1
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Bassani CL, van Anders G, Banin U, Baranov D, Chen Q, Dijkstra M, Dimitriyev MS, Efrati E, Faraudo J, Gang O, Gaston N, Golestanian R, Guerrero-Garcia GI, Gruenwald M, Haji-Akbari A, Ibáñez M, Karg M, Kraus T, Lee B, Van Lehn RC, Macfarlane RJ, Mognetti BM, Nikoubashman A, Osat S, Prezhdo OV, Rotskoff GM, Saiz L, Shi AC, Skrabalak S, Smalyukh II, Tagliazucchi M, Talapin DV, Tkachenko AV, Tretiak S, Vaknin D, Widmer-Cooper A, Wong GCL, Ye X, Zhou S, Rabani E, Engel M, Travesset A. Nanocrystal Assemblies: Current Advances and Open Problems. ACS NANO 2024; 18:14791-14840. [PMID: 38814908 DOI: 10.1021/acsnano.3c10201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.
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Affiliation(s)
- Carlos L Bassani
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Greg van Anders
- Department of Physics, Engineering Physics, and Astronomy, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Uri Banin
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dmitry Baranov
- Division of Chemical Physics, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Qian Chen
- University of Illinois, Urbana, Illinois 61801, USA
| | - Marjolein Dijkstra
- Soft Condensed Matter & Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands
| | - Michael S Dimitriyev
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, USA
| | - Efi Efrati
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Nicola Gaston
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, The University of Auckland, Auckland 1142, New Zealand
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
| | - G Ivan Guerrero-Garcia
- Facultad de Ciencias de la Universidad Autónoma de San Luis Potosí, 78295 San Luis Potosí, México
| | - Michael Gruenwald
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Maria Ibáñez
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Matthias Karg
- Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Tobias Kraus
- INM - Leibniz-Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, Colloid and Interface Chemistry, 66123 Saarbrücken, Germany
| | - Byeongdu Lee
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53717, USA
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bortolo M Mognetti
- Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Arash Nikoubashman
- Leibniz-Institut für Polymerforschung Dresden e.V., 01069 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01069 Dresden, Germany
| | - Saeed Osat
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077 Göttingen, Germany
| | - Oleg V Prezhdo
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Grant M Rotskoff
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Leonor Saiz
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
| | - An-Chang Shi
- Department of Physics & Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Sara Skrabalak
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Ivan I Smalyukh
- Department of Physics and Chemical Physics Program, University of Colorado, Boulder, Colorado 80309, USA
- International Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Mario Tagliazucchi
- Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Ciudad Autónoma de Buenos Aires, Buenos Aires 1428 Argentina
| | - Dmitri V Talapin
- Department of Chemistry, James Franck Institute and Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alexei V Tkachenko
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Sergei Tretiak
- Theoretical Division and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - David Vaknin
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
| | - Asaph Widmer-Cooper
- ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Xingchen Ye
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Shan Zhou
- Department of Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota 57701, USA
| | - Eran Rabani
- Department of Chemistry, University of California and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- The Raymond and Beverly Sackler Center of Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Engel
- Institute for Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Alex Travesset
- Iowa State University and Ames Lab, Ames, Iowa 50011, USA
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2
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Xie X, Ji M, Yan X, Yu Y, Wang Y, Ma N, Xing H, Tian Y. Layer-Controllable "2.5D" DNA Origami Crystals Synthesized by a Hierarchical Assembly Strategy. Angew Chem Int Ed Engl 2024; 63:e202402312. [PMID: 38578652 DOI: 10.1002/anie.202402312] [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: 02/01/2024] [Revised: 03/30/2024] [Accepted: 04/04/2024] [Indexed: 04/06/2024]
Abstract
The finite periodic arrangement of functional nanomaterials on the two-dimensional scale enables the integration and enhancement of individual properties, making them an important research topic in the field of tuneable nanodevices. Although layer-controllable lattices such as graphene have been successfully synthesized, achieving similar control over colloidal nanoparticles remains a challenge. DNA origami technology has achieved remarkable breakthroughs in programmed nanoparticle assembly. Based on this technology, we proposed a hierarchical assembly strategy to construct a universal DNA origami platform with customized layer properties, which we called 2.5-dimensional (2.5D) DNA origami crystals. Methodologically, this strategy divides the assembly procedure into two steps: 1) array synthesis, and 2) lattice synthesis, which means that the layer properties, including layer number, interlayer distance, and surface morphology, can be flexibly customized based on the independent designs in each step. In practice, these synthesized 2.5D crystals not only pioneer the expansion of the DNA origami crystal library to a wider range of dimensions, but also highlight the technological potential for templating 2.5D colloidal nanomaterial lattices.
