Interaction between 3-(p-tolylamino)-1,5-azulenequinone and the deoxyguanosine residue in various oligonucleotides upon photolysis

Eight single-stranded oligodeoxyribonucleotides P-32-labeled at the 5'-end were synthesized; they were annealed with the complementary oligodeoxyribon ucleotides to form the corresponding double-stranded helices. These duplexe s possessed standard Watson-Crick base pairs, locally perturbed sites of a base mismatch, or a bulge. Further, 5'-P-32-labeled oligodeoxyribonucleotid es with a hairpin loop were also synthesized. Cleavage of these single- and double-stranded oligodeoxyribonucleotides selectively at the deoxyguanosin e residue was accomplished by use of 3-(p-tolylamino)-1,5-azulenequinone 1 upon irradiation with 350 nn UV light. The single strands were cleaved more efficiently than the double-helices. For the helices containing a deoxygua nosine residue at a bulge, at a hairpin loop or toward the end, the cleavin g efficiency was increased. Computation results indicate that two possibili ties exist for agent 1 to form two " Watson-Crick type " hydrogen bonds wit h guanine in single-stranded oligodeoxyribonucleotides; yet, only one possi bility exists in duplexes.