Strong sequence-dependent polymorphism in adduct-induced DNA structure: analysis of single N-2-acetylaminofluorene residues bound within the NarI mutation hot spot

We have used a set of chemical probes to characterize and to compare the structural deformation of double-stranded oligomers bearing a single N-2-acetylaminofluorene (AAF) adduct covalently bound to each of the three guanine residues located within the frameshift mutation hot spot sequence -G1G2CG3CC-(NarI site). Two classes of chemical probes have been used, probes that sense the geometry of the helix, giving rise to cuts at every nucleotide (for example, 1,10-phenanthroline-copper), and probes that react with specific bases depending on their conformation (e.g., diethyl pyrocarbonate). For all probes that were tested, a distinct pattern of reactivity was observed according to the position of the adduct within the DNA sequence, revealing an important polymorphism in the adduct-induced DNA structure. With 1,10-phenanthroline-copper at least three base pairs 3' of the AAF-modified guanine were reactive on each strand, showing that the deformation of the DNA helix extends over a region of 4-6 bases pairs centered around the adduct and sensed by the probe in both strands. With the base-specific probes, reactivities were limited to the base complementary to the modified guanine and to adjacent bases. Within this sequence context, the three possible AAF adducts have previously been shown to exhibit strong differences in biological responses such as excision repair Seeberg, E., & Fuchs, R. P. P. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 191-194] and mutagenesis Burnouf, D., Koehl, P., & Fuchs, R. P. P. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 4147-4151].(ABSTRACT TRUNCATED AT 250 WORDS)