Isolated mammalian Mus81-Eme endonuclease complexes comprise an Mus81 protein portion and an Eme protein portion. A method of identifying a chemical compound that modulates mammalian cellular response to DNA damage comprises contacting a chemical compound to be tested with a biochemical mixture containing an isolated mammalian Mus81-Eme1 endonuclease complex, a source of magnesium ion, and a suitable DNA substrate; measuring the activity level of mammalian Mus81-Eme endonuclease complex in the mixture; comparing the measured activity level to the activity level of a substantially similar mixture of isolated Mus81-Eme1 endonuclease, magnesium ion, and DNA substrate in the absence of the chemical compound to be tested; and selecting a chemical compound that increases or decreases the endonuclease activity. Isolated mammalian Eme1 and Eme2 proteins derived from humans and murine species and isolated nucleic acids encoding the proteins are also described.