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Affiliation(s)
- Xiaolin Xie
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Min Ji
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Xuehui Yan
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Yifan Yu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Yong Wang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Ningning Ma
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
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3
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Gavrilović S, Brüggenthies GA, Weck JM, Heuer-Jungemann A, Schwille P. Protein-Assisted Large-Scale Assembly and Differential Patterning of DNA Origami Lattices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309680. [PMID: 38229553 DOI: 10.1002/smll.202309680] [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: 10/24/2023] [Revised: 11/20/2023] [Indexed: 01/18/2024]
Abstract
Nanofabrication has experienced a big boost with the invention of DNA origami, enabling the production and assembly of complex nanoscale structures that may be able to unlock fully new functionalities in biology and beyond. The remarkable precision with which these structures can be designed and produced is, however, not yet matched by their assembly dynamics, which can be extremely slow, particularly when attached to biological templates, such as membranes. Here, the rapid and controlled formation of DNA origami lattices on the scale of hundreds of micrometers in as little as 30 minutes is demonstrated, utilizing active patterning by the E.coli Min protein system, thereby yielding a remarkable improvement over conventional passive diffusion-based assembly methods. Various patterns, including spots, inverse spots, mazes, and meshes can be produced at different scales, tailored through the shape and density of the assembled structures. The differential positioning accomplished by Min-induced diffusiophoresis even allows the introduction of "pseudo-colors", i.e., complex core-shell patterns, by simultaneously patterning different DNA origami species. Beyond the targeted functionalization of biological surfaces, this approach may also be promising for applications in plasmonics, catalysis, and molecular sensing.
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Affiliation(s)
- Svetozar Gavrilović
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | | | - Johann Moritz Weck
- Research Group DNA Hybridnanomaterials, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Amelie Heuer-Jungemann
- Research Group DNA Hybridnanomaterials, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
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4
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Liu H, Matthies M, Russo J, Rovigatti L, Narayanan RP, Diep T, McKeen D, Gang O, Stephanopoulos N, Sciortino F, Yan H, Romano F, Šulc P. Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments. Science 2024; 384:776-781. [PMID: 38753798 DOI: 10.1126/science.adl5549] [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: 10/27/2023] [Accepted: 03/19/2024] [Indexed: 05/18/2024]
Abstract
Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. We use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization.
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Affiliation(s)
- Hao Liu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Michael Matthies
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Thong Diep
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Daniel McKeen
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Flavio Romano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30171 Venezia-Mestre, Italy
- European Centre for Living Technology (ECLT), Ca' Bottacin, 3911 Dorsoduro Calle Crosera, 30123 Venice, Italy
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748 Garching, Germany
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5
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Pham TT, Abe S, Date K, Hirata K, Suzuki T, Ueno T. Displaying a Protein Cage on a Protein Crystal by In-Cell Crystal Engineering. NANO LETTERS 2023; 23:10118-10125. [PMID: 37955329 DOI: 10.1021/acs.nanolett.3c02117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The development of solid biomaterials has rapidly progressed in recent years in applications in bionanotechnology. The immobilization of proteins, such as enzymes, within protein crystals is being used to develop solid catalysts and functionalized materials. However, an efficient method for encapsulating protein assemblies has not yet been established. This work presents a novel approach to displaying protein cages onto a crystalline protein scaffold using in-cell protein crystal engineering. The polyhedra crystal (PhC) scaffold, which displays a ferritin cage, was produced by coexpression of polyhedrin monomer (PhM) and H1-ferritin (H1-Fr) monomer in Escherichia coli. The H1-tag is derived from the H1-helix of PhM. Our technique represents a unique strategy for immobilizing protein assemblies onto in-cell protein crystals and is expected to contribute to various applications in bionanotechnology.
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Affiliation(s)
- Thuc Toan Pham
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| | - Koki Date
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun 679-5148, Hyogo, Japan
| | - Taiga Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
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6
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Huang S, Ji M, Wang Y, Tian Y. Geometry guided crystallization of anisotropic DNA origami shapes. Chem Sci 2023; 14:11507-11514. [PMID: 37886088 PMCID: PMC10599470 DOI: 10.1039/d3sc02722h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/01/2023] [Indexed: 10/28/2023] Open
Abstract
Three-dimensional assembly based on DNA origami structures is an ideal method to precisely fabricate nano-scale materials. Additionally, applying an anisotropic assembly unit facilitates constructing complex materials with extraordinary structure. However, it still remains challenging to crystallize anisotropic DNA nano-structures using simple design, because the assembly of low-symmetry monomers often requires harsh auxiliary conditions and more complicated crystallization processes. In this work, we managed to crystallize the anisotropic elongated octahedral DNA origami frames by non-specific connections, and acquired two kinds of highly ordered superlattices purely by conducting multiple annealing processes and increasing the rigidity of the connection parts. In the case where the connection parts were composed of soft DNA sticky ends, we obtained the theoretically inaccessible simple cubic superlattices by this anisotropic DNA origami shape. Through characterization by small-angle X-ray scattering and scanning electron microscopy, we found that the DNA monomers are arbitrarily arranged due to the stress buffering of the soft DNA SEs, while in the stiffer case, simple tetragonal superlattices with translational arrangement of most anisotropic DNA origami shapes were synthesized as expected. This work deepened the understanding of geometry-guided crystallization of DNA origami shapes and provided a new path for constructing three-dimensional functional devices with simple design.
