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

Abstract

The OPdG adduct N 2 -(3-oxo-1-propenyl)dG, formed in DNA exposed to malondialdehyde, was introduced into 5′-d(ATCGCXCGGCATG)-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-(β-D-ribofuranosyl) pyrimido[1,2-a]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 twobase 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 M 1 dG 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 M 1 dG 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 ∼140 days at pH 7 and 25 °C. (Tables S1 and S2, respectively) and chemical shifts of exchangeable protons for the OPdG-and M 1 dG-2BD duplexes (Tables S3 and S4, respectively). This material is available free of charge via the Internet at

Chemistry and Structural Biology of DNA Damage and Biological Consequences

“…Structural studies have also been conducted when M 1 dG and OPdG adducts are placed opposite a 2-base deletion (2BD) complementary strand in the 5′-(CpG) 3 sequence [215–217]. M 1 dG is stable in the 2BD duplex and remains ring-closed when it is the 5′-nucleotide of a two-nucleotide bulge [215].…”

“…Both bulged nucleotides are in the anti conformation about the glycosyl bond and appear inside the helix, but lack H-bonding interactions [216]. On the other hand, the OPdG-2BD duplex undergoes bulge migration from the 3′-neighbor base pairs to the adduct region [217]. The bulge migration transiently positions OPdG opposite dC in the complementary strand and, consequently, hinders the conversion of OPdG to M 1 dG.…”

Palliative care benefits patients with lung cancer

“…Although the adduct was originally observed in vitro in reactions of the lipid peroxidation product, malondialdehyde, with dG and DNA, it also arises in reactions of DNA with the base propenal products of 4′‐oxidation of DNA 123–126. In light of the potential mobility of M 1 dG in the genome127–132 and the potential for transfer of the oxopropenyl group to and from DNA via N ε ‐oxopropenyllysine adducts in histone proteins,133 it will be difficult to precisely define the source of M 1 G adducts in vivo .…”

3′-Intercalation of a N2-dG 1R-trans-anti-Benzo[c]phenanthrene DNA Adduct in an Iterated (CG)3 Repeat

“…DNA adducts located in iterated repeat sequences may be processed differently than adducts located in noniterated sequences (41). The iterated CG repeat sequence within the S. typhimurium hisD3052 gene represents a hotspot for frameshift mutations, which has been examined in the context of exocyclic 1,N 2 -dG adducts arising endogenously in DNA as the result of oxidative damage (42)(43)(44)(45)(46) (3) and mutagenic in the TA 98 and TA 100 strains of S. typhimurium (14). Structural refinement was achieved using molecular dynamics calculations restrained by interproton distances and torsion angle restraints obtained from NMR data.…”

“…DNA adducts located in iterated repeat sequences may be processed differently than adducts located in noniterated sequences . The iterated CG repeat sequence within the S. typhimurium hisD3052 gene represents a hotspot for frameshift mutations, which has been examined in the context of exocyclic 1, N 2 -dG adducts arising endogenously in DNA as the result of oxidative damage – .…”