Analysis of Topoisomerase-DNA Interactions by Electrophoretic Mobility Shift Assay

DNA topoisomerases break and rejoin DNA strands through a covalent pro-tein-DNA intermediate. The reaction chemistry involves nucleophilic attack by a tyrosine moiety of the enzyme on the phosphodiester backbone of DNA to form a phosphotyrosyl linkage to one (in the case of type I enzymes) or both (type II enzymes) of the DNA strands. Although the distribution of topoisomerase cleavage sites in DNA is nonrandom, the principles governing cleavage site choice are not fully understood. The question of how topoisomerases recognize their DNA cleavage sites is of definite interest, insofar as site specificity may have implications for topoisomerase action in vivo, and because the topoisomerase-DNA complex is the pharmacological target of many antimicrobial and anticancer drugs. An extensive battery of footprinting techniques has been applied to analyzing the topoisomerase-DNA interface in selected model systems, including deoxyribonuclease protection, base-specific modification protection, base-specific modification interference, phosphate modification interference, and site-specific photocrosslinking. This chapter focuses on the use of the electrophoretic mobility shift assay (EMSA) to study topoisomerase binding to DNA.