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Modified Outer Membrane Protein-G Nanopores with Expanded and Truncated β-Hairpins for Recognition of Double-Stranded DNA

Tosaka, Toshiyuki and Kamiya, Koki (2022) Modified Outer Membrane Protein-G Nanopores with Expanded and Truncated β-Hairpins for Recognition of Double-Stranded DNA. ACS Applied Nano Materials, 5 (5). pp. 6149-6158. ISSN 2574-0970. doi:10.1021/acsanm.1c04417. https://resolver.caltech.edu/CaltechAUTHORS:20220406-35628030

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Abstract

The detection of single molecules such as single-stranded DNA (ssDNA) and other small molecules through biological nanopores is a powerful approach for analyzing DNA sequences and DNA shapes, as well as for disease diagnostics. The fixed diameter of biological nanopores restricts the size of biomolecules translocated through them. Although some nanopores such as ClyA, FraC, Phi29p, and γ-hemolysin have been shown to translocate double-stranded DNA (dsDNA), identifying the difference between dsDNA and three-way junction DNA is difficult using these native biological nanopores. OmpG, a major outer membrane protein, forms a nanosized pore with 14 β-strands. Here, we create a modified OmpG that expands and truncates β-hairpins, allowing the generation of small or large nanopores compared to that of wild-type (WT) OmpG nanopores. To determine the pore diameters of modified OmpGs, the change in the current amplitude of the various modified OmpGs was measured in the presence or absence of poly(ethylene glycol) at different molecular weights. Finally, we demonstrated the detection of various structures of DNA (branched DNA) depending on the nanopore size using OmpG WT or mutated OmpG nanopores. Insights into the changes in pore diameters will be crucial to form precise pore diameters for the detection of various types of single biomolecules and for sequencing DNA, peptides, and proteins.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1021/acsanm.1c04417DOIArticle
ORCID:
AuthorORCID
Kamiya, Koki0000-0001-9143-9841
Additional Information:© 2022 American Chemical Society. Received: December 20, 2021; Accepted: March 22, 2022; Published: April 4, 2022. This work was partly supported by a Grant-in-Aid for Challenging Research (Exploratory) JP21K19039, Scientific Research on Innovative Areas “Chemistry for Multimolecular Crowding Biosystems” JP20H0492, the Leading Initiative for Excellent Young Researchers (LEADER) from the Japan Society for the Promotion of Science (JSPS), and the Nakatani Foundation for Advancement of Measuring Technologies in Biomedical Engineering. Author Contributions. K.K. designed the project and experiments. T.T. performed the experiments and analyzed the data. T.T. and K.K. wrote the manuscript; K.K. and T.T. revised the text. K.K. secured funding for the project. The authors declare no competing financial interest.
Funders:
Funding AgencyGrant Number
Japan Society for the Promotion of Science (JSPS)JP21K19039
Japan Society for the Promotion of Science (JSPS)JP20H0492
Nakatani Foundation for Advancement of Measuring Technologies in Biomedical EngineeringUNSPECIFIED
Subject Keywords:outer membrane protein; single-molecule detection; nanopores; lipid bilayer; biomolecule sensing
Issue or Number:5
DOI:10.1021/acsanm.1c04417
Record Number:CaltechAUTHORS:20220406-35628030
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20220406-35628030
Official Citation:Modified Outer Membrane Protein-G Nanopores with Expanded and Truncated β-Hairpins for Recognition of Double-Stranded DNA Toshiyuki Tosaka and Koki Kamiya. ACS Applied Nano Materials 2022 5 (5), 6149-6158; DOI: 10.1021/acsanm.1c04417
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:114176
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:06 Apr 2022 13:36
Last Modified:02 Aug 2022 22:33

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