We present a reaction scheme of silver containing 5-substituted uracils (N) bridge formation with two silver ions to a silver-mediated base pair [N-Ag(2)-N] by using the conductor-like polarizable continuum model (CPCM)-B3LYP/aug-cc-pVDZ level of theory. The whole reaction scheme is divided into the following three steps: (1) silver ion binding and deprotonation, (2) silver ion transfer, and (3) dimer formation and structural fluctuation. With a new pK(a) computing scheme proposed in our previous studies, it is found that a silver coordination decreases the pK(a) of N by 2.5-3.0 pK(a) units, which is an important clue for silver-ion selectivity by N. Judging from the calculation, we revealed that the silver ion transfer reaction and the dimerization reaction occur spontaneously. Moreover, both reactions are independent of the C5 ligand in N so that the deprotonation reaction, which is the first step of this scheme, plays a key role in forming the [N-Ag(2)-N] pairing.