Base Sequence-Dependent Bends in Site-Specific Benzo[a]pyrene Diol Epoxide-Modified Oligonucleotide Duplexes

A metabolite of the pollutant benzopyrene r7,t8-dihydroxy-t9,10-epoxy-7,8,9,10-tetrahydrobenzopyrene (racemic plus and minus anti-BPDE), has been shown to be mutagenic. In order to elucidate the structural features of adduct derived from the binding of anti-BPDE to nucleic acids, the site specifically modified oligonucleotides 5{prime}-d(TCCTCCTG{sub 1}G{sub 2}CCTCTC) (I) and 5{prime}-d(CTATG{sub 1})(CTATG{sub 1}G{sub 2}G{sub 3} TATC)(II) were synthesized with single modified guanine residues at positions G{sub 1}, G{sub 2}, or G{sub 3}. In denaturing 20% polyacrylamide gels, the electrophoretic mobilities of the (+)-anti-BPDE-modified oligonucleotides I and II are slower than the mobilities of the respective unmodified oligonucleotides and independent of the positions of the BPDE-modified guanines. However, in the double-stranded forms in native 8% polyacrylamide gels, the electrophoretic mobilities of the duplexes with lesions at G{sub 2} or G{sub 3} are remarkably slower (reductions in mobilities up to {approx}40%) than to duplexes with lesions at G{sub 1} and are attributed to physical bends or flexible hinge joints at the sites of the BPDE lesions. These sequence-dependent mobility effects occur whenever the BPDE-modified guanine residues with (+)-trans-stereochemistry are flanked by unmodified G`s on the 5{prime}-side. These retarded electrophoretic mobilities are attributed to bending induced by steric hindrance effects involving the bulky 5{prime}-flanking guanines and themore » pyrenyl residues that are known to point into the 5{prime}-direction relative to the modified G. These anomalous electrophoretic mobility effects are not observed in the case of (-)-anti-BPDE-modified sequences I with trans-(-)-anti-BPDE-N{sup 2}dG adduct stereochemistry. 51 refs., 6 figs., 1 tab.« less