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Updated: Aug 3, 2026

Studying DNA Looping by Single-Molecule FRET
Published on: June 28, 2014
An investigation of the ionic and solvation patterns of dsDNG versus dsDNA by use of molecular dynamics simulations
Joseph W Toporowski1, Swarnalatha Y Reddy, Thomas C Bruice
1Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA.
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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