Theoretical ab initio study of the effects of methylation on structure and stability of G:C Watson-Crick base pair.
Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) of pyrimidines. Methylated bases are continuously formed through endogenous and exogenous mechanisms. The results of a theoretical ab initio study on the methylation of G:C base pair components are reported. The geometries of the local minima were optimized without symmetry restrictions by the gradient procedure at DFT level of theory and were verified by energy second derivative calculations. The standard 6-31G(d) basis set was used. The single-point calculations have been performed at the MP2/6-31G(d,p), MP2/6-31++G(d,p), and MP2/6-311++G(2d,2p) levels of theory. The geometrical parameters, relative stability and counterpoise corrected interaction energies are reported. Also, using a variation-perturbation energy decomposition scheme we have found the vital contributions to the total interaction energy.
Forde
Gareth
G
Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217, USA. gforde@ccmsi.us
Flood
Aviane
A
Salter
Latasha
L
Hill
Glake
G
Gorb
Leonid
L
Leszczynski
Jerzy
J
D020029:Base Pairing; D019295:Computational Biology; D003596:Cytosine / Q000737:chemistry*; D019175:DNA Methylation; D006147:Guanine / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D013816:Thermodynamics
D006147:Guanine; D003596:Cytosine