[HTML][HTML] Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides
…, A Noy, KHS Main, V Velasco-Berrelleza… - Nature …, 2021 - nature.com
In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled)
structures. It remains unclear how this supercoiling affects the detailed double-helical …
structures. It remains unclear how this supercoiling affects the detailed double-helical …
[HTML][HTML] 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-…
Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity
…, JAL Howard, V Velasco-Berrelleza… - Nucleic Acids …, 2021 - academic.oup.com
Nucleoid-associated proteins (NAPs) are crucial in organizing prokaryotic DNA and regulating
genes. Vital to these activities are complex nucleoprotein structures, however, how these …
genes. Vital to these activities are complex nucleoprotein structures, however, how these …
[PDF][PDF] Combining high-resolution AFM with MD simulations shows that DNA supercoiling induces kinks and defects that enhance flexibility and recognition
A Pyne, A Noy, K Main, V Velasco-Berrelleza… - bioRxiv, 2019 - researchgate.net
In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled)
structures. It remains unclear how this supercoiling affects the double-helical structure of …
structures. It remains unclear how this supercoiling affects the double-helical structure of …
Study of the flexibility of DNA using molecular dynamics simulations
VM Velasco Berrelleza - 2022 - etheses.whiterose.ac.uk
Biological processes manipulating DNA test its physical properties. Atomistic molecular
dynamics simulations are a powerful tool to study the mechanical properties of DNA at atomic …
dynamics simulations are a powerful tool to study the mechanical properties of DNA at atomic …
A π-calculus Model of Supercoiling DNA Circuits
PF Rainford, A Mogre, V Velasco-Berrelleza… - Artificial Life …, 2023 - direct.mit.edu
Synthetic biology is one facet of Artificial Life which designs novel biological components,
eg DNA, RNA, membranes, to produce new behaviours. Here, we are interested in DNA “…
eg DNA, RNA, membranes, to produce new behaviours. Here, we are interested in DNA “…
Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments
Atomic-level computer simulations are a very useful tool for describing the structure and
dynamics of complex biomolecules such as DNA and for providing detail at a resolution where …
dynamics of complex biomolecules such as DNA and for providing detail at a resolution where …
[PDF][PDF] A nucleoid-associated protein bends and bridges DNA in a multiplicity of topological states with varying specificity
…, GD Watson, JAL Howard, V Velasco-Berrelleza… - bioRxiv, 2020 - biorxiv.org
Nucleoid-associated proteins perform crucial roles in compacting prokaryotic DNA, but how
they generate higher-order nucleoprotein structures by perturbing DNA topology is unclear. …
they generate higher-order nucleoprotein structures by perturbing DNA topology is unclear. …
[PDF][PDF] Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and recognition
ALB Pyne, A Noy, K Main, V Velasco-Berrelleza… - scholar.archive.org
In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled)
structures. It remains unclear how this supercoiling affects the detailed double-helical …
structures. It remains unclear how this supercoiling affects the detailed double-helical …
Atomistic Simulations of Supercoiled Linear DNA Under Tension
M Burman - 2023 - etheses.whiterose.ac.uk
DNA in living beings is constantly subject to torsional stress as a result of processes such as
transcription and replication, as well as the action of nucleosomes and nucleiod-associated …
transcription and replication, as well as the action of nucleosomes and nucleiod-associated …