High propeller twist and unusual hydrogen bonding patterns from the MD simulation of (dG)6.(dC)6.
A molecular dynamics (MD) study of (dG)6.(dC)6 including counter ions and 292 water molecules was made. The hydrogen bonding pattern and propeller twist angles for the mini-helix are reported as averages for times spanning 21-30, 31-40, 41-50, and 51-60 ps. The propeller twist angles range from 18 degrees to 38 degrees. Bifurcated and interstrand neighboring base (twisted) hydrogen bonding patterns were found.
Zielinski
T J
TJ
Department of Chemistry, Niagara University, NY 14109.
Shibata
M
M
Rein
R
R
D006860:Hydrogen Bonding; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D011089:Polydeoxyribonucleotides; D014867:Water
D011089:Polydeoxyribonucleotides; D014867:Water; C016681:poly(dG).poly(dC)