An investigation of the ionic and solvation patterns of dsDNG versus dsDNA by use of molecular dynamics simulations

Biophysical Chemistry
Joseph W ToporowskiThomas C Bruice

Abstract

Molecular dynamics has been employed to analyze the counterion and water atmospheres around the deoxynucleic guanidine (DNG) duplex G(12)-C(12). These features are compared to those of DNA G(12)-C(12). The chloride counterions of cationic DNG demonstrate fewer penetrations and only fleeting residence times in the minor groove, as opposed to the multi-nanosecond visits seen by sodium ions in DNA minor grooves. The 10 ns simulations also show the differences in hydration patterns between the DNG and DNA duplexes.

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Citations

Sep 21, 2010·Journal of Molecular Modeling·Kentaro DoiSatoyuki Kawano
Jul 27, 2011·The Journal of Chemical Physics·X ShenF S Zhang
Jun 19, 2007·Current Opinion in Structural Biology·Pascal Auffinger, Yaser Hashem
Aug 1, 2013·Journal of the American Chemical Society·Christian ReusMatthias Wagner
Sep 12, 2014·The Journal of Physical Chemistry. a·Toshiaki Matsubara, Chikako Ueta

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