Conformational Preferences of DNA in Reduced Dielectric Environments

The effect of reduced dielectric environments on the conformational sampling of DNA was examined through molecular dynamics simulations. Different dielectric environments were used to model one aspect of cellular environments. Implicit solvent based on the Generalized Born methodology was used to re...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2014-09, Vol.118 (37), p.10874-10881
Main Authors: Yildirim, Asli, Sharma, Monika, Varner, Bradley Michael, Fang, Liang, Feig, Michael
Format: Article
Language:English
Subjects:
DNA, A-Form - chemistry
DNA, A-Form - metabolism
DNA, B-Form - chemistry
DNA, B-Form - metabolism
Molecular Dynamics Simulation
Nucleic Acid Conformation
Solvents - chemistry
Thermodynamics
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Summary:The effect of reduced dielectric environments on the conformational sampling of DNA was examined through molecular dynamics simulations. Different dielectric environments were used to model one aspect of cellular environments. Implicit solvent based on the Generalized Born methodology was used to reflect different dielectric environments in the simulations. The simulation results show a tendency of DNA structures to favor noncanonical A-like conformations rather than canonical A- and B-forms as a result of the reduced dielectric environments. The results suggest that the reduced dielectric response in cellular environments may be sufficient to enhance the sampling of A-like DNA structures compared to dilute solvent conditions.
ISSN:1520-6106
1520-5207
DOI:10.1021/jp505727w