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The Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore

submitted on 29.05.2018, 11:54 and posted on 30.05.2018, 12:20 by Xin Shi, Qiao Li, Rui Gao, Wei Si, Shao-Chuang Liu, Aleksei Aksimentiev, Yi-Tao Long
Docking of a protein-DNA complex onto a nanopore can provide ample observation time for a detailed inspection of the complex, enabling collection of biophysical data for detection, identification, and characterization of the biomolecules. While docking of a protein-DNA complex onto a biological nanopore has enabled analytic applications of nanopores including DNA sequencing, the application of the same principle to solid-state nanopores is tempered by poor understanding of the docking process. Here, we elucidate the behaviour of individual protein-DNA complexes docked onto a solid-state nanopore by monitoring the nanopore ionic current. Repeat docking of monovalent streptavidin-DNA complexes is found to produce ionic current blockades that fluctuate between discrete levels within the same current blockade. We elucidate the roles of the protein plug and the DNA tether in the docking process, finding the docking configurations to determine the multitude of the current blockade levels whereas the frequency of the current level switching to be determined by the interactions between the molecules and the solid-state membrane. Finally, we prove the feasibility of using the nanopore docking principle for single molecule sensing using solid-state nanopores by detecting conformational changes of a tethered DNA molecule from a random coil to an i-motif states.


National Natural Science Foundation of China (21421004, 21327807), the Programme of Introducing Talents of Discipline to Universities (B16017), United States National Institutes of Health (R01-HG007406 and P41-GM104601), and China Scholarship Council (CSC201506090040 for W.S and CSC201606740021 for X. S.).


Email Address of Submitting Author


East China University of Science and Technology



ORCID For Submitting Author


Declaration of Conflict of Interest

no conflict of interest


Read the published paper

in The Journal of Physical Chemistry Letters