Six crystals of protonated DNA bases, [adenine (N₁,N₇)H₂]Cl₂ ([A(N₁,N₇)H₂]Cl₂), [adenine(N₁)H] PF₆ ([A(N₁)H]PF₆), [cytosine(N₇)H]Cl ([C(N₇)H]Cl), [cytosine(N₃)H]PF₆ ([C(N₃)H]PF₆), [guanine(N₁₀)H]Cl ([G(N₁₀)H]Cl) and [guanine(N₇)H]H₂PO₄ ([G(N₇)H]P) were newly prepared by the reaction of DNA bases, where A = adenine, C = cytosine, G = guanine, and P = H₂PO₄^- anion, with concentrated HCl or H₃PO₄. They were characterized by X-ray analysis and ultraviolet-visible (UV-vis) spectroscopy. Comparison of calculated bond lengths and angles between ground states and singlet excited states for the compounds were examined using density functional theory (DFT). A weak emission in H₂O solution was observed in [A(N₁,N₇)H₂]Cl₂ due to the formation of hydrogen bond between the protonated base and the Cl^- anion.