Based on the properties of intercalating molecules, i.e. fluorescing upon binding to DNA and unwinding of DNA base-pairs, in 2016, a single-molecule technique has been introduced to directly visualize individual plectonemes along supercoiled DNA which would further allow to study the interactions of DNA processing proteins with supercoiled DNA. In that study, Sytox Orange (an intercalating dye) was used to induce supercoiling on surface tethered DNA molecules.
Using this assay, it was found that the DNA sequence encodes for the position of plectonemic supercoils. Furthermore, DNA supercoils were found to be enriched at the transcription start sites in prokaryotes.