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Li D, Dong J, Zhou Y, Wang Q. Toward Precise Fabrication of Finite-Sized DNA Origami Superstructures. SMALL METHODS 2024:e2401629. [PMID: 39632670 DOI: 10.1002/smtd.202401629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 11/22/2024] [Indexed: 12/07/2024]
Abstract
DNA origami enables the precise construction of 2D and 3D nanostructures with customizable shapes and the high-resolution organization of functional materials. However, the size of a single DNA origami is constrained by the length of the scaffold strand, and since its inception, scaling up the size and complexity has been a persistent pursuit. Hierarchical self-assembly of DNA origami units offers a feasible approach to overcome the limitation. Unlike periodic arrays, finite-sized DNA origami superstructures feature well-defined structural boundaries and uniform dimensions. In recent years, increasing attention has been directed toward precise control over the hierarchical self-assembly of DNA origami structures and their applications in fields such as nanophotonics, biophysics, and material science. This review summarizes the strategies for fabricating finite-sized DNA origami superstructures, including heterogeneous self-assembly, self-limited self-assembly, and templated self-assembly, along with a comparative analysis of the advantages and limitations of each approach. Subsequently, recent advancements in the application of these structures are discussed from a structure design perspective. Finally, an outlook on the current challenges and potential future directions is provided, highlighting opportunities for further research and development in this rapidly evolving field.
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Affiliation(s)
- Dongsheng Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Yihao Zhou
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Qiangbin Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China
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2
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Luu MT, Berengut JF, Li J, Chen JB, Daljit Singh JK, Coffi Dit Glieze K, Turner M, Skipper K, Meppat S, Fowler H, Close W, Doye JPK, Abbas A, Wickham SFJ. Reconfigurable nanomaterials folded from multicomponent chains of DNA origami voxels. Sci Robot 2024; 9:eadp2309. [PMID: 39602517 DOI: 10.1126/scirobotics.adp2309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 10/30/2024] [Indexed: 11/29/2024]
Abstract
In cells, proteins rapidly self-assemble into sophisticated nanomachines. Bioinspired self-assembly approaches, such as DNA origami, have been used to achieve complex three-dimensional (3D) nanostructures and devices. However, current synthetic systems are limited by low yields in hierarchical assembly and challenges in rapid and efficient reconfiguration between diverse structures. Here, we developed a modular system of DNA origami "voxels" with programmable 3D connections. We demonstrate multifunctional pools of up to 12 unique voxels that can assemble into many shapes, prototyping 50 structures. Programmable switching of local connections between flexible and rigid states achieved rapid and reversible reconfiguration of global structures in three dimensions. Multistep assembly pathways were then explored to increase the yield. Voxels were assembled via flexible chain intermediates into rigid structures, increasing yield up to 100-fold. We envision that foldable chains of DNA origami voxels can achieve increased complexity in reconfigurable nanomaterials, providing modular components for the assembly of nanorobotic systems with future applications in synthetic biology, assembly of inorganic materials, and nanomedicine.
