ArticleThe journal of physical chemistry. B2022
RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations.
Article in The journal of physical chemistry. B, 2022. 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.
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Insights into siRNA Duplex Stability by UV Spectrophotometry Absorbance and Melting Temperature Analyses.ACS omega · 2026Article
- Selective binding of divalent cations reshapes nucleosome mechanics and unlocks histone tail dynamics.Communications biology · 2026Article
- Local cation-clamping distorts and softens RNA duplex.Communications biology · 2026Article
- Molecular drivers of RNA phase separation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Importance of Solution Studies for the Structural Characterization of the Enterovirus 5' Cloverleaf.Viruses · 2025Article
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- Interference of small compounds and MgScientific reports · 2024Article
- Molecular Dynamics Simulations of the miR-155 Duplex: Impact of Ionic Strength on Structure and NaMolecules (Basel, Switzerland) · 2024Article
- Barium Concentration-Dependent Anomalous Electrophoresis of Synthetic DNA Motifs.ACS applied bio materials · 2024Article
- The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.Nucleic acids research · 2024Article
- Enhancing Endosomal Escape and Gene Regulation Activity for Spherical Nucleic Acids.Small (Weinheim an der Bergstrasse, Germany) · 2024Article
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
- Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.Biophysical journal · 2023Article
- Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.Journal of chemical theory and computation · 2023Article
- Universality in RNA and DNA deformations induced by salt, temperature change, stretching force, and protein binding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Biomolecular Electrostatic Phenomena: An Evergreen Field.The journal of physical chemistry. B · 2023Article
- Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs.bioRxiv : the preprint server for biology · 2023Article
- Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.Journal of chemical information and modeling · 2023Article
- Molecular dynamics study of collective water vibrations in a DNA hydration shell.European biophysics journal : EBJ · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The distribution of cations around nucleic acids is essential for a broad variety of processes ranging from DNA condensation and RNA folding to the detection of biomolecules in biosensors. Predicting the exact distribution of ions remains challenging since the distribution and, hence, a broad variety of nucleic acid properties depend on the salt concentration, the valency of the ions, and the ion type. Despite the importance, a general theory to quantify ion-specific effects for highly charged biomolecules is still lacking. Moreover, recent experiments reveal that despite their similar building blocks, DNA and RNA duplexes can react differently to the same ionic conditions. The aim of our current work is to provide a comprehensive set of molecular dynamics simulations using more than 180 μs of simulation time. For the mono- and divalent cations Li
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