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 …

Molecular recognition of synthetic RNAs by phenothiazinium dyes methylene blue and new methylene blue: Thermodynamic approach

P Paul - Journal of Molecular Structure, 2024 - Elsevier
Many biological process and function centers around recognition of double stranded RNA
as it impacts numerous pathways associated with maturation of cellular RNA. This work …

Modeling and analysis of intercalant effects on circular DNA conformation

E Krueger, J Shim, A Fathizadeh, AN Chang, B Subei… - ACS …, 2016 - ACS Publications
The large-scale conformation of DNA molecules plays a critical role in many basic elements
of cellular functionality and viability. By targeting the structural properties of DNA, many …

The theory of interceptor-protector action of DNA binding drugs

MP Evstigneev, AS Buchelnikov… - Progress in Biophysics and …, 2019 - Elsevier
The review discusses the theory of interceptor-protector action (the IPA theory) as the new
self-consistent biophysical theory establishing a quantitative interrelation between …

[HTML][HTML] Thermal analysis of ligand-DNA interaction: determination of binding parameters

E Bereznyak, N Gladkovskaya, E Dukhopelnykov… - Aims …, 2015 - aimspress.com
The review discusses the methods of thermodynamic analysis of reactions of non-covalent
binding of biologically active compounds with DNA, which is a key constituent of cell …

Investigations on the interactions of 5-fluorouracil with herring sperm DNA: Steady state/time resolved and molecular modeling studies

S Chinnathambi, S Karthikeyan… - … Reviews and Letters, 2015 - World Scientific
In the present study, the interaction of 5-Fluorouracil with herring sperm DNA is reported
using spectroscopic and molecular modeling techniques. This binding study of 5-FU with hs …

Ligand binding to nucleic acids in solution and on microchips

YD Nechipurenko, AS Buchelnikov - Biophysics, 2022 - Springer
The equilibrium binding of ligands (proteins, biologically active compounds, and
oligonucleotides) to nucleic acids underlies many processes in the living cell. Model study …

Investigation of differential absorption of DNA complexes with ligands

MV Minasyants - Proceedings of the YSU B: Chemical and …, 2014 - journals.ysu.am
The investigation of complexes of ethidium bromide (EtBr) and methylene blue (MB) with
DNA at 0.02 M Na+ ionic strength of solution has been carried out. Absorption and …

Effects of Intercalating Molecules on the Polymer Properties of DNA

J Tibbs, SMA Tabei, TE Kidd… - The Journal of Physical …, 2020 - ACS Publications
Atomic force microscopy (AFM) enables determination of physical properties from single
DNA molecules. Insertion of aromatic molecules into the structure of DNA results in …

Thermodynamic analysis of ligand-DNA complex formation from the spectrophotometric data

H Anastasiia - 2015 International Young Scientists Forum on …, 2015 - ieeexplore.ieee.org
DNA is the target for many anticancer and antitumor drugs. Therefore determination of the
thermodynamic parameters of ligands-DNA interaction for prediction of biological activity at …