Dynamics of alkene radical cation/phosphate anion pair formation from nucleotide C4' radicals. The DNA/RNA paradox revisited.

The fragmentation of nucleotide C4' radicals generated by thiyl radical addition to C4'C5' exocyclic glycals has been re-examined and found to be a function of the thiol and, probably, the initiating system employed. It has been demonstrated that C4' radicals of DNA and RNA models fragment even in the very nonpolar benzene solution if the correct (aliphatic) thiol is employed. (17)O-Labeling experiments are used to demonstrate that the fragmentation of nucleotide C4' radicals (2-deoxyribo- and ribo-) to contact ion pairs is either irreversible or so rapidly reversible as to preclude prior reorganization of the contact ion pair. Formation of the solvent-separated ion pair is an irreversible step, with all such ion pairs proceeding to product formation.