Local dielectric environment of B-DNA in solution: results from a 14 ns molecular dynamics trajectory

Article Abstract:

The dielectric behavior of solvent water around DNA from a 14 ns molecular dynamics trajectory of B-form DNA was analyzed in terms of the Kirkwood-Grunwald theory. The computed dielectric profile near the DNA increases rapidly with distance and displays bulk behavior beyond 15 angstrom. The first DNA shell shows major groove with larger permittivities than minor groove and phosphate backbone with larger permittivities than major groove. These estimates garnered from local dielectric constants agree with fluorescence measurements.

Electric properties, Water, Solvents

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Molecular dynamics studies of the conformational preferences of a DNA double helix in water and an ethanol/water mixture: theoretical considerations of the A (both double arrow) B transition

Article Abstract:

The conformational preferences of sodium salt of the DNA double helix d(CGCGAATTCGCG) in water and in a mixed solvent composed of 85% ethanol/water were investigated using a series of molecular dynamics computer simulations. The DNA sequence was found to have a B-form structure in the solid state and in aqueous solution and is assumed to acquire an A-form structure in the mixed solvent environment. The use of conformational preferences as a performance index for nucleic acids force fields was discussed.

Proteins, Alcohol, Ethanol, Molecular dynamics, Water chemistry, Protein conformation

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Energetics of base pairs in B-DNA in solution: an appraisal of potential functions and dielectric treatments

Article Abstract:

A study was conducted to estimate the energetics of base pairs in B-DNA in solution suing empirical potential energy functions. The structures were produced in the canonical B-DNA conformation using the BIOSYM computer software. A single structure was utilized to compare the performance of different parameter sets and dielectric frameworks. Results suggested the applicability of a sigmoidal function for solution conditions in implicit solvent treatments.

Polymers

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