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Structure of hydrated Na + ions around a region of A‐ or B‐DNA helix
Author(s) -
Lee W. K.,
Gao Y.,
Prohofsky E. W.
Publication year - 1984
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360230207
Subject(s) - chemistry , helix (gastropod) , molecule , ion , crystallography , counterion , dna , molecular dynamics , guanine , nucleotide , computational chemistry , ecology , biochemistry , organic chemistry , snail , gene , biology
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.