1
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Mathew SS, Ahamed AAS, Abraham I, Prabhu DD, John F, George J. Self‐Assemblies of DNA ‐ Amphiphiles Nanostructures for New Design Strategies of Varied Morphologies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - A A Subuhan Ahamed
- School of Chemistry University of Hyderabad Hyderabad 500046 Telangana India
| | - Ignatious Abraham
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Deepak D Prabhu
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Franklin John
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Jinu George
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
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2
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Zhang Z, Nakata E, Dinh H, Saimura M, Rajendran A, Matsuda K, Morii T. Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation. Chemistry 2021; 27:18118-18128. [PMID: 34747070 DOI: 10.1002/chem.202103304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Indexed: 11/09/2022]
Abstract
Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.
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Affiliation(s)
- Zhengxiao Zhang
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | | | - Kazunari Matsuda
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
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3
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Burgahn T, Garrecht R, Rabe KS, Niemeyer CM. Solid-Phase Synthesis and Purification of Protein-DNA Origami Nanostructures. Chemistry 2019; 25:3483-3488. [PMID: 30609150 DOI: 10.1002/chem.201805506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/07/2018] [Indexed: 12/13/2022]
Abstract
We present a facile method for the combined synthesis and purification of protein-decorated DNA origami nanostructures (DONs). DONs bearing reductively cleavable biotin groups in addition to ligands for ligation of recombinant proteins are bound to magnetic beads. Protein immobilization is conducted with a large protein excess to achieve high ligation yields. Subsequent to cleavage from the solid support, pure sample solutions are obtained which are suitable for direct AFM analysis of occupation patterns. We demonstrate the method's utility using three different orthogonal ligation methods, the "halo-based oligonucleotide binder" (HOB), a variant of Halo-tag, the "SpyTag/SpyCatcher" (ST/SC) system, and the enzymatic "ybbR tag" coupling. We find surprisingly low efficiency for ST/SC ligation, presumably due to electrostatic repulsion and steric hindrance, whereas the ybbR method, despite its ternary nature, shows good ligation yields. Our method is particularly useful for the development of novel ligation methods and the synthesis of mechanically fragile DONs that present protein patterns for surface-based cell assays.
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Affiliation(s)
- Teresa Burgahn
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ruben Garrecht
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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4
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Kurokawa T, Kiyonaka S, Nakata E, Endo M, Koyama S, Mori E, Tran NH, Dinh H, Suzuki Y, Hidaka K, Kawata M, Sato C, Sugiyama H, Morii T, Mori Y. DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K +
Channels. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tatsuki Kurokawa
- Department of Synthetic Chemistry and Biological Chemistry; Graduate School of Engineering; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
| | - Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry; Graduate School of Engineering; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Department of Technology and Ecology, Hall of Global Environmental Studies; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
| | - Eiji Nakata
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Institute of Advanced Energy; Kyoto University, Gokasho, Uji; Kyoto 611-0011 Japan
| | - Masayuki Endo
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku; Kyoto 606-8501 Japan
| | - Shohei Koyama
- Department of Synthetic Chemistry and Biological Chemistry; Graduate School of Engineering; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
| | - Emiko Mori
- Department of Synthetic Chemistry and Biological Chemistry; Graduate School of Engineering; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
| | - Nam Ha Tran
- Department of Technology and Ecology, Hall of Global Environmental Studies; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
| | - Huyen Dinh
- Institute of Advanced Energy; Kyoto University, Gokasho, Uji; Kyoto 611-0011 Japan
| | - Yuki Suzuki
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Department of Chemistry; Graduate School of Science; Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku; Kyoto 606-8502 Japan
| | - Kumi Hidaka
- Department of Chemistry; Graduate School of Science; Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku; Kyoto 606-8502 Japan
| | - Masaaki Kawata
- Biomedical Research Institute; National Institute of Advanced Industrial Science and Technology; 1-1-1 Higashi, Tsukuba Ibaraki 305-8566 Japan
| | - Chikara Sato
- Biomedical Research Institute; National Institute of Advanced Industrial Science and Technology; 1-1-1 Higashi, Tsukuba Ibaraki 305-8566 Japan
| | - Hiroshi Sugiyama
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku; Kyoto 606-8501 Japan
- Department of Chemistry; Graduate School of Science; Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku; Kyoto 606-8502 Japan
| | - Takashi Morii
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Institute of Advanced Energy; Kyoto University, Gokasho, Uji; Kyoto 611-0011 Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry; Graduate School of Engineering; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
- Core Research for Evolutional Science and Technology (Japan); Science and Technology Agency; 4-1-8 Hon-cho, Kawaguchi Saitama 332-0012 Japan
- Department of Technology and Ecology, Hall of Global Environmental Studies; Kyoto University, Kyotodaigakukatsura, Nishikyo-ku; Kyoto 615-8510 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku; Kyoto 606-8501 Japan
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5