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Affiliation(s)
- Shujing Huang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 China
| | - Min Ji
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 China
| | - Yong Wang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 China
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7
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Voltà-Durán E, Alba-Castellón L, Serna N, Casanova I, López-Laguna H, Gallardo A, Sánchez-Chardi A, Villaverde A, Unzueta U, Vázquez E, Mangues R. High-precision targeting and destruction of cancer-associated PDGFR-β + stromal fibroblasts through self-assembling, protein-only nanoparticles. Acta Biomater 2023; 170:543-555. [PMID: 37683965 DOI: 10.1016/j.actbio.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
The need for more effective and precision medicines for cancer has pushed the exploration of new materials appropriate for drug delivery and imaging, and alternative receptors for targeting. Among the most promising strategies, finding suitable cell surface receptors and targeting agents for cancer-associated platelet derived growth factor receptor β (PDGFR-β)+ stromal fibroblasts is highly appealing. As a neglected target, this cell type mechanically and biologically supports the growth, progression, and infiltration of solid tumors in non-small cell lung, breast, pancreatic, and colorectal cancers. We have developed a family of PDGFR-β-targeted nanoparticles based on biofabricated, self-assembling proteins, upon hierarchical and iterative selective processes starting from four initial candidates. The modular protein PDGFD-GFP-H6 is well produced in recombinant bacteria, resulting in structurally robust oligomeric particles that selectively penetrates into PDGFR-β+ stromal fibroblasts in a dose-dependent manner, by means of the PDGFR-β ligand PDGFD. Upon in vivo administration, these GFP-carrying protein nanoparticles precisely accumulate in tumor tissues and enlighten them for IVIS observation. When GFP is replaced by a microbial toxin, selective tumor tissue destruction is observed associated with a significant reduction in tumor volume growth. The presented data validate the PDGFR-β/PDGFD pair as a promising toolbox for targeted drug delivery in the tumor microenvironment and oligomeric protein nanoparticles as a powerful instrument to mediate highly selective biosafe targeting in cancer through non-cancer cells. STATEMENT OF SIGNIFICANCE: We have developed a transversal platform for nanoparticle-based drug delivery into cancer-associated fibroblasts. This is based on the engineered modular protein PDGFD-GFP-H6 that spontaneously self-assemble and selectively penetrates into PDGFR-β+ stromal fibroblasts in a dose-dependent manner, by means of the PDGFR-β ligand PDGFD. In vivo, these protein nanoparticles accumulate in tumor and when incorporating a microbial toxin, they destroy tumor tissues with a significant reduction in tumor volume, in absence of side toxicities. The data presented here validate the PDGFR-β/PDGFD pair as a fully versatile toolbox for targeted drug delivery in the tumor microenvironment intended as a synergistic treatment.
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Affiliation(s)
- Eric Voltà-Durán
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Lorena Alba-Castellón
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona 08041, Spain; Josep Carreras Leukaemia Research Institute, Barcelona 08025, Spain.
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Isolda Casanova
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona 08041, Spain; Josep Carreras Leukaemia Research Institute, Barcelona 08025, Spain
| | - Hèctor López-Laguna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Alberto Gallardo
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona 08041, Spain; Department of Pathology, Hospital de la Santa Creu i Sant Pau, Barcelona 08025, Spain
| | - Alejandro Sánchez-Chardi
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, Barcelona 08028, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain.
| | - Ugutz Unzueta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona 08041, Spain; Josep Carreras Leukaemia Research Institute, Barcelona 08025, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona 08041, Spain; Josep Carreras Leukaemia Research Institute, Barcelona 08025, Spain.
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8
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Su Y, Liu B, Huang Z, Teng Z, Yang L, Zhu J, Huo S, Liu A. Virus-like particles nanoreactors: from catalysis towards bio-applications. J Mater Chem B 2023; 11:9084-9098. [PMID: 37697810 DOI: 10.1039/d3tb01112g] [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: 09/13/2023]
Abstract
Virus-like particles (VLPs) are self-assembled supramolecular structures found in nature, often used for compartmentalization. Exploiting their inherent properties, including precise nanoscale structures, monodispersity, and high stability, these architectures have been widely used as nanocarriers to protect or enrich catalysts, facilitating catalytic reactions and avoiding interference from the bulk solutions. In this review, we summarize the current progress of virus-like particles (VLPs)-based nanoreactors. First, we briefly introduce the physicochemical properties of the most commonly used virus particles to understand their roles in catalytic reactions beyond the confined space. Next, we summarize the self-assembly of nanoreactors forming higher-order hierarchical structures, highlighting the emerging field of nanoreactors as artificial organelles and their potential biomedical applications. Finally, we discuss the current findings and future perspectives of VLPs-based nanoreactors.
