Structures of 2-acetylaminofluorene modified DNA revisited: insight into conformational heterogeneity

Abstract

Despite the extensive data on dG-AAF, the major DNA adduct derived from the model carcinogen 2-acetylaminofluorene, little is known with respect to its solution structures. Here, we provide NMR/CD evidence for three conformers of dG-AAF in duplex DNA: major groove B-type (B), base-displaced stacked (S), and minor groove wedge (W). The S/B/W-conformational heterogeneities were found to be sensitive to the nature of the flanking DNA sequence contexts and pH.

Figure 1

(a) Structures of dG-AF, dG-AAF and their fluoro models, dG-FAF, dG-FAAF; (b) 12-mer duplexes I and II used in the present study; (c) Views from the major-grooves of a duplex for three FAAF-induced conformational motifs: B, S, and W-conformers. Color code: modified G (yellow) and complementary C (cyan) at the lesion site; fluorene (red) and N-acetyl (pink). Inset shows the minor groove view of W-conformer.

Figure 2

Temperature dependence of 1D ¹⁹F NMR (−114 ~ −121 ppm) spectra of the FAAF-modified duplex (a) I and (b) II recorded in 10% H₂O buffer at pH 6.8. ss (single strand, blue), B (green), S (red), W (purple) conformers. ≠ impurity.

Figure 3

pH dependence of (a) fluorine NMR (5°C, ≠ impurity) and (b) CD spectra (20°C)[pH 7.0 (red); pH 7.0→9.0 (blue); pH 7.0→9.0 →7.0 (green)] of the FAAF-modified duplex II. c) a Hoogsteen-type syn-dG[FAAF]:anti-dC alignment.