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Kurokawa T, Kiyonaka S, Nakata E, Endo M, Koyama S, Mori E, Tran NH, Dinh H, Suzuki Y, Hidaka K, Kawata M, Sato C, Sugiyama H, Morii T, Mori Y. DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K + Channels. Angew Chem Int Ed Engl 2018; 57:2586-2591. [PMID: 29341462 DOI: 10.1002/anie.201709982] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/15/2017] [Indexed: 01/17/2023]
Abstract
In native systems, scaffolding proteins play important roles in assembling proteins into complexes to transduce signals. This concept is yet to be applied to the assembly of functional transmembrane protein complexes in artificial systems. To address this issue, DNA origami has the potential to serve as scaffolds that arrange proteins at specific positions in complexes. Herein, we report that Kir3 K+ channel proteins are assembled through zinc-finger protein (ZFP)-adaptors at specific locations on DNA origami scaffolds. Specific binding of the ZFP-fused Kir3 channels and ZFP-based adaptors on DNA origami were confirmed by atomic force microscopy and gel electrophoresis. Furthermore, the DNA origami with ZFP binding sites nearly tripled the K+ channel current activity elicited by heterotetrameric Kir3 channels in HEK293T cells. Thus, our method provides a useful template to control the oligomerization states of membrane protein complexes in vitro and in living cells.
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Affiliation(s)
- Tatsuki Kurokawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan
| | - Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Department of Technology and Ecology, Hall of Global Environmental Studies, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Eiji Nakata
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Masayuki Endo
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shohei Koyama
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Emiko Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan
| | - Nam Ha Tran
- Department of Technology and Ecology, Hall of Global Environmental Studies, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Yuki Suzuki
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masaaki Kawata
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Chikara Sato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hiroshi Sugiyama
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takashi Morii
- Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Core Research for Evolutional Science and Technology (Japan), Science and Technology Agency, 4-1-8 Hon-cho, Kawaguchi, Saitama, 332-0012, Japan.,Department of Technology and Ecology, Hall of Global Environmental Studies, Kyoto University, Kyotodaigakukatsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
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6
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Ouyang X, De Stefano M, Krissanaprasit A, Bank Kodal AL, Bech Rosen C, Liu T, Helmig S, Fan C, Gothelf KV. Docking of Antibodies into the Cavities of DNA Origami Structures. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China; Key Laboratory of Modern Separation Science in Shaanxi Province; College of Chemistry & Material Science; Northwest University; Xi'an 710127 China
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Mattia De Stefano
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Abhichart Krissanaprasit
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Present address: Department of Materials Science and Engineering; North Carolina State University; Raleigh NC 27606 USA
| | - Anne Louise Bank Kodal
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Christian Bech Rosen
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Tianqiang Liu
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Sarah Helmig
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Chunhai Fan
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Kurt V. Gothelf
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
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7
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Ouyang X, De Stefano M, Krissanaprasit A, Bank Kodal AL, Bech Rosen C, Liu T, Helmig S, Fan C, Gothelf KV. Docking of Antibodies into the Cavities of DNA Origami Structures. Angew Chem Int Ed Engl 2017; 56:14423-14427. [DOI: 10.1002/anie.201706765] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/18/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China; Key Laboratory of Modern Separation Science in Shaanxi Province; College of Chemistry & Material Science; Northwest University; Xi'an 710127 China
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Mattia De Stefano
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Abhichart Krissanaprasit
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Present address: Department of Materials Science and Engineering; North Carolina State University; Raleigh NC 27606 USA
| | - Anne Louise Bank Kodal
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Christian Bech Rosen
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Tianqiang Liu
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Sarah Helmig
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Chunhai Fan
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Kurt V. Gothelf
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
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8
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Rajendran A, Nakata E, Nakano S, Morii T. Nucleic-Acid-Templated Enzyme Cascades. Chembiochem 2017; 18:696-716. [DOI: 10.1002/cbic.201600703] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Indexed: 11/08/2022]
Affiliation(s)
| | - Eiji Nakata
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Shun Nakano
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Takashi Morii
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
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9
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Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X. Beyond the Fold: Emerging Biological Applications of DNA Origami. Chembiochem 2016; 17:1081-9. [PMID: 26928725 DOI: 10.1002/cbic.201600038] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/22/2023]
Abstract
The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.
