Journal of Chemical Theory and Computation 2022, 18 Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA. The Journal of Physical Chemistry B 2022, 126 Nearest-Neighbor dsDNA Stability Analysis Using Alchemical Free-Energy Simulations. The Journal of Physical Chemistry Letters 2022, 13 Microscopic Insight into pH-Dependent Conformational Dynamics and Noncanonical Base Pairing in Telomeric i-Motif DNA. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA–Protein Complexes. Tucker, Stefano Piana, Dazhi Tan, Michael V. Studying the Dynamics of a Complex G-Quadruplex System: Insights into the Comparison of MD and NMR Data. Matteo Castelli, Filippo Doria, Mauro Freccero, Giorgio Colombo, Elisabetta Moroni.Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA. RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis. Şölen Ekesan, Erika McCarthy, David A.Journal of Chemical Information and Modeling 2022, 62 Preserving the Integrity of Empirical Force Fields. Orr, Suliman Sharif, Junmei Wang, Alexander D. Improving All-Atom Force Field to Accurately Describe DNA G-Quadruplex Loops. This article is cited by 248 publications. We recommend using β OL1 in combination with our previously introduced corrections, εζ OL1 and χ OL4, (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. We suggest a refinement of this potential, β OL1, which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. We show that this underprediction can be attributed to an inaccurate potential for the sugar–phosphate backbone torsion angle β. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. Z-DNA duplexes are a particularly complicated test case for current force fields.
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