ArticleJournal of chemical theory and computation2012
Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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Who cites it
99 citing papers in PubMed.
- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- Programmable kinetic barcoding for multiplexed RNA detection with Cas13a.Nature biomedical engineering · 2026Article
- Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge.Journal of chemical information and modeling · 2026Article
- Structural basis of bis-quinolinium ligands binding to quadruplex-duplex hybrids from PIM1 oncogene.Nucleic acids research · 2025Article
- Atomistic Insights Into Interaction of Doxorubicin With DNA: From Duplex to Nucleosome.Journal of computational chemistry · 2025Article
- Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field.Journal of chemical theory and computation · 2025Article
- Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.Journal of computational chemistry · 2025Article
- Stabilization of Hoogsteen H-bonds in G-quartet sheets by coordinated KBioImpacts : BI · 2025Article
- Complex Biophysical and Computational Analyses of G-Quadruplex Ligands: The Porphyrin Stacks Back.Chemistry (Weinheim an der Bergstrasse, Germany) · 2024Article
- Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations.Journal of chemical information and modeling · 2024Article
- van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.Journal of chemical theory and computation · 2024Article
- WhiA transcription factor provides feedback loop between translation and energy production in a genome-reduced bacterium.Frontiers in microbiology · 2024Article
- Feasibility of the inhibitor development for cancer: A systematic approach for drug design.PloS one · 2024Article
- Insight into Tetramolecular DNA G-Quadruplexes Associated with ALS and FTLD: Cation Interactions and Formation of Higher-Ordered Structure.International journal of molecular sciences · 2023Article
- The development of nucleic acids force fields: From an unchallenged past to a competitive future.Biophysical journal · 2023Review
- Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.Journal of chemical theory and computation · 2023Article
- Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.Journal of chemical information and modeling · 2023Article
- High-entropy alloy nanopatterns by prescribed metallization of DNA origami templates.Nature communications · 2023Article
- Mechanism of Chiral-Selective Aminoacylation of an RNA Minihelix Explored by QM/MM Free-Energy Simulations.Life (Basel, Switzerland) · 2023Article
- Inhibited complete folding of consecutive human telomeric G-quadruplexes.Nucleic acids research · 2023Article
39 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
Refinement of empirical force fields for nucleic acids requires their extensive testing using as wide range of systems as possible. However, finding unambiguous reference data is not easy. In this paper, we analyze four systems which we suggest should be included in standard portfolio of molecules to test nucleic acids force fields, namely, parallel and antiparallel stranded DNA guanine quadruplex stems, RNA quadruplex stem, and Z-DNA. We highlight parameters that should be monitored to assess the force field performance. The work is primarily based on 8.4 μs of 100-250 ns trajectories analyzed in detail followed by 9.6 μs of additional selected back up trajectories that were monitored to verify that the results of the initial analyses are correct. Four versions of the Cornell et al. AMBER force field are tested, including an entirely new parmχ(OL4) variant with χ dihedral specifically reparametrized for DNA molecules containing syn nucleotides. We test also different water models and ion conditions. While improvement for DNA quadruplexes is visible, the force fields still do not fully represent the intricate Z-DNA backbone conformation.
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