ArticleNucleic acids research2019
Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Rational Polyligand Design for G-Quadruplex Multimer Stabilization.Journal of chemical information and modeling · 2026Article
- Sequence-Encoded Frustration Directs the Formation of Abridged G-Quadruplex Architectures.Angewandte Chemie (International ed. in English) · 2026Article
- U2 snRNP recognizes the branch site through a loaded-spring strand-invasion mechanism.Nucleic acids research · 2026Article
- Telomeric G-quadruplex intermediates unveiled by complex Markov network analysis.Scientific reports · 2026Article
- Hyperpolarized NMR Reveals Low-Populated Folding Intermediates in DNA.Journal of the American Chemical Society · 2025Article
- Auto-luminescence study of thermal unfolding of DNA G-quadruplexes.RSC advances · 2025Article
- RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.Nucleic acids research · 2025Article
- Polymeric Properties of Telomeric G-Quadruplex Multimers: Effects of Chemically Inert Crowders.Biomacromolecules · 2025Article
- Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.Journal of computational chemistry · 2025Article
- A TeZla micromixer for interrogating the early and broad folding landscape of G-quadruplex via multistage velocity descending.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy.Nucleic acids research · 2024Article
- Benzimidazole-based small molecules as anticancer agents targeting telomeric G-quadruplex and inhibiting telomerase enzyme.Future medicinal chemistry · 2024Review
- Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations.Journal of chemical information and modeling · 2023Article
- Factors Impacting Invader-Mediated Recognition of Double-Stranded DNA.Molecules (Basel, Switzerland) · 2022Article
- 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
- Dynamic interaction of BRCA2 with telomeric G-quadruplexes underlies telomere replication homeostasis.Nature communications · 2022Article
- Remodeling the conformational dynamics of I-motif DNA by helicases in ATP-independent mode at acidic environment.iScience · 2022Article
- The effects of molecular crowding and CpG hypermethylation on DNA G-quadruplexes formed by the C9orf72 nucleotide repeat expansion.Scientific reports · 2021Article
- Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy.Biomolecules · 2021Review
- Nanomechanics of G-quadruplexes within the promoter of the KIT oncogene.Nucleic acids research · 2021Article
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7 authors.
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Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acids structures common in important genomic regions. Parallel-stranded G4 folds are the most abundant, but their folding mechanism is not fully understood. Recent research highlighted that G4 DNA molecules fold via kinetic partitioning mechanism dominated by competition amongst diverse long-living G4 folds. The role of other intermediate species such as parallel G-triplexes and G-hairpins in the folding process has been a matter of debate. Here, we use standard and enhanced-sampling molecular dynamics simulations (total length of ∼0.9 ms) to study these potential folding intermediates. We suggest that parallel G-triplex per se is rather an unstable species that is in local equilibrium with a broad ensemble of triplex-like structures. The equilibrium is shifted to well-structured G-triplex by stacked aromatic ligand and to a lesser extent by flanking duplexes or nucleotides. Next, we study propeller loop formation in GGGAGGGAGGG, GGGAGGG and GGGTTAGGG sequences. We identify multiple folding pathways from different unfolded and misfolded structures leading towards an ensemble of intermediates called cross-like structures (cross-hairpins), thus providing atomistic level of description of the single-molecule folding events. In summary, the parallel G-triplex is a possible, but not mandatory short-living (transitory) intermediate in the folding of parallel-stranded G4.
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