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Affiliation(s)
- Yuqing Su
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Beibei Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zhenkun Huang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zihao Teng
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Jie Zhu
- National-Local Joint Engineering Research and High-Quality Utilization, Changzhou University, Changzhou 213164, China
| | - Shuaidong Huo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Aijie Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
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9
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Adhikari S, Minevich B, Redeker D, Michelson AN, Emamy H, Shen E, Gang O, Kumar SK. Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions. J Am Chem Soc 2023; 145:19578-19587. [PMID: 37651692 DOI: 10.1021/jacs.3c03181] [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: 09/02/2023]
Abstract
Recent studies have demonstrated novel strategies for the organization of nanomaterials into three-dimensional (3D) ordered arrays with prescribed lattice symmetries using DNA-based self-assembly strategies. In one approach, the nanomaterial is sequestered into DNA origami frames or "material voxels" and then coordinated into ordered arrays based on the voxel geometry and the corresponding directional interactions based on its valency. While the lattice symmetry is defined by the valency of the bonds, a larger-scale morphological development is affected by assembly processes and differences in energies of anisotropic bonds. To facilely model this assembly process, we investigate the self-assembly behavior of hard particles with six interacting vertices via theory and Monte Carlo simulations and exploration of corresponding experimental systems. We demonstrate that assemblies with different 3D crystalline morphologies but the same lattice symmetry can be formed depending on the relative strength of vertex-to-vertex interactions in orthogonal directions. We observed three distinct assembly morphologies for such systems: cube-like, sheet-like, and cylinder-like. A simple analytical theory inspired by well-established ideas in the areas of protein crystallization, based on calculating the second virial coefficient of patchy hard spheres, captures the simulation results and thus represents a straightforward means of modeling this self-assembly process. To complement the theory and simulations, experimental studies were performed to investigate the assembly of octahedral DNA origami frames with varying binding energies at their vertices. X-ray scattering confirms the robustness of the formed nanoscale lattices for different binding energies, while both optical and electron microscopy imaging validated the theoretical predictions on the dependence of the distinct morphologies of assembled state on the interaction strengths in the three orthogonal directions.
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Affiliation(s)
- Sabin Adhikari
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Daniel Redeker
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Aaron Noam Michelson
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Hamed Emamy
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Eric Shen
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Sanat K Kumar
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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10
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McRae EKS, Rasmussen HØ, Liu J, Bøggild A, Nguyen MTA, Sampedro Vallina N, Boesen T, Pedersen JS, Ren G, Geary C, Andersen ES. Structure, folding and flexibility of co-transcriptional RNA origami. NATURE NANOTECHNOLOGY 2023; 18:808-817. [PMID: 36849548 PMCID: PMC10566746 DOI: 10.1038/s41565-023-01321-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
RNA origami is a method for designing RNA nanostructures that can self-assemble through co-transcriptional folding with applications in nanomedicine and synthetic biology. However, to advance the method further, an improved understanding of RNA structural properties and folding principles is required. Here we use cryogenic electron microscopy to study RNA origami sheets and bundles at sub-nanometre resolution revealing structural parameters of kissing-loop and crossover motifs, which are used to improve designs. In RNA bundle designs, we discover a kinetic folding trap that forms during folding and is only released after 10 h. Exploration of the conformational landscape of several RNA designs reveal the flexibility of helices and structural motifs. Finally, sheets and bundles are combined to construct a multidomain satellite shape, which is characterized by individual-particle cryo-electron tomography to reveal the domain flexibility. Together, the study provides a structural basis for future improvements to the design cycle of genetically encoded RNA nanodevices.
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Affiliation(s)
- Ewan K S McRae
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Helena Østergaard Rasmussen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andreas Bøggild
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Michael T A Nguyen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | | | - Thomas Boesen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cody Geary
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Ebbe Sloth Andersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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11
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Martínez-Torró C, Alba-Castellón L, Carrasco-Díaz LM, Serna N, Imedio L, Gallardo A, Casanova I, Unzueta U, Vázquez E, Mangues R, Villaverde A. Lymphocyte infiltration and antitumoral effect promoted by cytotoxic inflammatory proteins formulated as self-assembling, protein-only nanoparticles. Biomed Pharmacother 2023; 164:114976. [PMID: 37276641 DOI: 10.1016/j.biopha.2023.114976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023] Open
Abstract
Two human proteins involved in the inflammatory cell death, namely Gasdermin D (GSDMD) and the Mixed Lineage Kinase Domain-Like (MLKL) protein have been engineered to accommodate an efficient ligand of the tumoral cell marker CXCR4, and a set of additional peptide agents that allow their spontaneous self-assembling. Upon production in bacterial cells and further purification, both proteins organized as stable nanoparticles of 46 and 54 nm respectively, that show, in this form, a moderate but dose-dependent cytotoxicity in cell culture. In vivo, and when administered in mouse models of colorectal cancer through repeated doses, the nanoscale forms of tumor-targeted GSDMD and, at a lesser extent, of MLKL promoted CD8+ and CD20+ lymphocyte infiltration in the tumor and an important reduction of tumor size, in absence of systemic toxicity. The potential of these novel pharmacological agents as anticancer drugs is discussed in the context of synergistic approaches to more effective cancer treatments.
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Affiliation(s)
- Carlos Martínez-Torró
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Lorena Alba-Castellón
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Luis Miguel Carrasco-Díaz
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Laura Imedio
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Alberto Gallardo
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Department of Pathology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Isolda Casanova
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Ugutz Unzueta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain.
