© 2021 Elsevier Ltd Nucleobase editing is a powerful tool in genetic disease therapy. We have reported the photochemical transition of cytosine to uracil using an ultrafast DNA photo-cross-linking. In this study, we used cytosine derivatives such as methylcytosine, hydroxymethylcytosine, and trifluoromethylcytosine to evaluate the effect of 5-position substitution of cytosine on deamination. The conversion of cytosine to uracil was the fastest, and the conversion of trifluoromethylcytosine to trifluoromethyluracil was the slowest. The order was correlated with the hydrophilicity of the double strand containing these cytosine derivatives.