Stereochemistry-dependent bending in oligonucleotide duplexes induced by site-specific covalent benzo[a]pyrene diol epoxide-guanine lesions

The apparent persistence length of enzymatically linearized plBI30 plasmid DNA molecules ̃2300 bp long, as measured by a hydrodynamic linear flow dlchroism method, Is markedly decreased after covalent binding of the highly tumorigenic benzo[a]pyrene metabolite 7R,8S-dlhydroxy-9S, 10R-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(+)-anti-BPDE]. In striking contrast, the binding of the non-tumorigenlc, mirror-image 7S,8R,9R,10S enantiomer [(-)-anfi-BPDE] to DNA has no measurable effect on Its alignment in hydrodynamic flow gradients (≤22.2% of the DNA bases modified). In order to relate this effect to BPDE-nucleotide lesions of defined stereochemistry, the bending induced by site-specifically placed and stereochemlcally defined (+)- and (-)-anti-BPDE-N²-dG lesions in an 11mer deoxyoligonucleotide duplex was studied by ligation and gel electrophoresls methods. Out of the four stereochemically isomerlc anti-BPDE-N²-deoxyguanosyl (dG) adducts with either (+)-trans, (-)-trans, (+)-cls, and (-)-cls adduct stereochemistry, only the (+ytrans adduct gives rise to prominent bends or flexible hinge joints In the modified oligonucleotide duplexes. Since both antf-BPDE enantlomers are known to bind preferentially to dG (≤85%), these observations can account for the differences in persistence lengths of DNA modified with either (+)-anti-BPDE or the chiral (-)-anti-BPDE isomer.