Electron paramagnetic resonance evidence for a C3' sugar radical in crystalline d(CTCTCGAGAG) X-irradiated at 4 K

A neutral sugar radical formed by the net loss of hydrogen from C3' has been identified in crystalline DNA X-irradiated at 4 K. Crystals of duplex d(CTCTCGAGAG), known to be of B conformation, were studied using electron paramagnetic resonance (EPR) spectroscopy. The C3' radical was identified by using information from dose saturation, power saturation, thermal annealing, and spectrum simulation. The yield of the C3' radical, G(C3'), is 0.03 ± 0.01 µmol/J, and its concentration does not appear to saturate up to at least 100 kGy. In the region in which total radical concentration increases linearly with dose, the C3' radical makes up about 4.5% of the total radical population trapped in the oligodeoxynucleotide crystal at 4 K. Based on free base release measured in other oligodeoxynucleotides, we suggest that in d(CTCTCGAGAG) the C3' radical is responsible for about one-third of the strand breakage events.