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Neyra K, Everson HR, Mathur D. Dominant Analytical Techniques in DNA Nanotechnology for Various Applications. Anal Chem 2024; 96:3687-3697. [PMID: 38353660 PMCID: PMC11261746 DOI: 10.1021/acs.analchem.3c04176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
DNA nanotechnology is rapidly gaining traction in numerous applications, each bearing varying degrees of tolerance to the quality and quantity necessary for viable nanostructure function. Despite the distinct objectives of each application, they are united in their reliance on essential analytical techniques, such as purification and characterization. This tutorial aims to guide the reader through the current state of DNA nanotechnology analytical chemistry, outlining important factors to consider when designing, assembling, purifying, and characterizing a DNA nanostructure for downstream applications.
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Affiliation(s)
- Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Heather R Everson
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
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2
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Kröll S, Niemeyer CM. Nucleic Acid-based Enzyme Cascades-Current Trends and Future Perspectives. Angew Chem Int Ed Engl 2024; 63:e202314452. [PMID: 37870888 DOI: 10.1002/anie.202314452] [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: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
The natural micro- and nanoscale organization of biomacromolecules is a remarkable principle within living cells, allowing for the control of cellular functions by compartmentalization, dimensional diffusion and substrate channeling. In order to explore these biological mechanisms and harness their potential for applications such as sensing and catalysis, molecular scaffolding has emerged as a promising approach. In the case of synthetic enzyme cascades, developments in DNA nanotechnology have produced particularly powerful scaffolds whose addressability can be programmed with nanometer precision. In this minireview, we summarize recent developments in the field of biomimetic multicatalytic cascade reactions organized on DNA nanostructures. We emphasize the impact of the underlying design principles like DNA origami, efficient strategies for enzyme immobilization, as well as the importance of experimental design parameters and theoretical modeling. We show how DNA nanostructures have enabled a better understanding of diffusion and compartmentalization effects at the nanometer length scale, and discuss the challenges and future potential for commercial applications.
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Affiliation(s)
- Sandra Kröll
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1, Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1, Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
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3
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Kröll S, Burgahn T, Rabe KS, Franzreb M, Niemeyer CM. Nano- and Microscale Confinements in DNA-Scaffolded Enzyme Cascade Reactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304578. [PMID: 37732702 DOI: 10.1002/smll.202304578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/24/2023] [Indexed: 09/22/2023]
Abstract
Artificial reconstruction of naturally evolved principles, such as compartmentalization and cascading of multienzyme complexes, offers enormous potential for the development of biocatalytic materials and processes. Due to their unique addressability at the nanoscale, DNA origami nanostructures (DON) have proven to be an exceptionally powerful tool for studying the fundamental processes in biocatalytic cascades. To systematically investigate the diffusion-reaction network of (co)substrate transfer in enzyme cascades, a model system of stereoselective ketoreductase (KRED) with cofactor regenerating enzyme is assembled in different spatial arrangements on DNA nanostructures and is located in the sphere of microbeads (MB) as a spatially confining nano- and microenvironment, respectively. The results, obtained through the use of highly sensitive analytical methods, Western blot-based quantification of the enzymes, and mass spectrometric (MS) product detection, along with theoretical modeling, provide strong evidence for the presence of two interacting compartments, the diffusion layers around the microbead and the DNA scaffold, which influence the catalytic efficiency of the cascade. It is shown that the microscale compartment exerts a strong influence on the productivity of the cascade, whereas the nanoscale arrangement of enzymes has no influence but can be modulated by the insertion of a diffusion barrier.
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Affiliation(s)
- Sandra Kröll
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Teresa Burgahn
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Matthias Franzreb
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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4
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Schneider L, Richter M, Oelschlaeger C, Rabe KS, Domínguez CM, Niemeyer CM. Accurate quantification of DNA content in DNA hydrogels prepared by rolling circle amplification. Chem Commun (Camb) 2023; 59:12184-12187. [PMID: 37750315 DOI: 10.1039/d3cc04374f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Accurate quantification of polymerized DNA in rolling circle amplification (RCA)-based hydrogels is challenging due to the high viscosity of these materials, however, it can be achieved with a photometric nucleotide depletion assay or qPCR. We show that the DNA content strongly depends on the template sequence and correlates with the mechanical properties of the hydrogels.
