A T5 Exonuclease-Based Assay for DNA Topoisomerases and DNA Intercalators

DNA topoisomerases,
essential enzymes to all living organisms,
are important targets of certain antibiotics and anticancer drugs.
Although efforts have been taken to identify new inhibitors targeting
DNA topoisomerases, limited high throughput screening (HTS) studies
have been conducted since a widely accessible HTS assay is not available.
We report here the establishment of a fluorescence-based, low-cost
HTS assay to identify topoisomerase inhibitors. This HTS assay is
based on a unique property of T5 exonuclease that can completely digest
supercoiled plasmid pAB1 containing an “AT” hairpin
structure and spare relaxed pAB1 and has been validated by screening
a small library that contains 50 compounds for various topoisomerases.
This T5 exonuclease-based HTS assay can also be used to identify DNA
intercalators, the major false positives for identifying topoisomerase
inhibitors using this HTS assay. Additionally, we found a new compound
that potently inhibits human and bacterial DNA topoisomerase I.