The proton transfer process from a guanine to its complementary cytosine in a B-form d[GG] radical cation is investigated theoretically. The d[GG] radical cation is optimized by the ONIOM + PCM method. In this two-layer ONIOM method, the high layer consists of the pi-stacked complementary base pairs with a hole charge; which is treated at the B97D/6-31G(d) level; The low layer includes the sugar-phosphate. backbone and sodium ions; which is treated with the Amber99SB/Parmbsc0 force field. Our calculations reveal that the stabilization of the deprotonated state in d[GG] oligomers is related to the location of sodium ions. When sodium ions are located near phosphate groups, the proton prefers bonding with the guanine, and 80% of the hole charge is delocalized on the guanine residues. When sodium ions are placed in the major groove, the deprotonated state is favorable, and 70% of the hole charge localizes on the corresponding guanine-cytosine pair. According to the natural bond orbital analysis, the N-H center dot center dot center dot N hydrogen bond between the guanine-cytosine pair provides an important contribution to the stabilization of. the deprotonated state. Stabilization of this hydrogen bond is very sensitive to the. d[GG] oligomer configuration. In summary, the proton transfer Process in a guanine-cytosine pair of poly(G)-poly(C) radical -cations is largely affected by the arrangement of counterions.