ArticleThe journal of physical chemistry. B2010
DNA duplex stability: the role of preorganized electrostatics.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
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- Insight into Inhibitory Mechanism of PDE4D by Dietary Polyphenols Using Molecular Dynamics Simulations and Free Energy Calculations.Biomolecules · 2021Article
- Molecular Dynamics Simulations Predict That rSNP Located in theBiomolecules · 2020Article
- Aflatoxin B₁⁻Formamidopyrimidine DNA Adducts: Relationships between Structures, Free Energies, and Melting Temperatures.Molecules (Basel, Switzerland) · 2019Article
- Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2.Physical chemistry chemical physics : PCCP · 2016Article
- Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment.Journal of chemical theory and computation · 2015Article
- Co-solvation effect on the binding mode of the α-mangostin/β-cyclodextrin inclusion complex.Beilstein journal of organic chemistry · 2015Article
- Free energy of binding of coiled-coil complexes with different electrostatic environments: the influence of force field polarisation and capping.Natural products and bioprospecting · 2014Article
- Effects of water models on binding affinity: evidence from all-atom simulation of binding of tamiflu to A/H5N1 neuraminidase.TheScientificWorldJournal · 2014Article
- Structure-based function prediction of uncharacterized protein using binding sites comparison.PLoS computational biology · 2013Article
- Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues.Journal of chemical information and modeling · 2012Article
- Intramolecular base stacking of dinucleoside monophosphate anions in aqueous solution.The journal of physical chemistry. B · 2012Article
- An abridged transition state model to derive structure, dynamics, and energy components of DNA polymerase β fidelity.Biochemistry · 2011Article
- Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor.Journal of biological physics · 2011Article
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Authors and funding
5 authors.
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Abstract
The insertion of a DNA base moiety at the end of a DNA duplex to form a Watson-Crick or wobble pair during DNA annealing or replication is a step of fundamental biological importance. Therefore, we investigated the energetics of a formation of the terminal G x C, G x T, and G x A base pairs in DNA containing a 5'-dangling G adjacent to the base insertion point using differential scanning calorimetry and computer simulations. The energies calculated along classical molecular dynamics trajectories in aqueous solution were analyzed in the framework of linear-response approximation (LRA) to obtain relative free energies for the base insertion and their electrostatic, van der Waals, and preorganization components. Using the generic set of LRA parameters, the calculated free energies disfavored the mispair formation by 2.5 (G x C --> G x T) and 1.7 (G x C --> G x A) kcal/mol, in reasonable agreement with the experimental free energy differences of 1.8 and 1.4 kcal/mol, respectively. The calculated preorganization components of these free energies of 0.6 (G x C --> G x T) and -0.1 (G x C --> G x A) kcal/mol show that electrostatic preorganization, which is an important source of DNA replication fidelity, plays a lesser role in the mispair destabilization in the absence of DNA polymerase.
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