ArticleJournal of chemical theory and computation2022
Studying the Dynamics of a Complex G-Quadruplex System: Insights into the Comparison of MD and NMR Data.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Effects of Loop Nucleobase Substitution on G-Quadruplex Thermal Stability in Aqueous Glycine Betaine, Proline, TMAO, and Urea Solutions.Biomolecules · 2026Article
- Exploring Nucleic Acid Structure and Function with Molecular Dynamics and Fragment Molecular Orbital Methods.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Molecular Tools for Precision Targeting and Detection of G-Quadruplex Structures.Molecules (Basel, Switzerland) · 2025Review
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.Nature communications · 2025Article
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.bioRxiv : the preprint server for biology · 2025Article
- Bridged Azobenzene Exhibits Fully Reversible Photocontrolled Binding to a G‑Quadruplex DNA/Duplex Junction.JACS Au · 2025Article
- Synthetic G-quadruplex components for predictable, precise two-level control of mammalian recombinant protein expression.Nucleic acids research · 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
- Base pair dynamics, electrostatics, and thermodynamics at the LTR-III quadruplex:duplex junction.Biophysical journal · 2024Article
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) simulations are coming of age in the study of nucleic acids, including specific tertiary structures such as G-quadruplexes. While being precious for providing structural and dynamic information inaccessible to experiments at the atomistic level of resolution, MD simulations in this field may still be limited by several factors. These include the force fields used, different models for ion parameters, ionic strengths, and water models. We address various aspects of this problem by analyzing and comparing microsecond-long atomistic simulations of the G-quadruplex structure formed by the human immunodeficiency virus long terminal repeat (HIV LTR)-III sequence for which nuclear magnetic resonance (NMR) structures are available. The system is studied in different conditions, systematically varying the ionic strengths, ion numbers, and water models. We comparatively analyze the dynamic behavior of the G-quadruplex motif in various conditions and assess the ability of each simulation to satisfy the nuclear magnetic resonance (NMR)-derived experimental constraints and structural parameters. The conditions taking into account K
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