Topoisomerase I-mediated DNA relaxation as a tool to study intercalation of small molecules into supercoiled DNA.

Paul Peixoto, Christian Bailly, Marie-Hélène David-Cordonnier

Journal: Methods in molecular biology (Clifton, N.J.) 2010;613():235-56

PMID: 19997888

Abstract

Several biochemical and biophysical methods are available to study the intercalation of a small molecule between two consecutive base pairs of DNA. Among them, the topoisomerase I-mediated DNA relaxation assay has proved highly efficient, relatively easy to handle and very informative to investigate drug binding to DNA. The test relies on the use of a supercoiled plasmid to mimic the topological constraints of genomic DNA. The three main components of the assay - the topoisomerase I enzyme, DNA helix and intercalating small molecules - are presented here in a structural context. The principle of the assay is described in detail, along with a typical experimental protocol.

Address: INSERM U-837, Jean-Pierre Aubert Research Center (JPARC), Institut de Recherches sur le Cancer de Lille, Lille, France.

DOI: 10.1007/978-1-60327-418-0_15

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MeSH Terms: Bacteria, Cell Death, Cesium, Chlorides, DNA Topoisomerases, Type I, DNA, Superhelical, Electrophoresis, Agar Gel, Ethidium, Genome, Bacterial, Humans, Intercalating Agents, Nucleic Acid Amplification Techniques, Plasmids