ArticleJournal of chemical theory and computation2025
Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Molecular Basis of pH-Dependent Activity in T7 RNA Polymerase Revealed by Constant pH Replica Exchange Molecular Dynamics.ACS physical chemistry Au · 2026Article
- Substrate-Specific Inactivation of Human AAG by Tumor-Associated Single Nucleotide Polymorphic Variants.International journal of molecular sciences · 2026Article
- The Effect of CuACS chemical neuroscience · 2026Article
- Mechanistic basis for improved activity of Engineered AsCas12a.Communications biology · 2026Article
- Force fields matter in DNA polProtein science : a publication of the Protein Society · 2026Article
- The Role of Active Site Hydrophobic Interactions in Facilitating Catalysis in Human Terminal Deoxynucleotidyl Transferase.International journal of molecular sciences · 2025Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition.Nucleic acids research · 2025Article
- Adaptation of DNA to Protein Binding Revealed by Spectroscopy and Molecular Simulation.The journal of physical chemistry. B · 2025Article
- Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats.Journal of chemical information and modeling · 2025Article
- High Bendability of Short RNA-DNA Hybrid Duplex Revealed by Single-Molecule Cyclization and Molecular Dynamics Simulations.Biomolecules · 2025Article
- Thermodynamic Parameter Estimation for Modified Oligonucleotides Using Molecular Dynamics Simulations.The journal of physical chemistry. B · 2025Article
- NMR structure study of DNA G-quadruplexes and ligand complexes.Progress in nuclear magnetic resonance spectroscopyReview
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3 authors.
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Abstract
The transition from B-DNA to A-DNA occurs in many protein-DNA interactions or in DNA/RNA hybrid duplexes, and thus plays a role in many important biomolecular processes that convey the biological function of DNA. However, the stability of A-DNA is severely underestimated in current AMBER force fields such as OL15, OL21 or bsc1, potentially leading to unstable or deformed protein-DNA complexes. In this study, we refine the deoxyribose dihedral potential to increase the stability of the north (N) puckering present in A-DNA. The new parameters, termed OL24, model A/B equilibrium in B-DNA duplexes in water in good agreement with nuclear magnetic resonance (NMR) experiment. They also improve the description of DNA/RNA hybrids and the transition of the DNA duplex to the A-form in concentrated ethanol solutions. These refinements significantly improve the modeling of protein-DNA complexes, increasing their structural stability and A-form population, while maintaining accurate representation of canonical B-DNA duplexes. Overall, the new parameters should allow more reliable modeling of the thermodynamic equilibrium between A- and B-DNA forms and the interactions of DNA with proteins.
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