C. Micheletti and E. Orlandini
Knotting and unknotting dynamics of DNA strands in nanochannels
ACS Macro Letters, 2014, 3 , 876-880
Link to online article
Abstract
The self-knotting dynamics of DNA strands confined in nanochannels is
studied with Brownian simulations. The model DNA chains are several
microns long and placed inside channels that are 50-300 nm wide. This
width range covers the transition between different metric scaling
regimes and the concomitant drop of DNA knotting probability for
channel widths below ~75 nm. We find that knots typically originate
from deep looping and backfoldings of the chain ends. Upon lowering
the channel width, backfoldings become shallower and rarer and the
lifetime of knots decreases while that of unknots increases. This
lifetimes interplay causes the dramatic reduction of knots incidence
for increasing confinement. The results can aid the design of
nanochannels capable of harnessing the self-knotting dynamics to
quench or relax the DNA topological state as desired.