ArticleNucleic acids research2013
Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Telomeric G-quadruplex intermediates unveiled by complex Markov network analysis.Scientific reports · 2026Article
- Biophysics in the Czech Republic: 70th anniversary of the institute of biophysics.European biophysics journal : EBJ · 2025Review
- RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.Nucleic acids research · 2025Article
- Enzymatic bypass of G-quadruplex structures containing oxidative lesions.Nucleic acids research · 2025Article
- Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.Journal of computational chemistry · 2025Article
- Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations.Journal of chemical information and modeling · 2024Article
- BG4 antibody can recognize telomeric G-quadruplexes harboring destabilizing base modifications and lesions.Nucleic acids research · 2024Article
- Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations.Journal of chemical information and modeling · 2023Article
- Phen-DCAngewandte Chemie (International ed. in English) · 2022Article
- Gaining Insights on the Interactions of a Class of Decorated (2-([2,2'-Bipyridin]-6-yl)phenyl)platinum Compounds with c-Myc Oncogene Promoter G-Quadruplex and Other DNA Structures.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Article
- Studying the Dynamics of a Complex G-Quadruplex System: Insights into the Comparison of MD and NMR Data.Journal of chemical theory and computation · 2022Article
- Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes.The journal of physical chemistry. B · 2022Article
- Mechanical diversity and folding intermediates of parallel-stranded G-quadruplexes with a bulge.Nucleic acids research · 2021Article
- Folding intermediate states of the parallel human telomeric G-quadruplex DNA explored using Well-Tempered Metadynamics.Scientific reports · 2020Article
- Streamlining effects of extra telomeric repeat on telomeric DNA folding revealed by fluorescence-force spectroscopy.Nucleic acids research · 2019Article
- Modulation of DNA structure formation using small molecules.Biochimica et biophysica acta. Molecular cell research · 2019Review
- Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes.Nucleic acids research · 2019Article
- The crystal structure of an antiparallel chair-type G-quadruplex formed by Bromo-substituted human telomeric DNA.Nucleic acids research · 2019Article
- Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA). We initiate early stages of unfolding of several G-DNAs by simulating them under no-salt conditions and then try to fold them back using standard excess salt simulations. There is a significant difference between G-DNAs with all-anti parallel stranded stems and those with stems containing mixtures of syn and anti guanosines. The most natural rearrangement for all-anti stems is a vertical mutual slippage of the strands. This leads to stems with reduced numbers of tetrads during unfolding and a reduction of strand slippage during refolding. The presence of syn nucleotides prevents mutual strand slippage; therefore, the antiparallel and hybrid quadruplexes initiate unfolding via separation of the individual strands. The simulations confirm the capability of G-DNA molecules to adopt numerous stable locally and globally misfolded structures. The key point for a proper individual folding attempt appears to be correct prior distribution of syn and anti nucleotides in all four G-strands. The results suggest that at the level of individual molecules, G-DNA folding is an extremely multi-pathway process that is slowed by numerous misfolding arrangements stabilized on highly variable timescales.
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