ArticleNucleic acids research2015
Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Stable Protein-Based G-Quadruplex-Derived Supramolecular Bioinks as Tunable ECM-Mimetic Constructs Assembled by Combining Non-Covalent and Covalent Strategies.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Telomeric G-quadruplex intermediates unveiled by complex Markov network analysis.Scientific reports · 2026Article
- i-Motif, not G-quadruplex, stability regulates insulin expression.Nucleic acids research · 2026Article
- Hyperpolarized NMR Reveals Low-Populated Folding Intermediates in DNA.Journal of the American Chemical Society · 2025Article
- RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.Nucleic acids research · 2025Article
- Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering.Nucleic acids research · 2025Article
- Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.Journal of computational chemistry · 2025Article
- Insights into the Molecular Structure, Stability, and Biological Significance of Non-Canonical DNA Forms, with a Focus on G-Quadruplexes and i-Motifs.Molecules (Basel, Switzerland) · 2024Review
- RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy.Nucleic acids research · 2024Article
- Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations.Journal of chemical information and modeling · 2023Article
- 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
- Article
- Thermally Induced Transitions of d(GLife (Basel, Switzerland) · 2022Article
- Remodeling the conformational dynamics of I-motif DNA by helicases in ATP-independent mode at acidic environment.iScience · 2022Article
- Insight into formation propensity of pseudocircular DNA G-hairpins.Nucleic acids research · 2021Article
- Ion Binding Properties and Dynamics of theJournal of chemical information and modeling · 2020Article
- Folding intermediate states of the parallel human telomeric G-quadruplex DNA explored using Well-Tempered Metadynamics.Scientific reports · 2020Article
- 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
- Adenine-Driven Structural Switch from a Two- to Three-Quartet DNA G-Quadruplex.Angewandte Chemie (International ed. in English) · 2018Article
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8 authors.
Funding
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Abstract
DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating ∼130 μs of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-μs scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best understood by the kinetic partitioning mechanism with a set of deep competing minima on the folding landscape, with only a small fraction of molecules directly folding to the native fold. The landscape should further include non-specific collapse processes where the molecules move via diffusion and consecutive random rare transitions, which could, e.g. structure the propeller loops.
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