Pore translocation of knotted DNA rings

Abstract

We use an accurate coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translocation of 10-kbp-long DNA rings that are knotted. By monitoring various topological and physical observables we find that there is not one, as previously assumed, but rather two qualitatively different modes of knot translocation. For both modes the pore obstruction caused by knot passage has a brief duration and typically occurs at a late translocation stage. Both effects are well in agreement with experiments and can be rationalized with a transparent model based on the concurrent tensioning and sliding of the translocating knotted chains. We also observed that the duration of the pore obstruction event is more controlled by the knot translocation velocity than the knot size. These features should advance the interpretation and design of future experiments aimed at probing the spontaneous knotting of biopolymers.

Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches

“…All the simulations presented in the current paper are performed using the sequence dependent variation of the OxDNA model 39 implemented in the LAMMPS 46 simulation software by Henrich et al 40 . The OxDNA model has previously been shown to reproduce the behavior of DNA under tension and torsional stress 33 and has also been used to study various structural features of DNA 41,[47][48][49][50] . In the following sections the simulation parameters are given in the reduced…”

TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami

“…Consequently, a specific value of supercoiling density σ corresponds to Lk = round((1 + σ ) ⋅ ( N /10.5)). The second step involves calculating the writhe Wr of the input conformation from which one obtains the desired twist as Tw = Lk ‐ Wr . This total twist is finally distributed uniformly along the reconstructed oxDNA filament.…”

“…The tools revolve around, but are not limited to, the oxDNA model. This model, which some of us helped develop, offers a good balance between a realistic description of nucleotides and their effective interactions and is amenable to extensive MD simulations of filaments with thousands of base pairs …”

Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking

“…These circular centerlines, discretised in 2000 segments, were next turned into the oxDNA double-helical representation by a fine-graining procedure, where each segment was mapped into the six interaction centers of the two paired nucleotides [48], see inset in Fig. 1A.…”

“…Here, we tackle these questions for 2kbp-long DNA rings using molecular dynamics simulations and oxDNA [45][46][47], an accurate model for DNA filaments based on mesoscopic representation of nucleotides and their interactions. This level of detail makes it possible to gather multi-ms trajectories for kbp-long DNAs while retaining the key structural details responsible for the frictional [48] and cholesteric effects [49] arising from selfcontacts in the knotted or superhelical regions. Specifically, we focus on DNA rings with 5% negative supercoiling -typical of plasmids -and tied in 5-crossings knots (5 1 and 5 2 topologies), a complex form of entanglement previously reported in 4kbp-long pBR322 plasmids [5,16].…”