Density functional theory calculations were employed to study the stabilization process of the guanine radical cation through amino acid interactions as well as to understand the protection mechanisms. On the basis of our calculations, several protection mechanisms are proposed in this work subject to the type of the amino acid. Our results indicate that a series of three-electron bonds can be formed between the amino acids and the guanine radical cation which may serve as relay stations supporting hole transport. In the three-electron-bonded, π–π-stacked, and H-bonded modes, amino acids can protect guanine from oxidation or radiation damage by sharing the hole, while amino acids with reducing properties can repair the guanine radical cation through proton-coupled electron transfer or electron transfer. Another important finding is that positively charged amino acids (ArgH+, LysH+, and HisH+) can inhibit ionization of guanine through raising its ionization potential. In this situation, a negative dissociation energy for hydrogen bonds in the hole-trapped and positively charged amino acid–Guanine dimer is observed, which explains the low hole-trapping efficiency. We hope that this work provides valuable information on how to protect DNA from oxidation- or radiation-induced damages in biological systems.