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      Single-molecule protein sensing in a nanopore: a tutorial

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          Abstract

          A guidebook and reference for detecting and characterizing proteins at the single-molecule level using nanopores.

          Abstract

          Proteins are the structural elements and machinery of cells responsible for a functioning biological architecture and homeostasis. Advances in nanotechnology are catalyzing key breakthroughs in many areas, including the analysis and study of proteins at the single-molecule level. Nanopore sensing is at the forefront of this revolution. This tutorial review provides readers a guidebook and reference for detecting and characterizing proteins at the single-molecule level using nanopores. Specifically, the review describes the key materials, nanoscale features, and design requirements of nanopores. It also discusses general design requirements as well as details on the analysis of protein translocation. Finally, the article provides the background necessary to understand current research trends and to encourage the identification of new biomedical applications for protein sensing using nanopores.

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          Ion-beam sculpting at nanometre length scales.

          J. Li, D. Stein, C McMullan … (2001)
          Manipulating matter at the nanometre scale is important for many electronic, chemical and biological advances, but present solid-state fabrication methods do not reproducibly achieve dimensional control at the nanometre scale. Here we report a means of fashioning matter at these dimensions that uses low-energy ion beams and reveals surprising atomic transport phenomena that occur in a variety of materials and geometries. The method is implemented in a feedback-controlled sputtering system that provides fine control over ion beam exposure and sample temperature. We call the method "ion-beam sculpting", and apply it to the problem of fabricating a molecular-scale hole, or nanopore, in a thin insulating solid-state membrane. Such pores can serve to localize molecular-scale electrical junctions and switches and function as masks to create other small-scale structures. Nanopores also function as membrane channels in all living systems, where they serve as extremely sensitive electro-mechanical devices that regulate electric potential, ionic flow, and molecular transport across cellular membranes. We show that ion-beam sculpting can be used to fashion an analogous solid-state device: a robust electronic detector consisting of a single nanopore in a Si3N4 membrane, capable of registering single DNA molecules in aqueous solution.
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            Fabrication of solid-state nanopores with single-nanometre precision.

            A. Storm, J. Chen, X. S. Ling … (2003)
            Single nanometre-sized pores (nanopores) embedded in an insulating membrane are an exciting new class of nanosensors for rapid electrical detection and characterization of biomolecules. Notable examples include alpha-hemolysin protein nanopores in lipid membranes and solid-state nanopores in Si3N4. Here we report a new technique for fabricating silicon oxide nanopores with single-nanometre precision and direct visual feedback, using state-of-the-art silicon technology and transmission electron microscopy. First, a pore of 20 nm is opened in a silicon membrane by using electron-beam lithography and anisotropic etching. After thermal oxidation, the pore can be reduced to a single-nanometre when it is exposed to a high-energy electron beam. This fluidizes the silicon oxide leading to a shrinking of the small hole due to surface tension. When the electron beam is switched off, the material quenches and retains its shape. This technique dramatically increases the level of control in the fabrication of a wide range of nanodevices.
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              Graphene as a sub-nanometer trans-electrode membrane

              S. Garaj, W. Hubbard, A. Reina … (2010)
              Isolated, atomically thin conducting membranes of graphite, called graphene, have recently been the subject of intense research with the hope that practical applications in fields ranging from electronics to energy science will emerge1. Here, we show that when immersed in ionic solution, a layer of graphene becomes a new electrochemical structure we call a trans-electrode. The trans-electrode's unique properties are the consequence of the atomic scale proximity of its two opposing liquid-solid interfaces together with graphene's well known in-plane conductivity. We show that several trans-electrode properties are revealed by ionic conductance measurements on a CVD grown graphene membrane that separates two aqueous ionic solutions. Although our membranes are only one to two atomic layers2,3 thick, we find they are remarkable ionic insulators with a very small stable conductance that depends on the ion species in solution. Electrical measurements on graphene membranes in which a single nanopore has been drilled show that the membrane's effective insulating thickness is less than one nanometer. This small effective thickness makes graphene an ideal substrate for very high-resolution, high throughput nanopore-based single molecule detectors. The sensitivity of graphene's in-plane electronic conductivity to its immediate surface environment, as influenced by trans-electrode potential, will offer new insights into atomic surface processes and sensor development opportunities.
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                Author and article information

                Journal
                Journal ID (publisher-id): CSRVBR
                Title: Chemical Society Reviews
                Abbreviated Title: Chem. Soc. Rev.
                Publisher: Royal Society of Chemistry (RSC)
                ISSN (Print): 0306-0012
                ISSN (Electronic): 1460-4744
                Publication date Created: November 26 2018
                Publication date (Electronic): 2018
                Volume: 47
                Issue: 23
                Pages: 8512-8524
                Affiliations
                [1 ]Department of Biomedical Engineering
                [2 ]Boston University
                [3 ]Boston
                [4 ]USA
                [5 ]Departments of Chemistry and Medicine
                Article
                DOI: 10.1039/C8CS00106E
                PMC ID: 6309966
                PubMed ID: 30328860
                SO-VID: f5f23c5a-84dd-44ff-93d8-eea9f645b364
                Copyright © © 2018
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                http://rsc.li/journals-terms-of-use

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