Ethidium bromide interactions with DNA: an exploration of a classic DNA–ligand complex with unbiased molecular dynamics simulations

R Galindo-Murillo, TE Cheatham III - Nucleic acids research, 2021 - academic.oup.com
Visualization of double stranded DNA in gels with the binding of the fluorescent dye
ethidium bromide has been a basic experimental technique in any molecular biology …

Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies

JY Lee, Y Kim, DN Kim - Nature Communications, 2024 - nature.com
Chemo-mechanical deformation of structured DNA assemblies driven by DNA-binding
ligands has offered promising avenues for biological and therapeutic applications. However …

DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site

XX Zhang, SL Brantley, SA Corcelli… - Communications …, 2020 - nature.com
Understanding the dynamic interactions of ligands to DNA is important in DNA-based
nanotechnologies. By structurally tracking the dissociation of Hoechst 33258-bound DNA (d …

Unique features of metformin: a combined experimental, theoretical, and simulation study of its structure, dynamics, and interaction energetics with DNA grooves

S Mondal, RN Samajdar, S Mukherjee… - The Journal of …, 2018 - ACS Publications
There are certain small molecules that exhibit extraordinarily diverse biological activities.
Metformin is one of them. It is widely used as an antidiabetic drug for type-two diabetes …

A Cu (II) complex targeting the translocator protein: in vitro and in vivo antitumor potential and mechanistic insights

D Montagner, B Fresch, K Browne, V Gandin… - Chemical …, 2017 - pubs.rsc.org
A new Cu-based anticancer metallodrug which targets the translocator protein is
reported.[CuBr2 (TZ6)] elicits a remarkable in vitro cytotoxicity in sensitive and multidrug …

Understanding the kinetic mechanism of RNA single base pair formation

X Xu, T Yu, SJ Chen - … of the National Academy of Sciences, 2016 - National Acad Sciences
RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA
folding is the closing and opening of a base pair. Understanding this elementary rate …

2D-IR spectroscopy shows that optimized DNA minor groove binding of Hoechst33258 follows an induced fit model

LAI Ramakers, G Hithell, JJ May… - The Journal of …, 2017 - ACS Publications
The induced fit binding model describes a conformational change occurring when a small
molecule binds to its biomacromolecular target. The result is enhanced noncovalent …

Combining steady state and temperature jump IR spectroscopy to investigate the allosteric effects of ligand binding to dsDNA

J Dale, CP Howe, H Toncrova, R Fritzsch… - Physical Chemistry …, 2021 - pubs.rsc.org
Changes in the structural dynamics of double stranded (ds) DNA upon ligand binding have
been linked to the mechanism of allostery without conformational change, but direct …

Coherent electronic and nuclear dynamics in a rhodamine heterodimer–DNA supramolecular complex

M Cipolloni, B Fresch, I Occhiuto, P Rukin… - Physical Chemistry …, 2017 - pubs.rsc.org
Elucidating the role of quantum coherences in energy migration within biological and
artificial multichromophoric antenna systems is the subject of an intense debate. It is also a …

Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes

AK Sahoo, B Bagchi, PK Maiti - The Journal of chemical physics, 2019 - pubs.aip.org
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding
mode. Although experimental studies have become available recently, a molecular-level …