Dynamics of ionic interactions at protein–nucleic acid interfaces
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 …
biological processes essential to life. Electrostatic interactions via ion pairs (salt bridges) of …
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 …
Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides
In the cell, DNA is arranged into highly-organised and topologically-constrained
(supercoiled) structures. It remains unclear how this supercoiling affects the detailed double …
(supercoiled) structures. It remains unclear how this supercoiling affects the detailed double …
Structural diversity of supercoiled DNA
By regulating access to the genetic code, DNA supercoiling strongly affects DNA
metabolism. Despite its importance, however, much about supercoiled DNA (positively …
metabolism. Despite its importance, however, much about supercoiled DNA (positively …
Coarse-graining DNA for simulations of DNA nanotechnology
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 …
coarse-grained description. Here we provide an overview of different approaches to such …
Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy
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 …
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
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 …
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 …
in the unintended consequence of a worldwide spread of antibiotic resistance. The problem …
Supercoiling and loo** 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 …
DNA supercoiling-induced shapes alter minicircle hydrodynamic properties
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 …
bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay …