ArticleNucleic acids research2015
Extended molecular dynamics of a c-kit promoter quadruplex.
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 20 papers.
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Who cites it
20 citing papers in PubMed.
- Enhancing G-Quadruplex Binding: Rational Design and Biophysical Evaluation of Dimeric Ligands.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.Nucleic acids research · 2025Article
- Insight into Tetramolecular DNA G-Quadruplexes Associated with ALS and FTLD: Cation Interactions and Formation of Higher-Ordered Structure.International journal of molecular sciences · 2023Article
- 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
- Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes.Molecules (Basel, Switzerland) · 2021Article
- Cation competition and recruitment around the c-kit1 G-quadruplex using polarizable simulations.Biophysical journal · 2021Article
- Polarizable Molecular Dynamics Simulations of TwoJournal of chemical theory and computation · 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
- Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus.RNA (New York, N.Y.) · 2019Article
- Article
- Structural dynamics of propeller loop: towards folding of RNA G-quadruplex.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Fast-Folding Pathways of the Thrombin-Binding Aptamer G-Quadruplex Revealed by a Markov State Model.Biophysical journal · 2018Article
- Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.Journal of chemical theory and computation · 2017Article
- Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery.Biochemistry. Biokhimiia · 2016Article
- Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad-a common structural unit of G-quadruplex DNA.Nucleic acids research · 2016Article
- Article
- Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations.Nucleic acids research · 2015Article
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7 authors.
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Abstract
The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 μs long, ∼50 μs in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal μs-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex.
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