Journal
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS
Volume 29, Issue 1, Pages 57-60Publisher
SPRINGER
DOI: 10.1007/s002490050251
Keywords
DNA; molecular dynamics simulation; sodium counterions; localisation; dynamics
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The localisation and dynamics of sodium counterions around the DNA duplex d(AGCGTACTAG-TACGCT)(2) corresponding to the trp operator fragment used in the crystal structure of the half site complex has been studied by a 1.4 ns molecular dynamics simulation in explicit solvent. A continuous and well-defined counterion density is shown to be present around the minor groove, while density patches are found in the major groove in regions where DNA bending is observed. A residence time analysis reveals the dynamic nature of these distributions. The resulting picture agrees with previous theoretical and experimental studies of A-tract DNA sequences, and is consistent with the polyelectrolyte, condensation model.
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