ArticlePloS one2012
Mg2+ in the major groove modulates B-DNA structure and dynamics.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 48 citations in OpenAlex.
- Pair Dynamics of Aqueous MgClChemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Direct evidence and quantification of homologous recognition between DNA duplexes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Spermidine is a common component of the eDNA-dependent biofilm matrix.NPJ biofilms and microbiomes · 2026Article
- Ion-Specific Modulation of the Conformation and Compactness of DNA Oligo-Catenanes.The journal of physical chemistry. B · 2026Article
- Rapid means of biofilm disruption induce the newly released (NRel) phenotype of enhanced antibiotic sensitivity.Frontiers in microbiology · 2026Article
- Bisulfite probing reveals DNA structural intricacies.Nucleic acids research · 2023Article
- Specific Zn(II)-binding site in the C-terminus of Aspf2, a zincophore from Aspergillus fumigatus.Metallomics : integrated biometal science · 2022Article
- Ferrocene-Containing DNA Monolayers: Influence of Electrostatics on the Electron Transfer Dynamics.Langmuir : the ACS journal of surfaces and colloids · 2021Article
- A perspective on the molecular simulation of DNA from structural and functional aspects.Chemical science · 2021Review
- The role of assembly parameters on polyplex poly(beta-amino ester) nanoparticle transfections.Biotechnology and bioengineering · 2019Article
- RecA requires two molecules of Mg2+ ions for its optimal strand exchange activity in vitro.Nucleic acids research · 2018Article
- Photochemical analysis of structural transitions in DNA liquid crystals reveals differences in spatial structure of DNA molecules organized in liquid crystalline form.Scientific reports · 2018Article
- Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions.PloS one · 2017Article
- Force regulated dynamics of RPA on a DNA fork.Nucleic acids research · 2016Article
- Article
- A targeted DNA substrate mechanism for the inhibition of HIV-1 integrase by inhibitors with antiretroviral activity.FEBS open bio · 2016Article
- All-atom crystal simulations of DNA and RNA duplexes.Biochimica et biophysica acta · 2015Article
- A repulsion mechanism explains magnesium permeation and selectivity in CorA.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Atomic level rendering of DNA-drug encounter.Biophysical journal · 2014Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This study investigates the effect of Mg(2+) bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5'-CpA or TpG. Based on this knowledge, molecular dynamics simulations were carried out on a DNA oligomer without or with Mg(2+) close to an ApG step. These simulations showed that the hydrated Mg(2+) forms a stable intra-strand cross-link between the two purines in solution. ApG generates an electrostatic potential in the major groove that is particularly attractive for cations; its intrinsic conformation is well-adapted to the formation of water-mediated hydrogen bonds with Mg(2+). The binding of Mg(2+) modulates the behavior of the 5'-neighboring step by increasing the BII (ε-ζ>0°) population of its phosphate group. Additional electrostatic interactions between the 5'-phosphate group and Mg(2+) strengthen both the DNA-cation binding and the BII character of the 5'-step. Cation binding in the major groove may therefore locally influence the DNA conformational landscape, suggesting a possible avenue for better understanding how strong DNA distortions can be stabilized in protein-DNA complexes.
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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.