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Affiliation(s)
- Leonie Schneider
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Madleen Richter
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Claude Oelschlaeger
- Institute for Mechanical Process Engineering and Mechanics, Karlsruhe Institute of Technology (KIT), Gotthard-Franz-Straße 3, 76131 Karlsruhe, Germany
| | - Kersten S Rabe
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Carmen M Domínguez
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Christof M Niemeyer
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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5
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Sentosa J, Djutanta F, Horne B, Showkeir D, Rezvani R, Leff C, Pradhan S, Hariadi RF. Gradient-mixing LEGO robots for purifying DNA origami nanostructures of multiple components by rate-zonal centrifugation. PLoS One 2023; 18:e0283134. [PMID: 37467178 DOI: 10.1371/journal.pone.0283134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/02/2023] [Indexed: 07/21/2023] Open
Abstract
DNA origami purification is essential for many fields, including biophysics, molecular engineering, and therapeutics. The increasing interest in DNA origami has led to the development of rate-zonal centrifugation (RZC) as a scalable, high yield, and contamination-free method for purifying DNA origami nanostructures. RZC purification uses a linear density gradient of viscous media, such as glycerol or sucrose, to separate molecules according to their mass and shape. However, many methods for creating density gradients are time-consuming because they rely on slow passive diffusion. To expedite the preparation time, we used a LEGO gradient mixer to generate rotational motion and rapidly create a quasi-continuous density gradient with a minimal layering of the viscous media. Rotating two layers of differing concentrations at an angle decreases the time needed to form the density gradient from a few hours to minutes. In this study, the density gradients created by the LEGO gradient mixer were used to purify 3 DNA origami shapes that have different aspect ratios and numbers of components, with an aspect ratio ranging from 1:1 to 1:100 and the number of components up to 2. The gradient created by our LEGO gradient mixer is sufficient to purify folded DNA origami nanostructures from excess staple strands, regardless of their aspect ratios. Moreover, the gradient was able to separate DNA origami dimers from DNA origami monomers. In light of recent advances in large-scale DNA origami production, our method provides an alternative for purifying DNA origami nanostructures in large (gram) quantities in resource-limited settings.
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Affiliation(s)
- Jason Sentosa
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Franky Djutanta
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States of America
| | - Brian Horne
- Department of Physics, Arizona State University, Tempe, AZ, United States of America
| | - Dominic Showkeir
- Department of Physics, Arizona State University, Tempe, AZ, United States of America
| | - Robert Rezvani
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States of America
| | - Chloe Leff
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Swechchha Pradhan
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States of America
| | - Rizal F Hariadi
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States of America
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6
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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: 44] [Impact Index Per Article: 44.0] [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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7
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Liu M, Wang Y, Jiang H, Han Y, Xia J. Synthetic Multienzyme Assemblies for Natural Product Biosynthesis. Chembiochem 2023; 24:e202200518. [PMID: 36625563 DOI: 10.1002/cbic.202200518] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.
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Affiliation(s)
- Min Liu
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yue Wang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Jiang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongxu Han
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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8
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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9
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Parsons MF, Allan MF, Li S, Shepherd TR, Ratanalert S, Zhang K, Pullen KM, Chiu W, Rouskin S, Bathe M. 3D RNA-scaffolded wireframe origami. Nat Commun 2023; 14:382. [PMID: 36693871 PMCID: PMC9872083 DOI: 10.1038/s41467-023-36156-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.
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Affiliation(s)
- Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew F Allan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shanshan Li
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Inscripta, Inc., Boulder, CO, 80027, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Krista M Pullen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Kröll S, Schneider L, Wadhwani P, Rabe KS, Niemeyer CM. Orthogonal protein decoration of DNA nanostructures based on SpyCatcher-SpyTag interaction. Chem Commun (Camb) 2022; 58:13471-13474. [PMID: 36383063 DOI: 10.1039/d2cc05335g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We present an efficient and readily applicable strategy for the covalent ligation of proteins to DNA origami by using the SpyCatcher-SpyTag (SC-ST) connector system. This approach showed orthogonality with other covalent connectors and has been used exemplarily for the immobilization and study of stereoselective ketoreductases to gain insight into the spatial arrangement of enzymes on DNA nanostructures.
