A universal, photocleavable DNA base: Nitropiperonyl 2 '-deoxyriboside

A universal, photochemically cleavable DNA base analogue would add desirabl e versatility to a number of methods in molecular biology. A novel C-nucleo side, nitropiperonyl deoxyriboside (NPdR, P*), has been investigated for th is purpose. NPdR can be converted to its 5 ' -DMTr-3 ' -CEphosphoramidite a nd was incorporated into pentacosanucleotides by conventional synthesis tec hniques. The destabilizing effect on hybrid formation with a complementary strand when this P* base opposes A, T, and G was found to be 3-5 kcal/mol, but 9 kcal/mol when it opposes C. Brief irradiation (lambda > 360 nm, 20 mi n) of DNA containing the P* base and piperidine treatment causes strand cle avage giving the 3 '- and 5 ' -phosphates. Two significant recent interests , universal/non-hydrogen-bonding base analogues and photochemical backbone cleavage, have thus been combined in a single molecule that serves as a lig ht-based DNA scissors.