Mapping the sites for selective oxidation of guanines in DNA.
The effective energy of a positive charge when it is localized at a specific guanine nucleobase in DNA was calculated using density functional theory. The results demonstrate that the efficiency of a guanine to act as a hole-trap in DNA strongly depends on the nature of the flanking nucleobases. The presence of a pyrimidine base at the 3' position adjacent to a guanine significantly increases the localization energy of the positive charge. The calculated distributions of a positive charge in sequences of two or three adjacent guanines, flanked by other nucleobases, provide an explanation for experimental literature data on the site-selective oxidation of DNA.
Radiation Chemistry Department, Interfaculty Reactor Institute, Delft University of Technology, Mekelweg 15, NL-2629 JB Delft, The Netherlands.
K
K
Senthilkumar
F C
FC
Grozema
C Fonseca
CF
Guerra
F M
FM
Bickelhaupt
L D A
LD
Siebbeles
D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006147:Guanine / Q000737:chemistry* / Q000378:metabolism; D008956:Models, Chemical; D010084:Oxidation-Reduction
D006147:Guanine; D004247:DNA