ArticleNucleic acids research2020
Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes.
Article in Nucleic acids research, 2020. 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, 43 citations in OpenAlex.
- Drude SILCS-Nucleic: harnessing explicit electronic polarization in targeting RNA and DNA for drug design.Nucleic acids research · 2026Article
- Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.bioRxiv : the preprint server for biology · 2025Article
- RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.Nucleic acids research · 2025Article
- Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems.Journal of chemical theory and computation · 2025Article
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.The Journal of chemical physics · 2024Article
- Hexaconazole exposure may lead to Parkinson via disrupting glucocerebrosidase and parkin: molecular interaction, dynamics, MMPBSA and DFT basedToxicology research · 2024Article
- RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy.Nucleic acids research · 2024Article
- Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes.Journal of chemical information and modeling · 2023Article
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Article
- 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
- G4-quadruplex-binding proteins: review and insights into selectivity.Biophysical reviews · 2022Review
- CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.Journal of computational chemistry · 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
- Ion Binding Properties and Dynamics of theJournal of chemical information and modeling · 2020Article
- Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides.Journal of molecular modeling · 2020Article
- Polarizable Molecular Dynamics Simulations of TwoJournal of chemical theory and computation · 2020Article
- Impact of electronic polarizability on protein-functional group interactions.Physical chemistry chemical physics : PCCP · 2020Article
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1 author at 1 institution in 1 country.
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Abstract
DNA and RNA sequences rich in guanine can fold into noncanonical structures called G-quadruplexes (GQs), which exhibit a common stem structure of Hoogsteen hydrogen-bonded guanine tetrads and diverse loop structures. GQ sequence motifs are overrepresented in promoters, origins of replication, telomeres, and untranslated regions in mRNA, suggesting roles in modulating gene expression and preserving genomic integrity. Given these roles and unique aspects of different structures, GQs are attractive targets for drug design, but greater insight into GQ folding pathways and the interactions stabilizing them is required. Here, we performed molecular dynamics simulations to study two bimolecular GQs, a telomeric DNA GQ and the analogous telomeric repeat-containing RNA (TERRA) GQ. We applied the Drude polarizable force field, which we show outperforms the additive CHARMM36 force field in both ion retention and maintenance of the GQ folds. The polarizable simulations reveal that the GQs bind bulk K+ ions differently, and that the TERRA GQ accumulates more K+ ions, suggesting different ion interactions stabilize these structures. Nucleobase dipole moments vary as a function of position and also contribute to ion binding. Finally, we show that the TERRA GQ is more sensitive than the telomeric DNA GQ to water-mediated modulation of ion-induced dipole-dipole interactions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.