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Affiliation(s)
- Minh Tri Luu
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
- School of Physics, University of Sydney, Sydney, NSW 2006, Australia
- School of Chemical and Biomolecular Engineering, University of Sydney, NSW 2006, Australia
- University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathan F Berengut
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
- University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, Australia
| | - Jiahe Li
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Jing-Bing Chen
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Jasleen Kaur Daljit Singh
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
- School of Chemical and Biomolecular Engineering, University of Sydney, NSW 2006, Australia
- University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Kanako Coffi Dit Glieze
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
- University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Matthew Turner
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Karuna Skipper
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
- University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Sreelakshmi Meppat
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
- University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Hannah Fowler
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - William Close
- Australian Centre for Microscopy & Microanalysis, University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Ali Abbas
- School of Chemical and Biomolecular Engineering, University of Sydney, NSW 2006, Australia
- University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Shelley F J Wickham
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
- School of Physics, University of Sydney, Sydney, NSW 2006, Australia
- University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
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Ye R, Wang Y, Liu Y, Cai P, Song J. Self-assembled methodologies for the construction of DNA nanostructures and biological applications. Biomater Sci 2024; 12:3712-3724. [PMID: 38912847 DOI: 10.1039/d4bm00584h] [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: 06/25/2024]
Abstract
Over the past decades, deoxyribonucleic acid (DNA), as a versatile building block, has been widely employed to construct functionalized nanostructures. Among the diverse types of materials, DNA related nanostructures have gained growing attention due to their intrinsic programmability, favorable biocompatibility, and strong molecular recognition capability. The conventional construction strategy for building DNA structures is based on Watson-Crick base-pairing rules, which are mainly driven by the hydrogen bonding of bases. However, hydrogen bonding-based DNA nanostructures cannot meet the requirements of specific morphology and multifunctionality. Currently, various functional elements have been introduced to expand the synthetic methodologies for constructing the DNA hybrid nanostructures, including small molecules, peptide polymers, organic ligands and transition metal ions. Besides, the potential applications for these DNA hybrid nanostructures have also been explored. It has been demonstrated that DNA hybrid structures with various properties can be extensively applied in the fields of magnetic resonance, luminescence imaging, biomedical detection, and drug delivery systems. In this review, we highlight the pioneering contributions to the methodologies of DNA-based nanostructure assembly. Furthermore, the recent advances in drug delivery systems and biomedical diagnosis based on DNA hybrid nanostructures are briefly summarized.
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Affiliation(s)
- Rui Ye
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yuqi Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
- Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ping Cai
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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Raghuram V, Datye AD, Fried SI, Timko BP. Transparent and Conformal Microcoil Arrays for Spatially Selective Neuronal Activation. DEVICE 2024; 2:100290. [PMID: 39184953 PMCID: PMC11343507 DOI: 10.1016/j.device.2024.100290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Micromagnetic stimulation (μMS) using small, implantable microcoils is a promising method for achieving neuronal activation with high spatial resolution and low toxicity. Herein, we report a microcoil array for localized activation of cortical neurons and retinal ganglion cells. We developed a computational model to relate the electric field gradient (activating function) to the geometry and arrangement of microcoils, and selected a design that produced an anisotropic region of activation <50 μm wide. The device was comprised of an SU-8/Cu/SU-8 tri-layer structure, which was flexible, transparent and conformal and featured four individually-addressable microcoils. Interfaced with cortex or retina explants from GCaMP6-expressing mice, we observed that individual neurons localized within 40 μm of a microcoil tip could be activated repeatedly and in a dose- (power-) dependent fashion. These results demonstrate the potential of μMS devices for brain-machine interfaces and could enable routes toward bioelectronic therapies including prosthetic vision devices.
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Affiliation(s)
- Vineeth Raghuram
- Dept. of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
- Boston Veterans Affairs Healthcare System, Boston, MA 02130, USA
- Dept. of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Aditya D. Datye
- Dept. of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Shelley I. Fried
- Dept. of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
- Boston Veterans Affairs Healthcare System, Boston, MA 02130, USA
- Dept. of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Brian P. Timko
- Dept. of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
- Lead Contact
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Berg WR, Berengut JF, Bai C, Wimberger L, Lee LK, Rizzuto FJ. Light-Activated Assembly of DNA Origami into Dissipative Fibrils. Angew Chem Int Ed Engl 2023; 62:e202314458. [PMID: 37903739 DOI: 10.1002/anie.202314458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif-protonated, self-complementary poly(adenine) sequences-can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology.
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Affiliation(s)
- Willi R Berg
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
- Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstraße 34-36, 14195, Berlin, Germany
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, 2052, Australia
| | - Changzhuang Bai
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Laura Wimberger
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, 2052, Australia
| | - Felix J Rizzuto
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
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Benson E, Bath J. Reconfigurable self-assembled DNA devices. Sci Robot 2023; 8:eadh8148. [PMID: 37099637 DOI: 10.1126/scirobotics.adh8148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Modular reconfigurable systems can be achieved with DNA origami, demonstrating the potential to generate molecular robots.
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Affiliation(s)
- Erik Benson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonathan Bath
- Department of Physics, University of Oxford, Clarendon Laboratory, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, New Biochemistry Building, Oxford, UK
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