1
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Liu Y, Wang R, Chen Q, Chang Y, Chen Q, Fukumoto K, Wang B, Yu J, Luo C, Ma J, Chen X, Murayama Y, Umeda K, Kodera N, Harada Y, Sekine SI, Li J, Tadakuma H. Organ-Specific Gene Expression Control Using DNA Origami-Based Nanodevices. NANO LETTERS 2024; 24:8410-8417. [PMID: 38920331 PMCID: PMC11249008 DOI: 10.1021/acs.nanolett.4c02104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
Nanodevices that function in specific organs or cells are one of the ultimate goals of synthetic biology. The recent progress in DNA nanotechnology such as DNA origami has allowed us to construct nanodevices to deliver a payload (e.g., drug) to the tumor. However, delivery to specific organs remains difficult due to the fragility of the DNA nanostructure and the low targeting capability of the DNA nanostructure. Here, we constructed tough DNA origami that allowed us to encapsulate the DNA origami into lipid-based nanoparticles (LNPs) under harsh conditions (low pH), harnessing organ-specific delivery of the gene of interest (GOI). We found that DNA origami-encapsulated LNPs can increase the functionality of payload GOIs (mRNA and siRNA) inside mouse organs through the contribution from different LNP structures revealed by cryogenic electron microscope (Cryo-EM). These data should be the basis for future organ-specific gene expression control using DNA origami nanodevices.
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Affiliation(s)
- Yuxiang Liu
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
| | - Ruixuan Wang
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
| | - Qimingxing Chen
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
| | - Yan Chang
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
| | - Qi Chen
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
| | - Kodai Fukumoto
- Institute
for Protein Research, Osaka University, Osaka 565-0871, Japan
- RIKEN
Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Bingxun Wang
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
| | - Jianchen Yu
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
| | - Changfeng Luo
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
| | - Jiayuan Ma
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
| | - Xiaoxia Chen
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
- Zhejiang
Provincial Key Laboratory of Pancreatic Disease Hangzhou, Zhejiang University School of Medicine First Affiliated
Hospital, Zhejiang 310009, People’s Republic
of China
| | - Yuko Murayama
- RIKEN
Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Kenichi Umeda
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Noriyuki Kodera
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Yoshie Harada
- Institute
for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Shun-ichi Sekine
- RIKEN
Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Jianfeng Li
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
- Gene Editing
Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, People’s
Republic of China
| | - Hisashi Tadakuma
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210 People’s
Republic of China
- Gene Editing
Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, People’s
Republic of China
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2
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Iinuma R, Chen X, Masubuchi T, Ueda T, Tadakuma H. Size-Selective Capturing of Exosomes Using DNA Tripods. J Am Chem Soc 2024; 146:10293-10298. [PMID: 38569597 PMCID: PMC11027911 DOI: 10.1021/jacs.3c11067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024]
Abstract
Fractionating and characterizing target samples are fundamental to the analysis of biomolecules. Extracellular vesicles (EVs), containing information regarding the cellular birthplace, are promising targets for biology and medicine. However, the requirement for multiple-step purification in conventional methods hinders analysis of small samples. Here, we apply a DNA origami tripod with a defined aperture of binders (e.g., antibodies against EV biomarkers), which allows us to capture the target molecule. Using exosomes as a model, we show that our tripod nanodevice can capture a specific size range of EVs with cognate biomarkers from a broad distribution of crude EV mixtures. We further demonstrate that the size of captured EVs can be controlled by changing the aperture of the tripods. This simultaneous selection with the size and biomarker approach should simplify the EV purification process and contribute to the precise analysis of target biomolecules from small samples.