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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12
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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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13
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Xue H, Zhang M, Liu J, Wang J, Ren G. Structure-based mechanism and inhibition of cholesteryl ester transfer protein. Curr Atheroscler Rep 2023; 25:155-166. [PMID: 36881278 PMCID: PMC10027838 DOI: 10.1007/s11883-023-01087-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
PURPOSE OF REVIEW Cholesteryl ester transfer proteins (CETP) regulate plasma cholesterol levels by transferring cholesteryl esters (CEs) among lipoproteins. Lipoprotein cholesterol levels correlate with the risk factors for atherosclerotic cardiovascular disease (ASCVD). This article reviews recent research on CETP structure, lipid transfer mechanism, and its inhibition. RECENT FINDINGS Genetic deficiency in CETP is associated with a low plasma level of low-density lipoprotein cholesterol (LDL-C) and a profoundly elevated plasma level of high-density lipoprotein cholesterol (HDL-C), which correlates with a lower risk of atherosclerotic cardiovascular disease (ASCVD). However, a very high concentration of HDL-C also correlates with increased ASCVD mortality. Considering that the elevated CETP activity is a major determinant of the atherogenic dyslipidemia, i.e., pro-atherogenic reductions in HDL and LDL particle size, inhibition of CETP emerged as a promising pharmacological target during the past two decades. CETP inhibitors, including torcetrapib, dalcetrapib, evacetrapib, anacetrapib and obicetrapib, were designed and evaluated in phase III clinical trials for the treatment of ASCVD or dyslipidemia. Although these inhibitors increase in plasma HDL-C levels and/or reduce LDL-C levels, the poor efficacy against ASCVD ended interest in CETP as an anti-ASCVD target. Nevertheless, interest in CETP and the molecular mechanism by which it inhibits CE transfer among lipoproteins persisted. Insights into the structural-based CETP-lipoprotein interactions can unravel CETP inhibition machinery, which can hopefully guide the design of more effective CETP inhibitors that combat ASCVD. Individual-molecule 3D structures of CETP bound to lipoproteins provide a model for understanding the mechanism by which CETP mediates lipid transfer and which in turn, guide the rational design of new anti-ASCVD therapeutics.
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Affiliation(s)
- Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jianjun Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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14
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Raza MT, Tandon A, Park S, Lee S, Nguyen TBN, Vu THN, Park SH. DNA lattice growth with single, double, and triple double-crossover boundaries by stepwise self-assembly. NANOTECHNOLOGY 2023; 34:245603. [PMID: 36881902 DOI: 10.1088/1361-6528/acc1ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Construction of various nanostructures with nanometre-scale precision through various DNA building blocks depends upon self-assembly, base-pair complementarity and sequence programmability. During annealing, unit tiles are formed by the complementarity of base pairs in each strand. Enhancement of growth of target lattices is expected if seed lattices (i.e. boundaries for growth of target lattices) are initially present in a test tube during annealing. Although most processes for annealing DNA nanostructures adopt a one-step high temperature method, multi-step annealing provides certain advantages such as reusability of unit tiles and tuneability of lattice formation. We can construct target lattices effectively (through multi-step annealing) and efficiently (via boundaries) by multi-step annealing and combining boundaries. Here, we construct efficient boundaries made of single, double, and triple double-crossover DNA tiles for growth of DNA lattices. Two unit double-crossover DNA tile-based lattices and copy-logic implemented algorithmic lattices were introduced to test the growth of target lattices on boundaries. We used multi-step annealing to tune the formation of DNA crystals during fabrication of DNA crystals comprised of boundaries and target lattices. The formation of target DNA lattices was visualized using atomic force microscopy (AFM). The borders between boundaries and lattices in a single crystal were clearly differentiable from AFM images. Our method provides way to construct various types of lattices in a single crystal, which might generate various patterns and enhance the information capacity in a given crystal.
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Affiliation(s)
- Muhammad Tayyab Raza
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Anshula Tandon
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Suyoun Park
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sungjin Lee
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Thi Bich Ngoc Nguyen
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Thi Hong Nhung Vu
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sung Ha Park
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
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15
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Walczak M, Brady RA, Leathers A, Kotar J, Di Michele L. Influence of hydrophobic moieties on the crystallization of amphiphilic DNA nanostructures. J Chem Phys 2023; 158:084501. [PMID: 36859089 DOI: 10.1063/5.0132484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Three-dimensional crystalline frameworks with nanoscale periodicity are valuable for many emerging technologies, from nanophotonics to nanomedicine. DNA nanotechnology has emerged as a prime route for constructing these materials, with most approaches taking advantage of the structural rigidity and bond directionality programmable for DNA building blocks. Recently, we have introduced an alternative strategy reliant on flexible, amphiphilic DNA junctions dubbed C-stars, whose ability to crystallize is modulated by design parameters, such as nanostructure topology, conformation, rigidity, and size. While C-stars have been shown to form ordered phases with controllable lattice parameter, response to stimuli, and embedded functionalities, much of their vast design space remains unexplored. Here, we investigate the effect of changing the chemical nature of the hydrophobic modifications and the structure of the DNA motifs in the vicinity of these moieties. While similar design variations should strongly alter key properties of the hydrophobic interactions between C-stars, such as strength and valency, only limited differences in self-assembly behavior are observed. This finding suggests that long-range order in C-star crystals is likely imposed by structural features of the building block itself rather than the specific characteristics of the hydrophobic tags. Nonetheless, we find that altering the hydrophobic regions influences the ability of C-star crystals to uptake hydrophobic molecular cargoes, which we exemplify by studying the encapsulation of antibiotic penicillin V. Besides advancing our understanding of the principles governing the self-assembly of amphiphilic DNA building blocks, our observations thus open up new routes to chemically program the materials without affecting their structure.
