Proton-transfer reactions in two DNA base pair anion and cation radicals are treated by density functional theory to aid our understanding of the possible contributions of these reactions to electron and hole transfer in DNA. The proton-transfer transition structures for both the GC and IC anion and cation radicals are found. For both anion and cation radicals, it is the proton at the N1 guanine (G) site, or hypoxanthine (I) site, that transfers to cytosine. The forward and reverse activation energies as well as reaction enthalpies and free energy changes are calculated. These calculations show that small activation energies of 1 and 3 kcal/mol are present for the GC anion and cation, respectively. The predicted free energy change for the proton transfer is favorable for GC anion radical (−3 kcal/mol) but is slightly unfavorable for the GC cation radical (1.4 kcal/mol). Both of these values compare well with experimental estimates. Remarkably, the IC anion radical system shows no activation energy toward proton transfer and a large free energy change favoring the proton transferred state (−7 kcal). Electron affinities (EA) and ionization potentials (IP) of the two base pairs are also calculated and reported.