It does so by the covalent modification of histidine (most strongly), lysine, cysteine, and tyrosine residues.

Higher concentrations of DEPC are capable of deactivating larger amounts of RNase, but remaining traces or byproducts may inhibit further biochemical reactions such as in vitro transcription.

DEPC is unstable in water and susceptible to hydrolysis to carbon dioxide and ethanol, especially in the presence of a nucleophile.

Modification of histidine by DEPC results in carbethoxylated derivates at the N-omega-2 nitrogen of the imidazole ring.

DEPC modification of histidines can be reversed by treatment with 0.5 M hydroxylamine at neutral pH.