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Affiliation(s)
| | - Nate Anderson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. , .,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. ,
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10
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Valero J, Lohmann F, Keppner D, Famulok M. Single-Stranded Tile Stoppers for Interlocked DNA Architectures. Chembiochem 2016; 17:1146-9. [DOI: 10.1002/cbic.201500685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Julián Valero
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Finn Lohmann
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Daniel Keppner
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Michael Famulok
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
- Center of Advanced European Studies and Research (CAESAR); Ludwig-Erhard-Allee 2 53175 Bonn Germany
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11
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Sagredo S, Pirzer T, Aghebat Rafat A, Goetzfried MA, Moncalian G, Simmel FC, de la Cruz F. Orthogonale Assemblierung von Proteinen auf DNA-Nanostrukturen mithilfe von Relaxasen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510313] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sandra Sagredo
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria; Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN; Albert Einstein 22 39011 Santander Spanien
| | - Tobias Pirzer
- Physik-Department E14 und ZNN/WSI; TU München; Am Coulombwall 4a 85748 Garching Deutschland
| | - Ali Aghebat Rafat
- Physik-Department E14 und ZNN/WSI; TU München; Am Coulombwall 4a 85748 Garching Deutschland
| | - Marisa A. Goetzfried
- Physik-Department E14 und ZNN/WSI; TU München; Am Coulombwall 4a 85748 Garching Deutschland
| | - Gabriel Moncalian
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria; Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN; Albert Einstein 22 39011 Santander Spanien
| | - Friedrich C. Simmel
- Physik-Department E14 und ZNN/WSI; TU München; Am Coulombwall 4a 85748 Garching Deutschland
| | - Fernando de la Cruz
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria; Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN; Albert Einstein 22 39011 Santander Spanien
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12
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Sagredo S, Pirzer T, Aghebat Rafat A, Goetzfried MA, Moncalian G, Simmel FC, de la Cruz F. Orthogonal Protein Assembly on DNA Nanostructures Using Relaxases. Angew Chem Int Ed Engl 2016; 55:4348-52. [PMID: 26915475 PMCID: PMC5067690 DOI: 10.1002/anie.201510313] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/17/2015] [Indexed: 12/19/2022]
Abstract
DNA-binding proteins are promising reagents for the sequence-specific modification of DNA-based nanostructures. Here, we investigate the utility of a series of relaxase proteins-TrwC, TraI, and MobA-for nanofunctionalization. Relaxases are involved in the conjugative transfer of plasmids between bacteria, and bind to their DNA target sites via a covalent phosphotyrosine linkage. We study the binding of the relaxases to two standard DNA origami structures-rodlike six-helix bundles and flat rectangular origami sheets. We find highly orthogonal binding of the proteins with binding yields of 40-50 % per binding site, which is comparable to other functionalization methods. The yields differ for the two origami structures and also depend on the position of the binding sites. Due to their specificity for a single-stranded DNA target, their orthogonality, and their binding properties, relaxases are a uniquely useful addition to the toolbox available for the modification of DNA nanostructures with proteins.
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Affiliation(s)
- Sandra Sagredo
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, Albert Einstein 22, 39011, Santander, Spain
| | - Tobias Pirzer
- Physik-Department E14 and ZNN/WSI, TU Munich, Am Coulombwall 4a, 85748, Garching, Germany
| | - Ali Aghebat Rafat
- Physik-Department E14 and ZNN/WSI, TU Munich, Am Coulombwall 4a, 85748, Garching, Germany
| | - Marisa A Goetzfried
- Physik-Department E14 and ZNN/WSI, TU Munich, Am Coulombwall 4a, 85748, Garching, Germany
| | - Gabriel Moncalian
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, Albert Einstein 22, 39011, Santander, Spain
| | - Friedrich C Simmel
- Physik-Department E14 and ZNN/WSI, TU Munich, Am Coulombwall 4a, 85748, Garching, Germany.
| | - Fernando de la Cruz
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, Albert Einstein 22, 39011, Santander, Spain.
