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Nanopore-Based DNA-Probe Sequence-Evolution Method Unveiling Characteristics of Protein–DNA Binding Phenomena in a Nanoscale Confined Space

Nannan Liu,Zekun Yang,Xiaoding Lou,Benmei Wei,Juntao Zhang,Pengcheng Gao,Ruizuo Hou,Fan Xia

Almost all of the important functions of DNA are realized by proteins which interact with specific DNA, which actually happens in a limited space. However, most of the studies about the protein–DNA binding are in an unconfined space. Here, we propose a new method, nanopore-based DNA-probe sequence-evolution (NDPSE), which includes up to 6 different DNA-probe systems successively designed in a nanoscale confined space which unveil the more realistic characteristics of protein–DNA binding phenomena. There are several features; for example, first, the edge-hindrance and core-hindrance contribute differently for the binding events, and second, there is an equilibrium between protein–DNA binding and DNA–DNA hybridization.