory & Simul., 20, 65-74, 2011, (3) Z. Benková, P. Cifra, Macomolecules, 45, 2597-2608, 2012