Solution structure of the aminofluorene [AF]-external conformer of the anti-[AF]-C8-dG adduct opposite dC in a DNA duplex

The Escherichia coli genome contains a C-G(1)-G(2)-C-G(3)-C-C NarI hot spot sequence for -2 deletion mutations at G(3) by aromatic amine carcinogens 2-acetylaminofluorene (AAF) and 2-aminofluorene (AF) that form covalent adducts at the C-8-position of the guanine ring, Each of the three guanines are positioned in different sequence contexts (C-G(1)-G, G-G(2)-C, and C-G(3)-C) which provides an opportunity to investigate the potential sequence dependent interconversion between AF-intercalated and AF-external conformers of the [AF]dG adduct positioned opposite dC within the NarI sequence at the duplex level. We have prepared and purified DNA duplexes containing the [AF]dG adduct positioned in C-[AF]G-G, G-[AF]G-C, and C-[AF]G-C NarI sequence contexts and observe the ratio of AF-intercalated to AF-external conformers to be 30:70, 10:90, and 50:50, respectively. We have applied a combined NMR-molecular mechanics approach to define the structure of the AF-external conformer in the G-[AF]G-C NarI sequence context where it is the predominant conformation (90%) in solution. The modified guanine of the [AF]dG adduct aligns through Watson-Crick pairing with its partner cytosine and is stacked into the helix between flanking Watson-Crick dG.dC base pairs, The AF-external conformer with its anti[AF]dG residue causes minimal perturbations in the DNA duplex at and adjacent to the lesion site with the covalently linked fluorenyl ring readily accommodated in the major groove and tilted toward the 5'-end of the modified strand of the helix. This paper on the structure of the AF-external conformer with an anti-[AF]dG adduct together with the preceding paper in this issue on the structure of the AF-intercalated conformer with a syn-[AF]dG adduct defines for the first time the capacity of the mutagenic [AF]dG lesion to adopt interconverting syn and anti alignments with the equilibrium shifting between the conformers depending on nearest neighbor and next-nearest neighbor sequences, Perhaps, recognition of the [AF]dG lesion by the repair machinery would be able to discriminate between the AF-intercalated conformer with its base displacement-fluorenyl ring insertion perturbation of the helix and the AF-external conformer where the DNA helix is essentially unperturbed at the lesion site and the fluorenyl ring is positioned with directionality in the major groove.