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A modular spring-loaded actuator for mechanical activation of membrane proteins. Nat Commun 2022; 13:3182. [PMID: 35902570 PMCID: PMC9334261 DOI: 10.1038/s41467-022-30745-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
How cells respond to mechanical forces by converting them into biological signals underlie crucial cellular processes. Our understanding of mechanotransduction has been hindered by technical barriers, including limitations in our ability to effectively apply low range piconewton forces to specific mechanoreceptors on cell membranes without laborious and repetitive trials. To overcome these challenges we introduce the Nano-winch, a robust, easily assembled, programmable DNA origami-based molecular actuator. The Nano-winch is designed to manipulate multiple mechanoreceptors in parallel by exerting fine-tuned, low- piconewton forces in autonomous and remotely activated modes via adjustable single- and double-stranded DNA linkages, respectively. Nano-winches in autonomous mode can land and operate on the cell surface. Targeting the device to integrin stimulated detectable downstream phosphorylation of focal adhesion kinase, an indication that Nano-winches can be applied to study cellular mechanical processes. Remote activation mode allowed finer extension control and greater force exertion. We united remotely activated Nano-winches with single-channel bilayer experiments to directly observe the opening of a channel by mechanical force in the force responsive gated channel protein, BtuB. This customizable origami provides an instrument-free approach that can be applied to control and explore a diversity of mechanotransduction circuits on living cells. Studies on mechanotransduction are limited by our ability to apply low range forces to specific mechanoreceptors on cell membranes. Here the authors report the Nano-winch, a programmable DNA origami-based molecular actuator, to manipulate multiple mechanoreceptors in parallel by exerting piconewton forces.
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De Fazio AF, Misatziou D, Baker YR, Muskens OL, Brown T, Kanaras AG. Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly. Chem Soc Rev 2021; 50:13410-13440. [PMID: 34792047 PMCID: PMC8628606 DOI: 10.1039/d1cs00632k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 12/26/2022]
Abstract
The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.
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Affiliation(s)
- Angela F De Fazio
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Doxi Misatziou
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Ysobel R Baker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Otto L Muskens
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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Wang H, Luo D, Wang H, Wang F, Liu X. Construction of Smart Stimuli-Responsive DNA Nanostructures for Biomedical Applications. Chemistry 2021; 27:3929-3943. [PMID: 32830363 DOI: 10.1002/chem.202003145] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/12/2020] [Indexed: 12/13/2022]
Abstract
DNA nanostructures have recently attracted increasing interest in biological and biomedical applications by virtue of their unique properties, such as structural programmability, multi-functionality, stimuli-responsive behaviors, and excellent biocompatibility. In particular, the intelligent responsiveness of smart DNA nanostructures to specific stimuli has facilitated their extensive development in the field of high-performance biosensing and controllable drug delivery. This minireview begins with different self-assembly strategies for the construction of various DNA nanostructures, followed by the introduction of a variety of stimuli-responsive functional DNA nanostructures for assembling metastable soft materials and for facilitating amplified biosensing. The recent achievements of smart DNA nanostructures for controllable drug delivery are highlighted. Finally, the current challenges and possible developments of this promising research are discussed in the fields of intelligent nanomedicine.
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Affiliation(s)
- Huimin Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China.,College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, P. R. China
| | - Dan Luo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Hong Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
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Keller A, Linko V. Challenges and Perspectives of DNA Nanostructures in Biomedicine. Angew Chem Int Ed Engl 2020; 59:15818-15833. [PMID: 32112664 PMCID: PMC7540699 DOI: 10.1002/anie.201916390] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/26/2020] [Indexed: 01/12/2023]
Abstract
DNA nanotechnology holds substantial promise for future biomedical engineering and the development of novel therapies and diagnostic assays. The subnanometer-level addressability of DNA nanostructures allows for their precise and tailored modification with numerous chemical and biological entities, which makes them fit to serve as accurate diagnostic tools and multifunctional carriers for targeted drug delivery. The absolute control over shape, size, and function enables the fabrication of tailored and dynamic devices, such as DNA nanorobots that can execute programmed tasks and react to various external stimuli. Even though several studies have demonstrated the successful operation of various biomedical DNA nanostructures both in vitro and in vivo, major obstacles remain on the path to real-world applications of DNA-based nanomedicine. Here, we summarize the current status of the field and the main implementations of biomedical DNA nanostructures. In particular, we focus on open challenges and untackled issues and discuss possible solutions.
