5-Chloro-2′-deoxyuridine (CldU) is used as a thymidine analogue to study the miscoding potential of hypochlorous acid damage to DNA and DNA precursors. When used with antibody based immunofluorescent imaging, 5-Chloro-2′-deoxyuridine incorporation may be used in protocols to identify sites of DNA replication. CldU may be used as a labeling substrate in conjunction with other halogenated uridine labeling substrates such as bromodeoxyuridine (BrdU) and/or iododeoxyuridine (IdU).