Dynamics of ionic interactions at protein–nucleic acid interfaces

B Yu, BM Pettitt, J Iwahara - Accounts of chemical research, 2020 - ACS Publications
Conspectus Molecular association of proteins with nucleic acids is required for many
biological processes essential to life. Electrostatic interactions via ion pairs (salt bridges) of …

A molecular view of DNA flexibility

A Marin-Gonzalez, JG Vilhena, R Perez… - Quarterly Reviews of …, 2021 - cambridge.org
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 …

Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides

ALB Pyne, A Noy, KHS Main… - 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 …

Structural diversity of supercoiled DNA

RN Irobalieva, JM Fogg, DJ Catanese Jr… - Nature …, 2015 - nature.com
By regulating access to the genetic code, DNA supercoiling strongly affects DNA
metabolism. Despite its importance, however, much about supercoiled DNA (positively …

Coarse-graining DNA for simulations of DNA nanotechnology

JPK Doye, TE Ouldridge, AA Louis… - Physical Chemistry …, 2013 - pubs.rsc.org
To simulate long time and length scale processes involving DNA it is necessary to use a
coarse-grained description. Here we provide an overview of different approaches to such …

Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy

A Pyne, R Thompson, C Leung, D Roy… - …, 2014 - eprints.whiterose.ac.uk
Based on soft‐touch atomic force microscopy, a method is described to reconstruct the
secondary structure of single extended biomolecules, without the need for crystallization …

A 2.8 Å Structure of Zoliflodacin in a DNA Cleavage Complex with Staphylococcus aureus DNA Gyrase

H Morgan, M Lipka-Lloyd, AJ Warren… - International Journal of …, 2023 - mdpi.com
Since 2000, some thirteen quinolones and fluoroquinolones have been developed and
have come to market. The quinolones, one of the most successful classes of antibacterial …

Wicked: The untold story of ciprofloxacin

ZC Conley, TJ Bodine, A Chou, L Zechiedrich - PLoS pathogens, 2018 - journals.plos.org
Antibiotics, long used in an attempt to solve the problem of bacterial infections, have resulted
in the unintended consequence of a worldwide spread of antibiotic resistance. The problem …

Supercoiling and looping promote DNA base accessibility and coordination among distant sites

JM Fogg, A Judge, E Stricker, HL Chan… - Biophysical …, 2021 - cell.com
Thursday, February 25, 2021 221a sequences to superhelical apices. Base pair disruption
allows sharp bending at superhelical apices, which facilitates DNA writhing and, thus …

DNA supercoiling-induced shapes alter minicircle hydrodynamic properties

R Waszkiewicz, M Ranasinghe, JM Fogg… - Nucleic acids …, 2023 - academic.oup.com
DNA in cells is organized in negatively supercoiled loops. The resulting torsional and
bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay …