ArticleNucleic acids research2008
Dissociation of minor groove binders from DNA: insights from metadynamics simulations.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Thermodynamics and Kinetics of the Deintercalation of a Novel Anthracycline from Double-Stranded Oligonucleotide DNA.The journal of physical chemistry. B · 2025Article
- DNA Damage and Chromatin Conformation Changes Confer Nonhost Resistance: A Hypothesis Based on Effects of Anti-cancer Agents on Plant Defense Responses.Frontiers in plant science · 2018Article
- Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands.Journal of molecular modeling · 2017Article
- Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Article
- Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models.Journal of chemical theory and computation · 2016Article
- Intermediate states in the binding process of folic acid to folate receptor α: insights by molecular dynamics and metadynamics.Journal of computer-aided molecular design · 2015Article
- Metadynamics simulations reveal a Na+ independent exiting path of galactose for the inward-facing conformation of vSGLT.PLoS computational biology · 2014Article
- Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.Journal of chemical theory and computation · 2014Article
- Mechanistic insight into ligand binding to G-quadruplex DNA.Nucleic acids research · 2014Article
- Role of the protein in the DNA sequence specificity of the cleavage site stabilized by the camptothecin topoisomerase IB inhibitor: a metadynamics study.Nucleic acids research · 2013Article
- Some ligands enhance the efflux of other ligands by the Escherichia coli multidrug pump AcrB.Biochemistry · 2013Article
- Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.The Journal of chemical physics · 2013Article
- A novel dendrimeric peptide with antimicrobial properties: structure-function analysis of SB056.Biophysical journal · 2012Article
- Article
- Molecular motions in drug design: the coming age of the metadynamics method.Journal of computer-aided molecular design · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have used metadynamics to investigate the mechanism of noncovalent dissociation from DNA by two representatives of alkylating and noncovalent minor groove (MG) binders. The compounds are anthramycin in its anhydrous form (IMI) and distamycin A (DST), which differ in mode of binding, size, flexibility and net charge. This choice enables to evaluate the influence of such factors on the mechanism of dissociation. Dissociation of IMI requires an activation free energy of approximately 12 kcal/mol and occurs via local widening of the MG and loss of contacts between the drug and one DNA strand, along with the insertion of waters in between. The detachment of DST occurs at a larger free energy cost, approximately 16.5 or approximately 18 kcal/mol depending on the binding mode. These values compare well with that of 16.6 kcal/mol extracted from stopped-flow experiments. In contrast to IMI, an intermediate is found in which the ligand is anchored to the DNA through its amidinium tail. From this conformation, binding and unbinding occur almost at the same rate. Comparison between DST and with kinetic models for the dissociation of Hoechst 33258 from DNA uncovers common characteristics across different classes of noncovalent MG ligands.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.