The process of stabilizing radiation damage in the base pair of 1-methylcytosine (1-MeC):5-fluorouracil (5-FU) has been investigated. The formation of free radicals in purines and pyrimidines is influenced by the matrix in which they are irradiated. Of particular interest are the systems in which two different nucleic acid bases are complexed, providing situations that approximate the close proximity of bases in nucleic acid polymers. Detailed EPR/electron-nuclear double resonance experiments show that only the N3 protonated cytosine anion and the N1 deprotonated uracil cation are observed in single crystals of 1-MeC:5-FU, X-irradiated, and observed at 10 K. Upon warming one observes a radical formed by net hydrogen addition to C6 on uracil, and an allylic radical on the C4-C5-C6 region of the uracil. No cytosine C5 or C6 H-addition radicals are observed. The implications that free radical damage is transferred from the cytosine moiety to the uracil moiety in 1-MeC:5-FU is discussed. Single point calculations were performed on the optimized geometries at the B3LYP/6-311G(2df,p) level to obtain accurate energies and spin population's. To obtain electron affinities of the neutral parent molecules, the larger 6-311+G(2df,p) basis set was used. Results show that the cytosine base will be the preferred site of electron addition, and the uracil base will be the site of electron loss. Additional studies were performed to investigate the influence of the hydrogen-bonded crystal matrix on the stabilities of the initial radical ions. On the basis of these studies, a proton shuttle mechanism is proposed that provides an efficient transfer of charge away from the initial sites of electron addition or electron loss, leaving behind neutral radical sites that are less susceptible to recombination.