Bulge migration of the malondialdehdye OPdG DNA adduct when placed opposite a two-base deletion in the (CpG)3 frameshift hotspot of the Salmonella typhimurium hisD3052 gene

The OPdG adduct N-2-(3-oxo-1-propenyl) dG, formed in DNA exposed to malondialdehyde, was introduced into 5'-d(ATCGC (X) under bar CGGCATG)-3'.5'-d(CATGCCGCGAT)-3' at pH 7 ( X) OPdG). The OPdG adduct is the base-catalyzed rearrangement product of the M(1)dG adduct, 3-(beta-D-ribofuranosyl) pyrimido[1,2a] purin-10(3H)-one. This duplex, named the OPdG-2BD oligodeoxynucleotide, was derived from a frameshift hotspot of the Salmonella typhimuium hisD3052 gene and contained a two-base deletion in the complementary strand. NMR spectroscopy revealed that the OPdG-2BD oligodeoxynucleotide underwent rapid bulge migration. This hindered its conversion to the M(1)dG-2BD duplex, in which the bulge was localized and consisted of the M1dG adduct and the 3'-neighbor dC [Schnetz-Boutaud, N. C., Saleh, S., Marnett, L. J., and Stone, M. P. ( 2001) Biochemistry 40, 15638-15649]. The spectroscopic data suggested that bulge migration transiently positioned OPdG opposite dC in the complementary strand, hindering formation of the M(1)dG-2BD duplex, or alternatively, reverting rapidly formed intermediates in the OPdG to M1dG reaction pathway when dC was placed opposite from OPdG. The approach of initially formed M(1)dG-2BD or OPdG-2BD duplexes to an equilibrium mixture of the M(1)dG-2BD and OPdG-2BD duplexes was monitored as a function of time, using NMR spectroscopy. Both samples attained equilibrium in similar to 140 days at pH 7 and 25 degrees C.