Ramesh, SubramaniSissel, JuulAlexandru, RotaruFelicie F, AndersenKurt V., GothelfWael, MamdouhFlemming, BesenbacherMingdong, DongBirgitta R, Knudsen2023-09-162023-09-162010-09-09https://doi.org/10.1021/nn101662aThe biologically and clinically important nuclear enzyme human topoisomerase I relaxes both positively and negatively supercoiled DNA and binds consequently DNA with supercoils of positive or negative sign with a strong preference over relaxed DNA. One scheme to explain this preference relies on the existence of a secondary DNA binding site in the enzyme facilitating binding to DNA nodes characteristic for plectonemic DNA. Here we demonstrate the ability of human topoisomerase I to induce formation of DNA synapses at protein containing nodes or filaments using atomic force microscopy imaging. By means of a two-dimensional (2D) DNA origami platform, we monitor the interactions between a single human topoisomerase I covalently bound to one DNA fragment and a second DNA fragment protruding from the DNA origami. This novel single molecule origami-based detection scheme provides direct evidence for the existence of a secondary DNA interaction site in human topoisomerase I and lends further credence to the theory of two distinct DNA interaction sites in human topoisomerase I, possibly facilitating binding to DNA nodes characteristic for plectonemic supercoils.en-USatomic force microscopy (AFM)functionalized 2D origamihuman topoisomerase Isecondary binding sitesupercoil recognitionArticle