A primer on the oxDNA model of DNA: when to use it, how to simulate it and how to interpret the results
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology,
biophysics and nanotechnology. It is currently available via two independent open source …
biophysics and nanotechnology. It is currently available via two independent open source …
A molecular view of DNA flexibility
DNA dynamics can only be understood by taking into account its complex mechanical
behavior at different length scales. At the micrometer level, the mechanical properties of …
behavior at different length scales. At the micrometer level, the mechanical properties of …
Discovery and design of soft polymeric bio-inspired materials with multiscale simulations and artificial intelligence
Materials chemistry is at the forefront of the global “Fourth Industrial Revolution”, in part by
establishing a “Materials 4.0” paradigm. A key aspect of this paradigm is developing …
establishing a “Materials 4.0” paradigm. A key aspect of this paradigm is developing …
DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles
Eukaryotic genome and methylome encode DNA fragments' propensity to form nucleosome
particles. Although the mechanical properties of DNA possibly orchestrate such encoding …
particles. Although the mechanical properties of DNA possibly orchestrate such encoding …
Supercoiling and looping promote DNA base accessibility and coordination among distant sites
Thursday, February 25, 2021 221a sequences to superhelical apices. Base pair disruption
allows sharp bending at superhelical apices, which facilitates DNA writhing and, thus …
allows sharp bending at superhelical apices, which facilitates DNA writhing and, thus …
Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded DNA
We introduce MADna, a sequence-dependent coarse-grained model of double-stranded
DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar, at …
DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar, at …
A Self‐Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High‐Resolution Structural Detail
DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to
its high programmability based on canonical Watson–Crick base pairing, with crystal …
its high programmability based on canonical Watson–Crick base pairing, with crystal …
Nanopore sequencing of short dsDNA after elongation by combination of ligation and PEAR
B Cheng, K Hu, Z Song, R An… - Bulletin of the Chemical …, 2023 - academic.oup.com
Nanopore sequencing technology, as a third-generation method for DNA sequencing at the
single-molecule level, has attracted much attention and developed quickly due to the …
single-molecule level, has attracted much attention and developed quickly due to the …
Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches
Damaged or mismatched DNA bases result in the formation of physical defects in double-
stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain …
stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain …
Characterizing the free-energy landscapes of DNA origamis
We show how coarse-grained modelling combined with umbrella sampling using distance-
based order parameters can be applied to compute the free-energy landscapes associated …
based order parameters can be applied to compute the free-energy landscapes associated …