Specific recognition of DNA bulge structure by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
This study reports a novel approach utilizing an octahedral CoII(HAPP)(TFA)2 reagent in the presence of H2O2 with analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to serve as an efficient probe for bulged DNA structures. Elucidation of DNA bulge-specific recognition pathways and cleavage mechanisms is demonstrated by characterization of bulge-specific cleavage products and other backbone lesion fragments. The cleavage specificity of CoII(HAPP)(TFA)2/H2O2 arises from sugar oxidative strand scission, for which the position of the abstracted hydrogen is unambiguously determined as the 4'-H of the deoxyribose moiety. Furthermore, differentiation between bulge-specific recognition and diffusion-controlled non-selective cleavage can be clarified through time-dependent MALDI-TOFMS studies. The present results demonstrate that MALDI-TOFMS can be a sensitive and efficient technique for complex mechanistic studies of this kind, providing information for future rational drug design targeting bulged DNA structures.
Chen
Yu-Ju
YJ
Institute of Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC. yjchen@chem.sinica.edu.tw
Chen
Po-Jui
PJ
Wang
Hsueh-Ting
HT
Cheng
Chien-Chung
CC
D001483:Base Sequence; D003035:Cobalt / Q000737:chemistry; D004278:DNA, Superhelical / Q000032:analysis / Q000737:chemistry*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
D004278:DNA, Superhelical; D003035:Cobalt