Structure of hydrated Na+ ions around a region of A- or B-DNA helix

✍ Scribed by W. K. Lee; Y. Gao; E. W. Prohofsky

• Publisher: Wiley (John Wiley & Sons)
• Year: 1984
• Tongue: English
• Weight: 600 KB
• Volume: 23
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.360230207

✦ Synopsis

Synopsis

A molecular-dynamics simulation was used to carry out an introductory study of the hydration of a section of a rigid single A-or B-DNA helix with one Na+ counterion per nucleotide. Four Na+ ions and four nucleotides and periodic boundary conditions were used to mimic an infinite helix. The atoms of the helix and the Na+ ions were assumed to be Lennard-Jones spheres that also carried charges. Stillinger four-point charge model water molecules were used. We carried out five calculations, for 26 and 46 water molecules in B-DNA and 20,32, and 46 in A-DNA fragments. The arrangements of the Na+ ions are found to have some similarities to those obtained by Clementi and Corongiu. In the calculations with 46 water molecules, we found that two Na+ ions can be bridged by about two water molecules and form a hydrated bound pair, which in turn forms a bridge between the guanine N7 and a near phosphate group. These bound pairs may be important in stabilizing the helix structure of DNA molecules.