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13
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Mallik L, Dhakal S, Nichols J, Mahoney J, Dosey AM, Jiang S, Sunahara RK, Skiniotis G, Walter NG. Electron Microscopic Visualization of Protein Assemblies on Flattened DNA Origami. ACS NANO 2015; 9:7133-41. [PMID: 26149412 PMCID: PMC5835357 DOI: 10.1021/acsnano.5b01841] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
DNA provides an ideal substrate for the engineering of versatile nanostructures due to its reliable Watson-Crick base pairing and well-characterized conformation. One of the most promising applications of DNA nanostructures arises from the site-directed spatial arrangement with nanometer precision of guest components such as proteins, metal nanoparticles, and small molecules. Two-dimensional DNA origami architectures, in particular, offer a simple design, high yield of assembly, and large surface area for use as a nanoplatform. However, such single-layer DNA origami were recently found to be structurally polymorphous due to their high flexibility, leading to the development of conformationally restrained multilayered origami that lack some of the advantages of the single-layer designs. Here we monitored single-layer DNA origami by transmission electron microscopy (EM) and discovered that their conformational heterogeneity is dramatically reduced in the presence of a low concentration of dimethyl sulfoxide, allowing for an efficient flattening onto the carbon support of an EM grid. We further demonstrated that streptavidin and a biotinylated target protein (cocaine esterase, CocE) can be captured at predesignated sites on these flattened origami while maintaining their functional integrity. Our demonstration that protein assemblies can be constructed with high spatial precision (within ∼2 nm of their predicted position on the platforms) by using strategically flattened single-layer origami paves the way for exploiting well-defined guest molecule assemblies for biochemistry and nanotechnology applications.
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Affiliation(s)
- Leena Mallik
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Soma Dhakal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph Nichols
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jacob Mahoney
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anne M. Dosey
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shuoxing Jiang
- The Biodesign Institute and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Roger K. Sunahara
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Georgios Skiniotis
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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14
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Yu JS, Lim MC, Huynh DTN, Kim HJ, Kim HM, Kim YR, Kim KB. Identifying the Location of a Single Protein along the DNA Strand Using Solid-State Nanopores. ACS NANO 2015; 9:5289-98. [PMID: 25938865 DOI: 10.1021/acsnano.5b00784] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Solid-state nanopore has been widely studied as an effective tool to detect and analyze small biomolecules, such as DNA, RNA, and proteins, at a single molecule level. In this study, we demonstrate a rapid identification of the location of zinc finger protein (ZFP), which is bound to a specific locus along the length of a double-stranded DNA (dsDNA) to a single protein resolution using a low noise solid-state nanopore. When ZFP labeled DNAs were driven through a nanopore by an externally applied electric field, characteristic ionic current signals arising from the passage of the DNA/ZFP complex and bare DNA were detected, which enabled us to identify the locations of ZFP binding site. We examined two DNAs with ZFP binding sites at different positions and found that the location of the additional current drop derived from the DNA/ZFP complex is well-matched with a theoretical one along the length of the DNA molecule. These results suggest that the protein binding site on DNA can be mapped or that genetic information can be read at a single molecule level using solid-state nanopores.
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Affiliation(s)
- Jae-Seok Yu
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Min-Cheol Lim
- ‡Graduate School of Biotechnology and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Duyen Thi Ngoc Huynh
- ‡Graduate School of Biotechnology and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Hyung-Jun Kim
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Hyun-Mi Kim
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
| | - Young-Rok Kim
- ‡Graduate School of Biotechnology and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Ki-Bum Kim
- †Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
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15
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Ryu Y, Jin Z, Lee JJ, Noh SH, Shin TH, Jo SM, Choi J, Park H, Cheon J, Kim HS. Size-Controlled Construction of Magnetic Nanoparticle Clusters Using DNA-Binding Zinc Finger Protein. Angew Chem Int Ed Engl 2014; 54:923-6. [DOI: 10.1002/anie.201408593] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/13/2014] [Indexed: 12/25/2022]
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16
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Ryu Y, Jin Z, Lee JJ, Noh SH, Shin TH, Jo SM, Choi J, Park H, Cheon J, Kim HS. Size-Controlled Construction of Magnetic Nanoparticle Clusters Using DNA-Binding Zinc Finger Protein. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Tintoré M, Eritja R, Fábrega C. DNA Nanoarchitectures: Steps towards Biological Applications. Chembiochem 2014; 15:1374-90. [DOI: 10.1002/cbic.201402014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/26/2022]
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18
