Topoisomerase I-mediated DNA relaxation as a tool to study intercalation of small molecules into supercoiled DNA.
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.
Peixoto
Paul
P
INSERM U-837, Jean-Pierre Aubert Research Center (JPARC), Institut de Recherches sur le Cancer de Lille, Lille, France.
Bailly
Christian
C
David-Cordonnier
Marie-Hélène
MH
D001419:Bacteria / Q000166:cytology / Q000235:genetics; D016923:Cell Death; D002586:Cesium / Q000494:pharmacology; D002712:Chlorides / Q000494:pharmacology; D004264:DNA Topoisomerases, Type I / Q000378:metabolism*; D004278:DNA, Superhelical / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D004587:Electrophoresis, Agar Gel; D004996:Ethidium / Q000378:metabolism / Q000494:pharmacology; D016680:Genome, Bacterial / Q000235:genetics; D006801:Humans; D007364:Intercalating Agents / Q000378:metabolism* / Q000494:pharmacology*; D021141:Nucleic Acid Amplification Techniques; D010957:Plasmids / Q000235:genetics / Q000302:isolation & purification
D002712:Chlorides; D004278:DNA, Superhelical; D007364:Intercalating Agents; D002586:Cesium; D004264:DNA Topoisomerases, Type I; D004996:Ethidium; C028019:cesium chloride