Potential energy surfaces of the microhydrated guanine...cytosine base pair and its methylated analogue.
A complete scan of the potential and free-energy surfaces of monohydrated and dihydrated guanine...cytosine and 9-methylguanine...1-methylcytosine base pairs was realized by the molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The most stable and populated structures localized were further fully reoptimized at the correlated ab initio level employing the resolution of identity Møller-Plesset method with a large basis set. A systematic study of microhydration of these systems using a high-level correlated ab initio approach is presented for the first time. The different behavior of guanine...cytosine and adenine...thymine complexes is also discussed. These studies of nucleic acid base pairs are important for finding binding sites of water molecules around bases and for better understanding of the influence of the solvent on the stability of the structure of DNA.
Zendlová
Lucie
L
The Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6 (Czech Republic).
Hobza
Pavel
P
Kabelác
Martin
M
D020029:Base Pairing; D003198:Computer Simulation; D003596:Cytosine / Q000031:analogs & derivatives / Q000737:chemistry*; D006147:Guanine / Q000031:analogs & derivatives / Q000737:chemistry*; D006860:Hydrogen Bonding; D008745:Methylation; D008958:Models, Molecular; D015394:Molecular Structure; D014867:Water / Q000737:chemistry*
D014867:Water; D006147:Guanine; D003596:Cytosine