ArticlePLoS computational biology2019
Why do G-quadruplexes dimerize through the 5'-ends? Driving forces for G4 DNA dimerization examined in atomic detail.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Collision-induced transfer enhances ligand-binding kinetics in guanine quadruplex DNA.Nucleic acids research · 2026Article
- Computational Analysis Uncovering Contrasts in G-Quadruplex Propensity and Aptamer Enrichment in SELEX-Derived Libraries.Chembiochem : a European journal of chemical biology · 2026Article
- Helical aromatic oligoamide foldamers as selective G-quadruplex ligands.Nucleic acids research · 2025Article
- Why Are Left-Handed G-Quadruplexes Scarce?The journal of physical chemistry letters · 2024Article
- Stacking Interactions and Flexibility of Human Telomeric Multimers.Journal of the American Chemical Society · 2023Article
- Higher-order G-quadruplexes in promoters are untapped drug targets.Frontiers in chemistry · 2023Review
- Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection.PLoS computational biology · 2022Article
- Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-Ras and c-Kit promoter sequences.Nucleic acids research · 2022Article
- Understanding self-assembly at molecular level enables controlled design of DNA G-wires of different properties.Nature communications · 2022Article
- Drug discovery of small molecules targeting the higher-order hTERT promoter G-quadruplex.PloS one · 2022Article
- How bioinformatics resources work with G4 RNAs.Briefings in bioinformatics · 2021Review
- Supramolecular Polymorphism of (GInternational journal of molecular sciences · 2021Article
- Covalent Bi-Modular Parallel and Antiparallel G-Quadruplex DNA Nanocostructs Reduce Viability of Patient Glioma Primary Cell Cultures.International journal of molecular sciences · 2021Article
- Aptamers against the β-Conglutin Allergen: Insights into the Behavior of the Shortest Multimeric (Intra)Molecular DNA G-Quadruplex.International journal of molecular sciences · 2021Article
- Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations.Computational and structural biotechnology journal · 2021Article
- Diversity of Parallel Guanine Quadruplexes Induced by Guanine Substitutions.International journal of molecular sciences · 2020Article
- The noncovalent dimerization of a G-quadruplex/hemin DNAzyme improves its biocatalytic properties.Chemical science · 2020Article
- Harnessing intrinsic fluorescence for typing of secondary structures of DNA.Nucleic acids research · 2020Article
- The hTERT core promoter forms three parallel G-quadruplexes.Nucleic acids research · 2020Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
G-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order G4 DNA structures. To understand the molecular driving forces for G4 association, here, we study the binding interaction between two parallel-stranded G-quadruplexes using all-atom molecular dynamics simulations. The predicted dimerization free energies show that direct binding through the 5'-G-tetrads is the most preferred of all possible end-to-end stacking orientations, consistently with all available experimental data. Decomposition of dimerization enthalpies in combination with simulations at varying ionic strength further indicate that the observed orientational preferences arise from a fine balance between the electrostatic repulsion of the sugar-phosphate backbones and favorable counterion binding at the dimeric interface. We also demonstrate how these molecular-scale findings can be used to devise means of controlling G4 dimerization equilibrium, e.g., by altering salt concentration and using G4-targeted ligands.
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