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Affiliation(s)
- Sandra Kröll
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany.
| | - Leonie Schneider
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany.
| | - Parvesh Wadhwani
- Department of Molecular Biophysics (IBG 2), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany.
| | - Christof M Niemeyer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany.
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11
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Lin P, Yang H, Nakata E, Morii T. Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold. Molecules 2022; 27:molecules27196309. [PMID: 36234845 PMCID: PMC9572797 DOI: 10.3390/molecules27196309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.
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12
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Kröll S, Rabe KS, Niemeyer CM. An Orthogonal Covalent Connector System for the Efficient Assembly of Enzyme Cascades on DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2105095. [PMID: 34825457 DOI: 10.1002/smll.202105095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/19/2021] [Indexed: 05/06/2023]
Abstract
Combining structural DNA nanotechnology with the virtually unlimited variety of enzymes offers unique opportunities for generating novel biocatalytic devices. However, the immobilization of enzymes is still restricted by a lack of efficient covalent coupling techniques. The rational re-engineering of the genetically fusible SNAP-tag linker is reported here. By replacing five amino acids that alter the electrostatic properties of the SNAP_R5 variant, up to 11-fold increased coupling efficiency with benzylguanine-modified oligonucleotides and DNA origami nanostructures (DON) was achieved, resulting in typical occupancy densities of 75%. The novel SNAP_R5 linker can be combined with the equally efficient Halo-based oligonucleotide binding tag (HOB). Since both linkers exhibit neither cross-reactivity nor non-specific binding, they allowed orthogonal assembly of an enzyme cascade consisting of the stereoselective ketoreductase Gre2p and the cofactor-regenerating isocitrate dehydrogenase on DON. The cascade showed approximately 1.6-fold higher activity in a stereoselective cascade reaction than the corresponding free solubilized enzymes. The connector system presented here and the methods used to validate it represent important tools for further development of DON-based multienzyme systems to investigate mechanistic effects of substrate channeling and compartmentalization relevant for exploitation in biosensing and catalysis.
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Affiliation(s)
- Sandra Kröll
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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13
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The biological applications of DNA nanomaterials: current challenges and future directions. Signal Transduct Target Ther 2021; 6:351. [PMID: 34620843 PMCID: PMC8497566 DOI: 10.1038/s41392-021-00727-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 02/08/2023] Open
Abstract
DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.
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14
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Knappe GA, Wamhoff EC, Read BJ, Irvine DJ, Bathe M. In Situ Covalent Functionalization of DNA Origami Virus-like Particles. ACS NANO 2021; 15:14316-14322. [PMID: 34490781 PMCID: PMC8628367 DOI: 10.1021/acsnano.1c03158] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
DNA origami is a powerful nanomaterial for biomedical applications due in part to its capacity for programmable, site-specific functionalization. To realize these applications, scalable and efficient conjugation protocols are needed for diverse moieties ranging from small molecules to biomacromolecules. Currently, there are no facile and general methods for in situ covalent modification and label-free quantification of reaction conversion. Here, we investigate the postassembly functionalization of DNA origami and the subsequent high-performance liquid chromatography-based characterization of these nanomaterials. Following this approach, we developed a versatile DNA origami functionalization and characterization platform. We observed quantitative in situ conversion using widely accessible click chemistry for carbohydrates, small molecules, peptides, polymers, and proteins. This platform should provide broader access to covalently functionalized DNA origami, as illustrated here by PEGylation for passivation and HIV antigen decoration to construct virus-like particle vaccines.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Benjamin J. Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Darrell J. Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States of America
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to
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15
