E. Orlandini and C. Micheletti
Knotting of linear DNA in nano-slits and nano-channels: a numerical study
Journal of Biological Physics, 2013, 39 , 267-275
Link to arXiv preprint ,
Abstract
The amount and type of self-entanglement of DNA filaments is
signficantly affected by spatial confinement, which is ubiquitous in
biological systems. Motivated by recent advancements in single DNA
molecule experiments based on nanofluidic devices, and by the
introduction of algorithms capable of detecting knots in open chains, we
investigate numerically the entanglement of linear, open DNA chains
confined inside nano-slits. The results regard the abundance, type and
length of occurring knots and are compared with recent findings for DNA
inside nano-channels. In both cases, the width of the confining region,
$D$, spans the 30nm- 1$\mu$m range and the confined DNA chains are 1 to
4$\mu$m long. It is found that the knotting probability is maximum for
slit widths in the 70-100nm range. However, over the considered DNA
contour lengths, the maximum incidence of knots remains below 20\%,
while for channel confinement it tops 50\%. Further differences of the
entanglement are seen for the average contour length of the knotted
region which drops significantly below $D\sim 100$nm for
channel-confinement, while it stays approximately constant for slit-like
confinement. These properties ought to reverberate in different kinetic
properties of linear DNA depending on confinement and could be
detectable experimentally or exploitable in nano-technological
applications.