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A molecular dynamics simulation of the (dG) 6 ·(dC) 6 minihelix including counterions and water
Author(s) -
Zielinski Theresa Julia,
Shibata Masayuki
Publication year - 1990
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.360290614
Subject(s) - counterion , chemistry , molecular dynamics , dynamics (music) , chemical physics , computational chemistry , statistical physics , ion , physics , organic chemistry , acoustics
The results of a 60 ps molecular dynamics (MD) simulation of (dG) 6 ·(dC) 6 including 10 Na + counterions and 292 water molecules are presented. All backbone angles and helix parameters for the hexamer are reported in this paper along with trajectory plots of selected angles. Hydrogen bonding between the bases along the helical axis was observed to flucturate with time, showing the dynamic nature of the base‐pairing interaction. These fluctuations gave rise to unusual hydrogen‐bonding patterns. Good intrastrad base stacking and no interstrand base stacking were also observed. The hexamer minihelix retains an essentially B‐DNA conformation throughout the entire simulation even though some helix parameters and backbone angles do not have strict B‐DNA values. The most striking feature obtained from the simulation was a high propeller twist, which resulted in a narrow minor groove for the minihelix. It is proposed that (dG) n ·(dC) n sequences are resistant to DNAase I because of this narrow minor groove in dilute aqueous solution.