DNA topoisomerase II (topo II), a fundamental nuclear enzyme, cleaves the double-stranded DNA molecule at preferred sequences within its recognition/binding sites. We have recently reported [F. Cortés, N. Pastor, S. Mateos, I. Domínguez, The nature of DNA plays a role in chromosome segregation: endoreduplication in halogen-substituted chromosomes, DNA Repair 2 (2003) 719-726] that when cells incorporate halogenated nucleosides analogues of thymidine into DNA, it interferes with normal chromosome segregation, as shown by an extraordinarily high yield of endoreduplication. The frequency of endoreduplicated cells paralleled the level of analogue substitution into DNA, lending support to the idea that thymidine analogue substitution into DNA is most likely responsible for the triggering of endoreduplication. Using the pulsed-field gel electrophoresis (PFGE) technique, we have now analyzed a possible protection provided by the incorporation of exogenous halogenated nucleosides against DNA breakage induced by the topo II poison m-AMSA. The result was that the different halogenated nucleosides were shown as able to protect DNA from double-strand breaks induced by m-AMSA depending such a protection upon the relative percent of incorporation of a given thymidine analogue into DNA. Our results clearly indicate that the presence of halogenated nucleosides in DNA diminishes the frequency of interaction of topo II with DNA and thus the frequency with which cleavage can occur.