Local Dielectric Environment of B-DNA in Solution:  Results from a 14 ns Molecular Dynamics Trajectory

• Published in: The journal of physical chemistry. B Vol. 102; no. 39; pp. 7666 - 7669
• Main Authors: Young, M. A, Jayaram, B, Beveridge, D. L
• Format: Journal Article
• Language: English
• Published: American Chemical Society 24.09.1998
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp9823188

The dielectric behavior of solvent water around DNA is elicited in terms of Kirkwood−Grunwald theory from a 14 ns molecular dynamics trajectory of B-DNA developed in a medium of explicit waters and sodium counterions with particle mesh Ewald for long-range electrostatics. The computed dielectric profile near DNA increases rather rapidly with distance and displays bulk behavior beyond 5 Å. A proximity analysis of the dielectric function reveals that the relative permittivities in the first shell of DNA obey the following trend in the simulations:  phosphate backbone > major groove > minor groove. Estimates of the local dielectric constants in the major groove are consistent with interpretations based on fluorescence measurements, indicating that MD models of solvent around DNA are providing a reasonably accurate account of the local solution environment of a complicated polyelectrolyte. The calculated dielectric profile is fit to a sigmoidal function, which can be used in estimating the strength of charge−charge interactions around DNA.