ArticleNucleic acids research2018
Structural dynamics of propeller loop: towards folding of RNA G-quadruplex.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Revealing G4 Structures as Drug Targets: Exploring the Potential of Novel Therapeutic Agents.Research (Washington, D.C.) · 2026Review
- RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.Nucleic acids research · 2025Article
- Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.Journal of computational chemistry · 2025Article
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA.NAR genomics and bioinformatics · 2024Article
- 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
- Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back.Nucleic acids research · 2020Article
- Stabilization of human telomeric RNA G-quadruplex by the water-compatible optically pure and biologically-active metallohelices.Scientific reports · 2020Article
- Polarizable Molecular Dynamics Simulations of TwoJournal of chemical theory and computation · 2020Article
- Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs.Nucleic acids research · 2020Article
- Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes.Nucleic acids research · 2019Article
- Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions.Journal of chemical theory and computation · 2019Article
- Folding Landscape of a Parallel G-Quadruplex.The journal of physical chemistry letters · 2019Article
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding mechanism of propeller loops suggested in this work may be common for their formation in RNA and DNA GQs.
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