ArticleNucleic acids research2017
How accurate are accurate force-fields for B-DNA?
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes.Biophysical journal · 2026Article
- Force fields matter in DNA polProtein science : a publication of the Protein Society · 2026Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers.Nucleic acids research · 2025Article
- The 'very moment' when UDG recognizes a flipped-out uracil base in dsDNA.Scientific reports · 2025Article
- Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism.Nucleic acids research · 2025Article
- Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications.NAR genomics and bioinformatics · 2024Article
- Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.Nucleic acids research · 2024Article
- Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair.ACS physical chemistry Au · 2024Article
- Temperature-dependent elasticity of DNA, RNA, and hybrid double helices.Biophysical journal · 2024Article
- Temperature-Dependent Twist of Double-Stranded RNA Probed by Magnetic Tweezer Experiments and Molecular Dynamics Simulations.The journal of physical chemistry. B · 2024Article
- Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations.Journal of chemical theory and computation · 2023Article
- Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations.The journal of physical chemistry. B · 2023Article
- Three-Dimensional Modeling of CpG DNA Binding with Matrix Lumican Shows Leucine-Rich Repeat Motif Involvement as in TLR9-CpG DNA Interactions.International journal of molecular sciences · 2023Article
- Experimental detection of conformational transitions between forms of DNA: problems and prospects.Biophysical reviews · 2023Review
- Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency.The journal of physical chemistry. B · 2023Article
- The development of nucleic acids force fields: From an unchallenged past to a competitive future.Biophysical journal · 2023Review
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides.Nucleic acids research · 2023Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Last generation of force-fields are raising expectations on the quality of molecular dynamics (MD) simulations of DNA, as well as to the belief that theoretical models can substitute experimental ones in several cases. However these claims are based on limited benchmarks, where MD simulations have shown the ability to reproduce already existing 'experimental models', which in turn, have an unclear accuracy to represent DNA conformation in solution. In this work we explore the ability of different force-fields to predict the structure of two new B-DNA dodecamers, determined herein by means of 1H nuclear magnetic resonance (NMR). The study allowed us to check directly for experimental NMR observables on duplexes previously not solved, and also to assess the reliability of 'experimental structures'. We observed that technical details in the annealing procedures can induce non-negligible local changes in the final structures. We also found that while not all theoretical simulations are equally reliable, those obtained using last generation of AMBER force-fields (BSC1 and BSC0OL15) show predictive power in the multi-microsecond timescale and can be safely used to reproduce global structure of DNA duplexes and fine sequence-dependent details.
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