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Affiliation(s)
- Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Strasse 10033098PaderbornGermany
| | - Veikko Linko
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
- HYBER CentreDepartment of Applied PhysicsAalto UniversityP. O. Box 1510000076AaltoFinland
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Yan Q, Wang Y, Shi J, Wei B. Allostery of DNA nanostructures controlled by enzymatic modifications. Nucleic Acids Res 2020; 48:7595-7600. [PMID: 32526030 PMCID: PMC7367186 DOI: 10.1093/nar/gkaa488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 01/10/2023] Open
Abstract
Allostery is comprehensively studied for natural macromolecules, such as proteins and nucleic acids. Here, we present controllable allostery of synthetic DNA nanostructure–enzyme systems. Rational designs of the synthetic allosteric systems are based on an in-depth understanding of allosteric sites with several types of strand placements, whose varying stacking strengths determine the local conformation and ultimately lead to a gradient level of allosteric transition. When enzymes in a molecular cloning toolbox such as DNA polymerase, exonuclease and ligase are applied to treat the allosteric sites, the resulting local conformational changes propagate through the entire structure for a global allosteric transition.
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Affiliation(s)
- Qi Yan
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yaqi Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Jile Shi
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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6
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Ribbon of DNA Lattice on Gold Nanoparticles for Selective Drug Delivery to Cancer Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Zhang S, Chen C, Xue C, Chang D, Xu H, Salena BJ, Li Y, Wu Z. Ribbon of DNA Lattice on Gold Nanoparticles for Selective Drug Delivery to Cancer Cells. Angew Chem Int Ed Engl 2020; 59:14584-14592. [DOI: 10.1002/anie.202005624] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/21/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Shuxin Zhang
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis, Chemoprevention and Chemotherapy National & Local Joint Biomedical Engineering Research Center on, Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Chang Chen
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis, Chemoprevention and Chemotherapy National & Local Joint Biomedical Engineering Research Center on, Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Chang Xue
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis, Chemoprevention and Chemotherapy National & Local Joint Biomedical Engineering Research Center on, Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - Huo Xu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis, Chemoprevention and Chemotherapy National & Local Joint Biomedical Engineering Research Center on, Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Bruno J. Salena
- Department of Medicine McMaster University 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - Zai‐Sheng Wu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis, Chemoprevention and Chemotherapy National & Local Joint Biomedical Engineering Research Center on, Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
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Keller A, Linko V. Herausforderungen und Perspektiven von DNA‐Nanostrukturen in der Biomedizin. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Adrian Keller
- Technische und Makromolekulare Chemie Universität Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Veikko Linko
- Biohybrid Materials Department of Bioproducts and Biosystems Aalto University P. O. Box 16100 00076 Aalto Finnland
- HYBER Centre Department of Applied Physics Aalto University P. O. Box 15100 00076 Aalto Finnland
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Li Z, Liu L, Zheng M, Zhao J, Seeman NC, Mao C. Making Engineered 3D DNA Crystals Robust. J Am Chem Soc 2019; 141:15850-15855. [PMID: 31553173 DOI: 10.1021/jacs.9b06613] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Engineered 3D DNA crystals are promising scaffolds for bottom-up construction of three-dimensional, macroscopic devices from the molecular level. Nevertheless, this has been hindered by the highly constrained conditions for DNA crystals to be stable. Here we report a method to prepare robust 3D DNA crystals by postassembly ligation to remove this constraint. Specifically, sticky ends at crystal contacts were enzymatically ligated, and the covalent bonds significantly enhanced crystal stability, e.g., being stable at 65 °C. This method also enabled the fabrication of DNA crystals with complex architectures including crystal shell, core-shell, and matryoshka dolls. Furthermore, we have demonstrated the applications of the robust DNA crystals in biocatalysis and protein entrapment. Our study removes one key obstacle for the applications of DNA crystals and offers many new opportunities in DNA nanotechnology.
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Affiliation(s)
- Zhe Li
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Longfei Liu
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Mengxi Zheng
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Jiemin Zhao
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Chengde Mao
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
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