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Rectification of protein translocation in truncated-pyramidal nanopores
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
IBM TJ Watson Res Ctr, Yorktown Hts, NY USA.
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
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2019 (English)In: Nature Nanotechnology, ISSN 1748-3387, E-ISSN 1748-3395, Vol. 14, p. 1056-1062Article in journal (Refereed) Published
Abstract [en]

Solid-state nanopore technology presents an emerging single-molecule-based analytical tool for the separation and analysis of nanoparticles. Different approaches have been pursued to attain the anticipated detection performance. Here, we report the rectification behaviour of protein translocation through silicon-based truncated pyramidal nanopores. When the size of translocating proteins is comparable to the smallest physical constriction of the nanopore, the frequency of translocation events observed is lower for proteins that travel from the larger to the small opening of the nanopore than for those that travel in the reverse direction. When the proteins are appreciably smaller than the nanopore, an opposite rectification in the frequency of translocation events is evident. The maximum rectification factor achieved is around ten. Numerical simulations reveal the formation of an electro-osmotic vortex in such asymmetric nanopores. The vortex–protein interaction is found to play a decisive role in rectifying the translocation in terms of polarity and amplitude. The reported phenomenon can be potentially exploitable for the discrimination of various nanoparticles.

Place, publisher, year, edition, pages
2019. Vol. 14, p. 1056-1062
National Category
Nano Technology Engineering and Technology
Identifiers
URN: urn:nbn:se:uu:diva-384656DOI: 10.1038/s41565-019-0549-0ISI: 000495608700014PubMedID: 31591525OAI: oai:DiVA.org:uu-384656DiVA, id: diva2:1321203
Funder
Swedish Research Council, 621-2014-6300Swedish Research Council, 2016/39Available from: 2019-06-07 Created: 2019-06-07 Last updated: 2019-12-16Bibliographically approved
In thesis
1. Solid-State Nanopores for Sensing: From Theory to Applications
Open this publication in new window or tab >>Solid-State Nanopores for Sensing: From Theory to Applications
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Nanopore based sensing technology has been widely studied for a broad range of applications including DNA sequencing, protein profiling, metabolite molecules, and ions detection. The nanopore technology offers an unprecedented technological solution to meeting the demands of precision medicine on rapid, in-field, and low-cost biomolecule analysis. In general, nanopores are categorized in two families: solid-state nanopore (SSNP) and biological nanopore. The former is formed in a solid-state membrane made of SiNx, SiO2, silicon, graphene, MoS2, etc., while the latter represents natural protein ion-channels in cell membranes. Compared to biological pores, SSNPs are mechanically robust and their fabrication is compatible with traditional semiconductor processes, which may pave the way to their large-scale fabrication and high-density integration with standard control electronics. However, challenges remain for SSNPs, including poor stability, low repeatability, and relatively high background noise level. This thesis explores SSNPs from basic physical mechanisms to versatile applications, by entailing a balance between theory and experiment.

The thesis starts with theoretical models of nanopores. First, resistance of the open pore state is studied based on the distribution of electric field. An important concept, effective transport length, is introduced to quantify the extent of the high field region. Based on this conductance model, the nanopores size of various geometrical shapes can be extracted from a simple resistance measurement. Second, the physical causality of ionic current rectification of geometrically asymmetrical nanopores is unveiled. Third, the origin of low-frequency noise is identified. The contribution of each noise component at different conditions is compared. Forth, a simple nano-disk model is used to describe the blockage of ionic current caused by DNA translocation. The signal and noise properties are analyzed at system level.

Then, nanopore sensing experiments are implemented on cylinder SiNx nanopores and truncated-pyramid silicon nanopores (TPP). Prior to a systematic study, a low noise electrical characterization platform for nanopore devices is established. Signal acquisition guidelines and data processing flow are standardized. The effects of electroosmotic vortex in TPP on protein translocation dynamics are excavated. The autogenic translocation of DNA and proteins driven by the pW-level power generated by an electrolyte concentration gradient is demonstrated. Furthermore, by extending to a multiple pore system, the group translocation behavior of nanoparticles is studied. Various application scenarios, different analyte categories and divergent device structures accompanying with flexible configurations clearly point to the tremendous potential of SSNPs as a versatile sensor.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 108
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1825
Keywords
solid-state nanopore, ionic current, current blockage, effective transport length, noise, surface charge, translocation, biomolecule, electroosmotic flow, vortex, autogenic translocation, multiple nanopores
National Category
Nano Technology Electrical Engineering, Electronic Engineering, Information Engineering
Research subject
Engineering Science with specialization in Electronics
Identifiers
urn:nbn:se:uu:diva-384667 (URN)978-91-513-0689-6 (ISBN)
Public defence
2019-09-06, Polhemsalen, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2019-08-12 Created: 2019-06-19 Last updated: 2019-08-23
2. Solid-state nanopores: fabrication and applications
Open this publication in new window or tab >>Solid-state nanopores: fabrication and applications
2020 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Nanopores are of great interest in study of DNA sequencing, protein profiling and power generation. Among them, solid-state nanopores show obvious advantages over their biological counterparts in terms of high chemical stability and reusability as well as compatibility with the existing CMOS fabrication techniques. Nanopore sensing is most frequently based on measuring ionic current through a nanopore while applying a voltage across it. When an analyte passes through the pore, the ionic current temporarily changes, providing information of the analyte such as its size, shape and surface charge. Although many magnificent reports on using solid-state nanopores have appeared in the literature, several challenges still remain for their wider applications, which include improvement of fabrication reproducibility for mass production of ultra-small nanopores and minimization of measurement instability as well as control of translocation speed and reduction of background noise. This thesis work explores different techniques to achieve robust and high throughput fabrication of sub-10 nm nanopores for different applications.

The thesis starts with presenting various fabrication techniques explored during my PhD studies. Focused ion beam method was firstly employed to drill nanopores in free-standing SiNx membranes. Sub-10 nm nanopores could be obtained with a focused helium ion beam. But the fabrication throughput was limited with this technique. A new fabrication process combing electron beam lithography (EBL) with reactive ion etching/ion beam etching, which is compatible with the existing CMOS fabrication technology, was developed to realize a high throughput, mass production of nanopores in free-standing SiNx membranes. However, the smallest size that could be controllably achieved with this process was around 40 nm, which is still far from sub-10 nm in size required for, e.g., DNA sequencing. Finally, by using anisotropic etching of single-crystal silicon in KOH solution, sub-5 nm truncated pyramidal nanopores were mass produced with good process controllability in a silicon-on-insulator (SOI) substrate. In addition, nanopore arrays were also successfully fabricated using a modified EBL based fabrication process.

Then, several sensing application examples using either single nanopores or nanopore arrays were investigated. Translocation of nanoparticles, DNA and proteins were demonstrated using the fabricated single nanopores or nanopore arrays in a single freestanding membrane. Moreover, the kinetics and mechanism of the lipid bilayer formation in nanopore array, aiming to prevent non-specific adsorption, were studied using ionic current measurements. In addition, individual addressability of a solid-state nanopore array on separated freestanding membranes was realized by integrating microfluidics and a customized multiplexer.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2020. p. 82
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1890
Keywords
solid-state nanopore, truncated-pyramidal nanopore, nanopore array, pore size reduction, individual addressability, microfluidics, translocation.
National Category
Engineering and Technology
Research subject
Engineering Science with specialization in Electronics
Identifiers
urn:nbn:se:uu:diva-399726 (URN)978-91-513-0838-8 (ISBN)
Public defence
2020-02-21, Polhemsalen, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2020-01-31 Created: 2019-12-16 Last updated: 2020-01-31

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