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Affiliation(s)
- Michal Walczak
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ryan A Brady
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Adrian Leathers
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Jurij Kotar
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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16
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He L, Zheng N, Wang Q, Du J, Wang S, Cao Z, Wang Z, Chen G, Mu J, Liu S, Chen X. Responsive Accumulation of Nanohybrids to Boost NIR-Phototheranostics for Specific Tumor Imaging and Glutathione Depletion-Enhanced Synergistic Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 10:e2205208. [PMID: 36373690 PMCID: PMC9811476 DOI: 10.1002/advs.202205208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Dynamic regulation of nanoparticles in a controllable manner has great potential in various areas. Compared to the individual nanoparticles, the assembled nanoparticles exhibit superior properties and functions, which can be applied to achieve desirable performances. Here, a pH-responsive i-motif DNA-mediated strategy to tailor the programmable behaviors of erbium-based rare-earth nanoparticles (ErNPs) decorated copper doped metal-organic framework (CPM) nanohybrids (ECPM) under physiological conditions is reported. Within the acidic tumor microenvironment, the i-motif DNA strands are able to form quadruplex structures, resulting in the assembly of nanohybrids and selective tumor accumulation, which further amplify the ErNPs downconversion emission (1550 nm) signal for imaging. Meanwhile, the ECPM matrix acts as a near-infrared (NIR) photon-activated reactive oxygen species (ROS) amplifier through the singlet oxygen generation of the matrix in combination with its ability of intracellular glutathione depletion upon irradiation. In short, this work displays a classical example of engineering of nanoparticles, which will manifest the importance of developing nanohybrids with structural programmability in biomedical applications.
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Affiliation(s)
- Liangcan He
- School of Medicine and Health, Key Laboratory of Micro‐systems and Micro‐structures Manufacturing (Ministry of Education)Harbin Institute of TechnologyHarbin150001China
| | - Nannan Zheng
- School of Medicine and Health, Key Laboratory of Micro‐systems and Micro‐structures Manufacturing (Ministry of Education)Harbin Institute of TechnologyHarbin150001China
| | - Qinghui Wang
- School of Medicine and Health, Key Laboratory of Micro‐systems and Micro‐structures Manufacturing (Ministry of Education)Harbin Institute of TechnologyHarbin150001China
- Institute of Precision MedicinePeking University Shenzhen HospitalShenzhen518036China
| | - Jiarui Du
- School of Chemistry and Chemical EngineeringHarbin Institute of TechnologyHarbin150090China
| | - Shumin Wang
- Institute of Precision MedicinePeking University Shenzhen HospitalShenzhen518036China
| | - Zhiyue Cao
- School of Medicine and Health, Key Laboratory of Micro‐systems and Micro‐structures Manufacturing (Ministry of Education)Harbin Institute of TechnologyHarbin150001China
| | - Zhantong Wang
- Laboratory of Cellular Imaging and Macromolecular BiophysicsNational Institute of Biomedical Imaging and BioengineeringNational Institutes of HealthBethesdaMD20892USA
| | - Guanying Chen
- School of Chemistry and Chemical EngineeringHarbin Institute of TechnologyHarbin150090China
| | - Jing Mu
- Institute of Precision MedicinePeking University Shenzhen HospitalShenzhen518036China
| | - Shaoqin Liu
- School of Medicine and Health, Key Laboratory of Micro‐systems and Micro‐structures Manufacturing (Ministry of Education)Harbin Institute of TechnologyHarbin150001China
| | - Xiaoyuan Chen
- Departments of Diagnostic RadiologySurgeryChemical and Biomolecular Engineering and Biomedical EngineeringYong Loo Lin School of Medicine and College of Design and EngineeringNational University of SingaporeSingapore117597Singapore
- Institute of Molecular and Cell BiologyAgency for Science, Technology, and Research (A*STAR)61 Biopolis Drive, ProteosSingapore138673Singapore
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17
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Winegar PH, Figg CA, Teplensky MH, Ramani N, Mirkin CA. Modular Nucleic Acid Scaffolds for Synthesizing Monodisperse and Sequence-Encoded Antibody Oligomers. Chem 2022; 8:3018-3030. [PMID: 36405374 PMCID: PMC9674055 DOI: 10.1016/j.chempr.2022.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthesizing protein oligomers that contain exact numbers of multiple different proteins in defined architectures is challenging. DNA-DNA interactions can be used to program protein assembly into oligomers; however, existing methods require changes to DNA design to achieve different numbers and oligomeric sequences of proteins. Herein, we develop a modular DNA scaffold that uses only six synthetic oligonucleotides to organize proteins into defined oligomers. As a proof-of-concept, model proteins (antibodies) are oligomerized into dimers and trimers, where antibody function is retained. Illustrating the modularity of this technique, dimer and trimer building blocks are then assembled into pentamers containing three different antibodies in an exact stoichiometry and oligomeric sequence. In sum, this report describes a generalizable method for organizing proteins into monodisperse, sequence-encoded oligomers using DNA. This advance will enable studies into how oligomeric protein sequences affect material properties in areas spanning pharmaceutical development, cascade catalysis, synthetic photosynthesis, and membrane transport.
