Combined Monte Carlo and quantum mechanics study of the hydration of the guanine-cytosine base pair.
We present a computer simulation study of the hydration of the guanine-cytosine (GC) hydrogen-bonded complex. Using first principles density-functional theory, with gradient-corrected exchange-correlation and Monte Carlo simulation, we include thermal contribution, structural effects, solvent polarization, and the water-water and water-GC hydrogen bond interaction to show that the GC interaction in an aqueous environment is weakened to about 70% of the value obtained for an isolated complex. We also analyze in detail the preferred hydration sites of the GC pair and show that on the average it makes around five hydrogen bonds with water.
Coutinho
Kaline
K
Universidade de Mogi das Cruzes, CP 411, 08701-970, Mogi das Cruzes, São Paulo, Brazil.
Ludwig
Valdemir
V
Canuto
Sylvio
S
D001482:Base Composition; D020029:Base Pairing; D001665:Binding Sites; D003596:Cytosine / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry*; D006860:Hydrogen Bonding; D046911:Macromolecular Substances; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009010:Monte Carlo Method; D044367:Phase Transition; D011789:Quantum Theory; D012996:Solutions; D014867:Water / Q000737:chemistry*
D046911:Macromolecular Substances; D012996:Solutions; D014867:Water; D006147:Guanine; D003596:Cytosine