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Affiliation(s)
- Ryosuke Iinuma
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- JSR
Corporation, Ibaraki, 305-0841, Japan
| | - Xiaoxia Chen
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, People’s Republic of China
| | - Takeya Masubuchi
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- Department
of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Takuya Ueda
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- Graduate
School of Science and Engineering, Waseda
University, Tokyo 162-8480, Japan
| | - Hisashi Tadakuma
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, People’s Republic of China
- Gene Editing
Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, People’s Republic
of China
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3
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Lachance-Brais C, Yao C, Reyes-Valenzuela A, Asohan J, Guettler E, Sleiman HF. Exceptional Nuclease Resistance of DNA and RNA with the Addition of Small-Molecule Nucleobase Mimics. J Am Chem Soc 2024; 146:5811-5822. [PMID: 38387071 DOI: 10.1021/jacs.3c07023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Nucleases present a formidable barrier to the application of nucleic acids in biology, significantly reducing the lifetime of nucleic acid-based drugs. Here, we develop a novel methodology to protect DNA and RNA from nucleases by reconfiguring their supramolecular structure through the addition of a nucleobase mimic, cyanuric acid. In the presence of cyanuric acid, polyadenine strands assemble into triple helical fibers known as the polyA/CA motif. We report that this motif is exceptionally resistant to nucleases, with the constituent strands surviving for up to 1 month in the presence of serum. The conferred stability extends to adjacent non-polyA sequences, albeit with diminishing returns relative to their polyA sections due to hypothesized steric clashes. We introduce a strategy to regenerate stability through the introduction of free polyA strands or positively charged amino side chains, enhancing the stability of sequences of varied lengths. The proposed protection mechanism involves enzyme failure to recognize the unnatural polyA/CA motif, coupled with the motif's propensity to form long, bundling supramolecular fibers. The methodology provides a fundamentally new mechanism to protect nucleic acids from degradation using a supramolecular approach and increases lifetime in serum to days, weeks, or months.
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Affiliation(s)
| | - Chihyu Yao
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
| | | | - Jathavan Asohan
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
| | - Elizabeth Guettler
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
| | - Hanadi F Sleiman
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
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4
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Xu G, Wang C, Yu H, Li Y, Zhao Q, Zhou X, Li C, Liu M. Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer. Nucleic Acids Res 2023; 51:7666-7674. [PMID: 37351632 PMCID: PMC10415127 DOI: 10.1093/nar/gkad541] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
The 26-mer DNA aptamer (AF26) that specifically binds aflatoxin B1 (AFB1) with nM-level high affinity is rare among hundreds of aptamers for small molecules. Despite its predicted stem-loop structure, the molecular basis of its high-affinity recognition of AFB1 remains unknown. Here, we present the first high-resolution nuclear magnetic resonance structure of AFB1-AF26 aptamer complex in solution. AFB1 binds to the 16-residue loop region of the aptamer, inducing it to fold into a compact structure through the assembly of two bulges and one hairpin structure. AFB1 is tightly enclosed within a cavity formed by the bulges and hairpin, held in a place between the G·C base pair, G·G·C triple and multiple T bases, mainly through strong π-π stacking, hydrophobic and donor atom-π interactions, respectively. We further revealed the mechanism of the aptamer in recognizing AFB1 and its analogue AFG1 with only one-atom difference and introduced a single base mutation at the binding site of the aptamer to increase the discrimination between AFB1 and AFG1 based on the structural insights. This research provides an important structural basis for understanding high-affinity recognition of the aptamer, and for further aptamer engineering, modification and applications.
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Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Chen Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yapiao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
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5
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Neitz H, Bessi I, Kuper J, Kisker C, Höbartner C. Programmable DNA Interstrand Crosslinking by Alkene-Alkyne [2 + 2] Photocycloaddition. J Am Chem Soc 2023; 145:9428-9433. [PMID: 37071840 DOI: 10.1021/jacs.3c01611] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical, and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2'-deoxyuridine (PhedU). The crosslinking ability of PhedU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2 + 2] cycloaddition within the DNA duplex, resulting in efficient formation of a PhedU dimer after short irradiation times of a few seconds. A PhedU-dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Irene Bessi
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jochen Kuper
- Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging, Universität Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging, Universität Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, 97074 Würzburg, Germany
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