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Affiliation(s)
- Peter H. Winegar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - C. Adrian Figg
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - Michelle H. Teplensky
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Namrata Ramani
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Lead contact
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18
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Torres-Huerta AL, Antonio-Pérez A, García-Huante Y, Alcázar-Ramírez NJ, Rueda-Silva JC. Biomolecule-Based Optical Metamaterials: Design and Applications. BIOSENSORS 2022; 12:962. [PMID: 36354471 PMCID: PMC9688573 DOI: 10.3390/bios12110962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.
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Affiliation(s)
- Ana Laura Torres-Huerta
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Aurora Antonio-Pérez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Yolanda García-Huante
- Departamento de Ciencias Básicas, Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional (UPIITA-IPN), Mexico City 07340, Mexico
| | - Nayelhi Julieta Alcázar-Ramírez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Juan Carlos Rueda-Silva
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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19
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de Pinho Favaro MT, Atienza-Garriga J, Martínez-Torró C, Parladé E, Vázquez E, Corchero JL, Ferrer-Miralles N, Villaverde A. Recombinant vaccines in 2022: a perspective from the cell factory. Microb Cell Fact 2022; 21:203. [PMID: 36199085 PMCID: PMC9532831 DOI: 10.1186/s12934-022-01929-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/30/2022] [Indexed: 12/02/2022] Open
Abstract
The last big outbreaks of Ebola fever in Africa, the thousands of avian influenza outbreaks across Europe, Asia, North America and Africa, the emergence of monkeypox virus in Europe and specially the COVID-19 pandemics have globally stressed the need for efficient, cost-effective vaccines against infectious diseases. Ideally, they should be based on transversal technologies of wide applicability. In this context, and pushed by the above-mentioned epidemiological needs, new and highly sophisticated DNA-or RNA-based vaccination strategies have been recently developed and applied at large-scale. Being very promising and effective, they still need to be assessed regarding the level of conferred long-term protection. Despite these fast-developing approaches, subunit vaccines, based on recombinant proteins obtained by conventional genetic engineering, still show a wide spectrum of interesting potentialities and an important margin for further development. In the 80’s, the first vaccination attempts with recombinant vaccines consisted in single structural proteins from viral pathogens, administered as soluble plain versions. In contrast, more complex formulations of recombinant antigens with particular geometries are progressively generated and explored in an attempt to mimic the multifaceted set of stimuli offered to the immune system by replicating pathogens. The diversity of recombinant antimicrobial vaccines and vaccine prototypes is revised here considering the cell factory types, through relevant examples of prototypes under development as well as already approved products.
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Affiliation(s)
- Marianna Teixeira de Pinho Favaro
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.,Laboratory of Vaccine Development, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jan Atienza-Garriga
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain
| | - Carlos Martínez-Torró
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain
| | - Eloi Parladé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain. .,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
| | - José Luis Corchero
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain. .,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain. .,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain. .,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
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20
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Wang Y, Yan X, Zhou Z, Ma N, Tian Y. pH-Induced Symmetry Conversion of DNA Origami Lattices. Angew Chem Int Ed Engl 2022; 61:e202208290. [PMID: 35934673 DOI: 10.1002/anie.202208290] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Indexed: 01/02/2023]
Abstract
DNA nanotechnology has provided credible approaches for assembly of three-dimensional (3D) lattices with complex patterns. However, the symmetries are strictly dependent on their initial configurations and difficult to alter via non-thermal treatments. While switchable nucleic acid structures have been employed to construct deformable DNA motifs, it remains challenging to arrange them anisotropically in 3D lattices to trigger directed collective shape transition and dynamic symmetry conversion. In this work, we used octahedral DNA origami frames to synthesize four DNA origami lattices by placing the pH-reactive i-motif sequences in the desired dimensions. Thereinto, lattices with an anisotropic design can switch between simple cubic (SC) and simple tetragonal (ST) upon pH change. Small angle X-ray scattering (SAXS) results reveal the feasibility of obtaining 3D lattices with sensitive responses to external stimuli, expanding the way to obtain low-symmetry lattices.
