Solution Structure of the Aminofluorene [AF]-Intercalated Conformer of the syn-[AF]-C⁸-dG Adduct Opposite dC in a DNA Duplex

Abstract

We report below on a conformational equilibrium between AF-intercalated and AF-external states in slow exchange for the [AF]dG lesion positioned opposite dC in the d(C-[AF]G-C).d(G-C-G) sequence context. The slow exchange between states is attributed to interconversion between syn glycosidic torsion angle in the AF-intercalated and anti torsion angle in AF-external conformers of the [AF]dG opposite dC containing duplex. The present paper describes an NMR-molecular mechanics study that defines the solution structure of the AF-intercalated conformer for the case of [AF]dG adduct positioned opposite dC in the d(C-[AF]G-C).d(G-C-G) sequence context. The structure is of the base displacement-intercalation type where the aminofluorene ring is intercalated into the helix between intact Watson-Crick dG.dC base pairs, which results in a displacement of the modified guanine ring into the major groove where it stacks with the major groove edge of its 5'-flanking cytosine in the adduct duplex. The conformational equilibrium between AF-intercalated conformer (approximately 70%) with a syn alignment and AF-external conformer (approximately 30%) with an anti alignment for the [AF]dG adduct positioned opposite dC in the d(C-[AF]G-C).d(G-C-G) sequence context can be contrasted with our earlier demonstration that the population is 100% for the AP-intercalated conformer with a synalignment at the N-(deoxyguanosin-8-yl)-2-aminopyrene ([AP]dG) adduct site positioned opposite dC in the same sequence context [Mao, B., Vyas, R. R., Hingerty, B. E., Broyde, S., Basu, A. K., and Patel, D. J. (1996) Biochemistry, 35, 12659-12670]. This shift in population may reflect the much larger size of the pyrenyl ring of the [AP]dG adduct compared to the fluorenyl ring of the [AF]dG adduct which in turn might provide for a greater overlap of the aromatic amine with the flanking base pairs in the intercalated conformer of the former adduct in DNA.

Conformational Differences of the C8-Deoxyguanosine Adduct of 2-Amino-3-methylimidazo[4,5-f]quinoline (IQ) within the NarI Recognition Sequence

“…Previous NMR analyses demonstrated that these oligonucleotides are in conformational exchange between the base-displaced intercalated and groove-bound conformations (37,38). The UV spectra of all three AF-modified oligonucleotides were nearly identical, and little or no change in the absorbance intensity of the AF chromophore was observed upon hybridization to a complementary strand.…”

Examination of the Long-range Effects of Aminofluorene-induced Conformational Heterogeneity and Its Relevance to the Mechanism of Translesional DNA Synthesis

“…In contrast, the N-deacetylated AF-adduct possesses flexiblility around the glycosidyl bond (χ), enabling it to adopt multiple conformational motifs depending upon the location of the aminofulorene moiety, including a major-groove binding "B-type" (B) conformation and a minor-groove binding "wedged" (W) conformation in addition to the S conformation ( Fig. 1b) (12)(13)(14)(15)(16)(17)(18). In general, fully base-paired DNA duplexes that have incorporated AF are present in an S/B equilibrium in which the tendency for the molecules to favor the S or the B conformation is dependent upon the flanking-sequence context (17)(18)(19).…”

Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis

“…Studies of the deacylated dG-AF adduct in double-stranded DNA by similar methods have revealed two interchangeable conformers of the modified nucleoside (21)(22)(23)(24). In one conformer, the fluorene ring of dG-AF is oriented outside the DNA helix, where it does not perturb base-pairing.…”