Suppression of Cyclobutane and <6-4> Dipyrimidines Formation in Triple-Stranded H-DNA

We have determined the effect of H-DNA formation on the distributions of two ultraviolet (UV) light induced photoproducts-cyclobutane dipyrimidines and <6-4> dipyrimidines. A region of DNA containing the sequence (dT-dC)_(18)^*(dA-dG)_(18) was treated under conditions that specifically yield the triple-stranded H-y3 or H-y5 DNA structure and then irradiated with UV. The positions of cyclobutane dipyrimidines and <6-4> dipyrimidines were determined by T4 endonuclease V cleavage and by hot piperidine cleavage, respectively. Formation of H-DNA structures greatly decreased the photoproduct yield in the (dT-dC)_(18)^*(dA-dG)_(18) region but not elsewhere in the DNA. Suppression of photoproduct formation is greater in half of the repeat, reflecting whether the DNA is in the H-y3 or H-y5 conformation. Within the repeat, the suppression was less in the middle and toward the ends. Models for the suppression of photoproduct formation in H-DNA and the possible utility of our findings are discussed.