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, Nanjing, 210023, China
| | - Xuehui Yan
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, Nanjing, 210023, China
| | - Zhaoyu Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, Nanjing, 210023, China
| | - Ningning Ma
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, Nanjing, 210023, China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, Nanjing, 210023, China.,Shenzhen Research Institute of Nanjing University, Shenzhen, 518000, China
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21
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Xue H, Zhang M, Liu J, Wang J, Ren G. Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination. Front Chem 2022; 10:889203. [PMID: 36110139 PMCID: PMC9468540 DOI: 10.3389/fchem.2022.889203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/13/2022] [Indexed: 11/28/2022] Open
Abstract
To understand the dynamic structure-function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.
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Affiliation(s)
- Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianjun Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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22
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Wang Y, Yan X, Zhou Z, Ma N, Tian Y. pH‐Induced Symmetry Conversion of DNA Origami Lattices. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yong Wang
- State Key Laboratory of Analytical Chemistry for Life Science College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials Collaborative Innovation Center of Advanced Microstructures Chemistry and Biomedicine Innovation Center Nanjing 210023 China
| | - Xuehui Yan
- State Key Laboratory of Analytical Chemistry for Life Science College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials Collaborative Innovation Center of Advanced Microstructures Chemistry and Biomedicine Innovation Center Nanjing 210023 China
| | - Zhaoyu Zhou
- State Key Laboratory of Analytical Chemistry for Life Science College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials Collaborative Innovation Center of Advanced Microstructures Chemistry and Biomedicine Innovation Center Nanjing 210023 China
| | - Ningning Ma
- State Key Laboratory of Analytical Chemistry for Life Science College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials Collaborative Innovation Center of Advanced Microstructures Chemistry and Biomedicine Innovation Center Nanjing 210023 China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials Collaborative Innovation Center of Advanced Microstructures Chemistry and Biomedicine Innovation Center Nanjing 210023 China
- Shenzhen Research Institute of Nanjing University Shenzhen 518000 China
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23
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Fabrini G, Minard A, Brady RA, Di Antonio M, Di Michele L. Cation-Responsive and Photocleavable Hydrogels from Noncanonical Amphiphilic DNA Nanostructures. NANO LETTERS 2022; 22:602-611. [PMID: 35026112 PMCID: PMC8796241 DOI: 10.1021/acs.nanolett.1c03314] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/01/2021] [Indexed: 05/26/2023]
Abstract
Thanks to its biocompatibility, versatility, and programmable interactions, DNA has been proposed as a building block for functional, stimuli-responsive frameworks with applications in biosensing, tissue engineering, and drug delivery. Of particular importance for in vivo applications is the possibility of making such nanomaterials responsive to physiological stimuli. Here, we demonstrate how combining noncanonical DNA G-quadruplex (G4) structures with amphiphilic DNA constructs yields nanostructures, which we termed "Quad-Stars", capable of assembling into responsive hydrogel particles via a straightforward, enzyme-free, one-pot reaction. The embedded G4 structures allow one to trigger and control the assembly/disassembly in a reversible fashion by adding or removing K+ ions. Furthermore, the hydrogel aggregates can be photo-disassembled upon near-UV irradiation in the presence of a porphyrin photosensitizer. The combined reversibility of assembly, responsiveness, and cargo-loading capabilities of the hydrophobic moieties make Quad-Stars a promising candidate for biosensors and responsive drug delivery carriers.
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Affiliation(s)
- Giacomo Fabrini
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Aisling Minard
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Ryan A. Brady
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Marco Di Antonio
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Lorenzo Di Michele
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
- Department
of Physics—Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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24
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Encoding hierarchical assembly pathways of proteins with DNA. Proc Natl Acad Sci U S A 2021; 118:2106808118. [PMID: 34593642 DOI: 10.1073/pnas.2106808118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2021] [Indexed: 11/18/2022] Open
Abstract
The structural and functional diversity of materials in nature depends on the controlled assembly of discrete building blocks into complex architectures via specific, multistep, hierarchical assembly pathways. Achieving similar complexity in synthetic materials through hierarchical assembly is challenging due to difficulties with defining multiple recognition areas on synthetic building blocks and controlling the sequence through which those recognition sites direct assembly. Here, we show that we can exploit the chemical anisotropy of proteins and the programmability of DNA ligands to deliberately control the hierarchical assembly of protein-DNA materials. Through DNA sequence design, we introduce orthogonal DNA interactions with disparate interaction strengths ("strong" and "weak") onto specific geometric regions of a model protein, stable protein 1 (Sp1). We show that the spatial encoding of DNA ligands leads to highly directional assembly via strong interactions and that, by design, the first stage of assembly increases the multivalency of weak DNA-DNA interactions that give rise to an emergent second stage of assembly. Furthermore, we demonstrate that judicious DNA design not only directs assembly along a given pathway but can also direct distinct structural outcomes from a single pathway. This combination of protein surface and DNA sequence design allows us to encode the structural and chemical information necessary into building blocks to program their multistep hierarchical assembly. Our findings represent a strategy for controlling the hierarchical assembly of proteins to realize a diverse set of protein-DNA materials by design.
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