The luminescent quantum yield of silver-cluster emitters stabilized by short oligonucleotides (AgN-DNA) may be efficiently tuned by replacing nucleobases in their stabilization DNA matrices with analogues. In the present study, we proposed a valuable and straightforward theoretical methodology for assessing the photophysical behaviors emerging in AgN-DNA emitters after excitation. Using green Ag10-DNA and near-IR Ag16-DNA emitters we demonstrate how point guanine/inosine replacement could affect the photophysical rate constants of radiative/nonradiative processes. The main deactivation channel of the fluorescence of Ag16-DNA is intersystem crossing, which is in line with experimental data, whereas for Ag10-DNA the calculations overestimate the intersystem crossing rate possibly due to pure solvent contributions.