Photochemical cleavage of phosphodiester bonds in oligoribonucleotides

The release of inorganic phosphate from a variety of mononucleotides and the generation of new phosphomonoester end groups as a result of chain cleavage in a number of oligoribonucleotides have been studied quantitatively as a function of irradiation with 254-nm light. The reaction cross sections for adenosine 5'-phosphate, guanosine 2'(3')-phosphate, cytidine 5'-phosphate, cytidine 3'-phosphate, cytidine 2'(3')-phosphate, uridine 5'-phosphate, uridine 2'(3')-phosphate, dihydrouridine 5'-phosphate, and ribose 5-phosphate are close to 2 X 10(-7) m2/J. The value for UpU is similar. The reaction cross sections, sigma, for (Ap)n where n = 3-10 as well as for the oligonucleotides ApUpGp, m1ApCpUpCpGp, CpCpCpCpCpGp, and DpDpDpApApGp increased linearly as a function of the number of phosphodiester bonds and gave values close to 6.4 X 10(-7) m2/J per bond. The cross sections for (Up)n were also about 6.4 X 10(-7) m2/J per bond for n = 2-5 and then, unexpectedly, increased rapidly for n = 6-10. By analogy to the carefully studied release of phosphate from ethyl phosphate and several sugar phosphates by 254-nm light [Halmann, M., & Platzner, I. (1965) J. Chem. Soc., 5380-5385], we conclude that the photolysis reactions we have observed are induced by absorption of photons by the sugar phosphate groups rather than the purine or pyrimidine rings. It follows that the quantum yields for chain cleavage of both RNA and DNA have been seriously underestimated since these calculations were based on the assumption that the observed photochemistry is due to absorption of photons by the purine and pyrimidine rings, and the absorption cross section of these rings is roughly 10 000 times greater than that of the sugar phosphate group itself.