ArticlePLoS computational biology2014
Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Rational Polyligand Design for G-Quadruplex Multimer Stabilization.Journal of chemical information and modeling · 2026Article
- From Triads to Tools: A Comprehensive Review of the Expanding Roles of G-Triplex Structures.Molecules (Basel, Switzerland) · 2025Review
- 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
- 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
- A backbone-dependent rotamer library with high (ϕ, ψ) coverage using metadynamics simulations.Protein science : a publication of the Protein Society · 2022Article
- Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes.The journal of physical chemistry. B · 2022Article
- Pre-folded structures govern folding pathways of human telomeric G-quadruplexes.Nucleic acids research · 2020Article
- Folding intermediate states of the parallel human telomeric G-quadruplex DNA explored using Well-Tempered Metadynamics.Scientific reports · 2020Article
- Why do G-quadruplexes dimerize through the 5'-ends? Driving forces for G4 DNA dimerization examined in atomic detail.PLoS computational biology · 2019Article
- Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes.Nucleic acids research · 2019Article
- Structural Flexibility of DNA-RNA Hybrid Duplex: Stretching and Twist-Stretch Coupling.Biophysical journal · 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
- Competitive Binding of MgBiophysical journal · 2018Article
- Fast-Folding Pathways of the Thrombin-Binding Aptamer G-Quadruplex Revealed by a Markov State Model.Biophysical journal · 2018Article
- Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level.Nucleic acids research · 2017Article
- 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
- Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.Journal of chemical theory and computation · 2017Article
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Abstract
In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and K(+) ions explicitly modeled. Enabled by the powerful bias-exchange metadynamics and large-scale conventional molecular dynamic simulations, the free energy landscape of this G-DNA was obtained for the first time and four folding intermediates were identified, including a triplex and a basically formed quadruplex. The simulations also provided atomistic pictures for the structures and cation binding patterns of the intermediates. The results showed that the structure formation and cation binding are cooperative and mutually supporting each other. The syn/anti reorientation dynamics of the intermediates was also investigated. It was found that the nucleotides usually take correct syn/anti configurations when they form native and stable hydrogen bonds with the others, while fluctuating between two configurations when they do not. Misfolded intermediates with wrong syn/anti configurations were observed in the early intermediates but not in the later ones. Based on the simulations, we also discussed the roles of the non-native interactions. Besides, the formation process of the parallel conformation in the first two G-repeats and the associated reversal loop were studied. Based on the above results, we proposed a folding pathway for the hybrid-1 type G-quadruplex with atomistic details, which is new and more complete compared with previous ones. The knowledge gained for this type of G-DNA may provide a general insight for the folding of the other G-quadruplexes.
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