O6-Methylguanine and A:C and G:T mismatches cause asymmetric structural defects in DNA that are affected by DNA sequence

Abstract

Mismatched and modified base pairs are central to questions of DNA mutation and repair. NMR and X-ray crystallography of mispairs indicate little to no local helical distortion, but these techniques are not sensitive to more global distortions of the DNA molecule. We used polyacrylamide gel electrophoresis and thermal denaturation to examine A.C, G.T, and O6-methylG.T and O6-methylG.C mismatches synthesized in place of either of two adjacent G.C base pairs in synthetic DNA duplexes. Substitution for G.C at either position decreased the stability of the duplex; O6-methylguanine was more destabilizing in place of the 5'G than in place of the 3'G. Comparisons between polymers synthesized so that lesions occurred regularly spaced on the same side of the helix and polymers synthesized so that the lesions alternated from side to side on the helix showed that these lesions introduced helical distortion composed of (i) a symmetric frictional component, probably caused by localized bubble formation, and (ii) an asymmetric component indicative of a more global effect on the DNA molecule. Comparisons between these effects at the two adjacent positions show that the extent of structural perturbation depends on sequence context.

DNA Sequence Context Affects Repair of the Tobacco-Specific Adduct O6-[4-Oxo-4-(3-pyridyl)butyl]guanine by Human O6-Alkylguanine-DNA Alkyltransferases

“…The markedly poor repair of O 6 -pobG in sequences 2 and 3 oligonucleotides is consistent with the presence of helical distortions or alternative DNA conformations that are known to influence repair (41)(42)(43). Although it is conceivable that these H-ras oligonucleotides could form secondary hairpin structures that inhibit repair (35), our studies with nondenaturing gels indicate that it is highly unlikely that DNA hairpin structures are stabilized by O 6 -pobG.…”

Sequence specific mutations induced by N-nitrosodimethylamine at two marker loci in metabolically competent human lymphoblastoid cells

“…However, the abundance of 5Ј-GG-3Ј sites is similar on both strands of the tk locus and a strand bias for mutations on the non-transcribed strand was still observed. Although O 6 meG has been reported to be a poor substrate for nucleotide excision repair in E.coli (58), the observation of a strand bias for mutations induced by O 6 meG in this and other studies (48,50), indicates that a repair process linked to transcription removes methylated DNA lesions during transcription. Conclusions with regard to strand bias are based on the assumption that G:C→A:T transitions were induced by the presence of O 6 meG lesions.…”

“…The preference for the recovery of O 6 meG-induced G:C→A:T mutations at positions 3Ј to purines may be attributable to a number of factors. It has been shown that the formation of O 6 meG lesions occurs preferentially at sites 3Ј to purines (57), and that O 6 meG is less stable when located at the 5Ј rather than 3Ј G in 5Ј-GG-3Ј sequences (58). Furthermore, the methyl group on the O 6 position of a guanine has been reported to be less susceptible to MGMT removal if it is located 3Ј to a purine than if it is located 3Ј to a pyrimidine (49).…”

DNA-binding mechanism of the Escherichia coli Ada O6-alkylguanine-DNA alkyltransferase

“…O 6 meG is thought to promote localised unstacking in the DNA duplex, which may in turn lead to slight kinking of the structure (56,57). In this manner a lesion could advertise its presence more dramatically to DNA repair proteins.…”