© Springer Science+Business Media LLC 2017. DNA gyrase is the only topoisomerase that can catalytically introduce negative supercoils into covalently closed DNA. The enzyme plays a critical role in many phases of DNA biochemistry. There are only a few methods that allow one to measure supercoiling in chromosomal DNA and analyze the role of gyrase in transcription and its interaction with the other three bacterial topoisomerases. Here, we provide molecular tools for measuring supercoil density in the chromosome and for connecting the dots between transcription and DNA topology.