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Flory JD, Simmons CR, Lin S, Johnson T, Andreoni A, Zook J, Ghirlanda G, Liu Y, Yan H, Fromme P. Low temperature assembly of functional 3D DNA-PNA-protein complexes. J Am Chem Soc 2014; 136:8283-95. [PMID: 24871902 DOI: 10.1021/ja501228c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Proteins have evolved to carry out nearly all the work required of living organisms within complex inter- and intracellular environments. However, systematically investigating the range of interactions experienced by a protein that influence its function remains challenging. DNA nanostructures are emerging as a convenient method to arrange a broad range of guest molecules. However, flexible methods are needed for arranging proteins in more biologically relevant 3D geometries under mild conditions that preserve protein function. Here we demonstrate how peptide nucleic acid (PNA) can be used to control the assembly of cytochrome c (12.5 kDa, pI 10.5) and azurin (13.9 kDa, pI 5.7) proteins into separate 3D DNA nanocages, in a process that maintains protein function. Toehold-mediated DNA strand displacement is introduced as a method to purify PNA-protein conjugates. The PNA-proteins were assembled within 2 min at room temperature and within 4 min at 11 °C, and hybridize with even greater efficiency than PNA conjugated to a short peptide. Gel electrophoresis and steady state and time-resolved fluorescence spectroscopy were used to investigate the effect of protein surface charge on its interaction with the negatively charged DNA nanocage. These data were used to generate a model of the DNA-PNA-protein complexes that show the negatively charged azurin protein repelled away from the DNA nanocage while the positively charged cytochrome c protein remains within and closely interacts with the DNA nanocage. When conjugated to PNA and incorporated into the DNA nanocage, the cytochrome c secondary structure and catalytic activity were maintained, and its redox potential was reduced modestly by 20 mV possibly due to neutralization of some positive surface charges. This work demonstrates a flexible new approach for using 3D nucleic acid (PNA-DNA) nanostructures to control the assembly of functional proteins, and facilitates further investigation of protein interactions as well as engineer more elaborate 3D protein complexes.
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Affiliation(s)
- Justin D Flory
- Department of Chemistry and Biochemistry, ‡Center for Bio-Inspired Solar Fuel Production, and §Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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19
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Li Z, Lavergne T, Malyshev DA, Zimmermann J, Adhikary R, Dhami K, Ordoukhanian P, Sun Z, Xiang J, Romesberg FE. Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet. Chemistry 2013; 19:14205-14209. [PMID: 24026962 DOI: 10.1002/chem.201302496] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Indexed: 12/20/2022]
Abstract
A class of replicable unnatural DNA base pairs formed between d5SICS and either dMMO2, dDMO, or dNaM were developed. To explore the use of these pairs to produce site-specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase-mediated replication, and subsequent site-specific modification of the amplified DNA by Click chemistry is reported. With the d5SICS scaffold a propynyl ether linker is accommodated better than its aliphatic analogue, but not as well as the protected propargyl amine linker explored previously. It was also found that with the dMMO2 and dDMO analogues, the dMMO2 position para to the glycosidic linkage is best suited for linker attachment and that although aliphatic and ether-based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogues, a variety of them were used to site-selectively attach a biotin tag to the amplified DNA. Finally, we use d5SICS(CO) -dNaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps "evolution" of nanomaterials.
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Affiliation(s)
- Zhengtao Li
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Thomas Lavergne
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Denis A Malyshev
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Jörg Zimmermann
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Ramkrishna Adhikary
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Kirandeep Dhami
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Phillip Ordoukhanian
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
| | - Zhelin Sun
- Department of Electrical and Computer Engineering 9500 Gilman Drive University of California, San Diego La Jolla, CA 92093
| | - Jie Xiang
- Department of Electrical and Computer Engineering 9500 Gilman Drive University of California, San Diego La Jolla, CA 92093
| | - Floyd E Romesberg
- Department of Chemistry and Dr. P. Ordoukhanian Center for Protein and Nucleic Acid Research The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037
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Endo M, Yang Y, Suzuki Y, Hidaka K, Sugiyama H. Single-Molecule Visualization of the Hybridization and Dissociation of Photoresponsive Oligonucleotides and Their Reversible Switching Behavior in a DNA Nanostructure. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205247] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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21
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Endo M, Yang Y, Suzuki Y, Hidaka K, Sugiyama H. Single-molecule visualization of the hybridization and dissociation of photoresponsive oligonucleotides and their reversible switching behavior in a DNA nanostructure. Angew Chem Int Ed Engl 2012; 51:10518-22. [PMID: 22965475 DOI: 10.1002/anie.201205247] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Indexed: 12/20/2022]
Abstract
A framed photo of DNA: A pair of photoresponsive oligonucleotides containing azobenzene moieties was introduced into double-stranded DNA within the cavity of a DNA nanostructure (see scheme). The two dsDNAs, in contact at the center, were dissociated using UV irradiation and hybridized with visible light; this was directly observed using high-speed atomic force microscopy.
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Affiliation(s)
- Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.
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