A perspective on the molecular simulation of DNA from structural and functional aspects
As genetic material, DNA not only carries genetic information by sequence, but also affects
biological functions ranging from base modification to replication, transcription and gene …
biological functions ranging from base modification to replication, transcription and gene …
Chromatin compaction multiscale modeling: a complex synergy between theory, simulation, and experiment
Understanding the mechanisms that trigger chromatin compaction, its patterns, and the
factors they depend on, is a fundamental and still open question in Biology. Chromatin …
factors they depend on, is a fundamental and still open question in Biology. Chromatin …
Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models
We investigate the influence of nonlocal couplings on the torsional and bending elasticities
of DNA. Such couplings have been observed in the past by several simulation studies. Here …
of DNA. Such couplings have been observed in the past by several simulation studies. Here …
SerraNA: a program to determine nucleic acids elasticity from simulation data
V Velasco-Berrelleza, M Burman… - Physical Chemistry …, 2020 - pubs.rsc.org
The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments
and is important for gene regulation and chromosome packing. However, their sequence …
and is important for gene regulation and chromosome packing. However, their sequence …
Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism
Torsional restraints on DNA change in time and space during the life of the cell and are an
integral part of processes such as gene expression, DNA repair and packaging. The …
integral part of processes such as gene expression, DNA repair and packaging. The …
Overtwisting induces polygonal shapes in bent DNA
By combining analytical results and simulations of various coarse-grained models, we
investigate the minimal energy shape of DNA minicircles which are torsionally constrained …
investigate the minimal energy shape of DNA minicircles which are torsionally constrained …
Sequence-dependent twist-bend coupling in DNA minicircles
Looping of double-stranded DNA molecules with 100–200 base pairs into minicircles,
catenanes, and rotaxanes has been suggested as a potential tool for DNA …
catenanes, and rotaxanes has been suggested as a potential tool for DNA …
Conformational and dynamic properties of short DNA minicircles in aqueous solution from atomistic molecular dynamics simulations
Detailed molecular dynamics (MD) simulations of aqueous solutions of short DNA
minicircles ranging in size from 30 to 180 bp were performed for the investigation of the …
minicircles ranging in size from 30 to 180 bp were performed for the investigation of the …
Spectral analysis of DNA superhelical dynamics from molecular minicircle simulations
JD Curuksu - The Journal of Chemical Physics, 2023 - pubs.aip.org
Torsional and bending deformations of DNA molecules often occur in vivo and are important
for biological functions. DNA “under stress” is a conformational state, which is by far the most …
for biological functions. DNA “under stress” is a conformational state, which is by far the most …
Structure and dynamics of double-stranded DNA rotaxanes
Y Song, JS Kim - Nanoscale, 2024 - pubs.rsc.org
A DNA rotaxane, with its unique mechanically interlocked architecture consisting of a
circular DNA molecule threaded onto a linear DNA axle, holds promise as a fundamental …
circular DNA molecule threaded onto a linear DNA axle, holds promise as a fundamental …