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Hellmeier J, Platzer R, Mühlgrabner V, Schneider MC, Kurz E, Schütz GJ, Huppa JB, Sevcsik E. Strategies for the Site-Specific Decoration of DNA Origami Nanostructures with Functionally Intact Proteins. ACS NANO 2021; 15:15057-15068. [PMID: 34463486 PMCID: PMC8482763 DOI: 10.1021/acsnano.1c05411] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/26/2021] [Indexed: 05/14/2023]
Abstract
DNA origami structures provide flexible scaffolds for the organization of single biomolecules with nanometer precision. While they find increasing use for a variety of biological applications, the functionalization with proteins at defined stoichiometry, high yield, and under preservation of protein function remains challenging. In this study, we applied single molecule fluorescence microscopy in combination with a cell biological functional assay to systematically evaluate different strategies for the site-specific decoration of DNA origami structures, focusing on efficiency, stoichiometry, and protein functionality. Using an activating ligand of the T-cell receptor (TCR) as the protein of interest, we found that two commonly used methodologies underperformed with regard to stoichiometry and protein functionality. While strategies employing tetravalent wildtype streptavidin for coupling of a biotinylated TCR-ligand yielded mixed populations of DNA origami structures featuring up to three proteins, the use of divalent (dSAv) or DNA-conjugated monovalent streptavidin (mSAv) allowed for site-specific attachment of a single biotinylated TCR-ligand. The most straightforward decoration strategy, via covalent DNA conjugation, resulted in a 3-fold decrease in ligand potency, likely due to charge-mediated impairment of protein function. Replacing DNA with charge-neutral peptide nucleic acid (PNA) in a ligand conjugate emerged as the coupling strategy with the best overall performance in our study, as it produced the highest yield with no multivalent DNA origami structures and fully retained protein functionality. With our study we aim to provide guidelines for the stoichiometrically defined, site-specific functionalization of DNA origami structures with proteins of choice serving a wide range of biological applications.
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Affiliation(s)
| | - René Platzer
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | - Vanessa Mühlgrabner
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | | | - Elke Kurz
- Kennedy
Institute of Rheumatology, University of
Oxford, Oxford, OX3 7FY, U.K.
| | | | - Johannes B. Huppa
- Center
for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University
of Vienna, Vienna, 1090, Austria
| | - Eva Sevcsik
- Institute
of Applied Physics, TU Wien, Vienna, 1060, Austria
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16
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Xu H, Zheng L, Zhou Y, Ye BC. An artificial enzyme cascade amplification strategy for highly sensitive and specific detection of breast cancer-derived exosomes. Analyst 2021; 146:5542-5549. [PMID: 34515703 DOI: 10.1039/d1an01071a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tumor-related exosomes, which are heterogeneous membrane-enclosed nanovesicles shed from cancer cells, have been widely recognized as potential noninvasive biomarkers for early cancer diagnosis. Herein, an artificial enzyme cascade amplification strategy based on a switchable DNA tetrahedral (SDT) scaffold was proposed for quantification of breast cancer-derived exosomes. The SDT scaffold is composed of G-quadruplex mimicking DNAzyme sequences on its two single-stranded edges and glucose oxidase (GOx) on the four termini of the complementary strands. In the initial state, the SDT scaffold is blocked by the switch strand which consists of partial complementary domains with the DNA tetrahedron and a MUC1 aptamer. MCF-7 exosomes could release the quadruplex-forming sequences through the recognition of the MUC1 aptamer. The newly formed DNAzyme brings GOx into spatial proximity and induces high-efficiency enzyme cascade catalytic reactions on the SDT. Consequently, high sensitivity toward MCF-7 exosome analysis was obtained with a wide linear range of 3.8 × 106 to 1.2 × 108 particles per mL and a limit of detection of 1.51 × 105 particles per mL. In addition, such a DNAzyme reconfiguration strategy was able to distinguish MCF-7 exosomes from other breast cancer cell derived exosomes, indicating its excellent method specificity. The proposed enzyme cascade strategy not only provides a novel signal transformation and amplification nanoplatform for quantifying the specific populations of exosomes, but also can be further expanded to the analysis of multiple cancer biomarkers.
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Affiliation(s)
- Huiying Xu
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Lu Zheng
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yu Zhou
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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17
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Lin P, Dinh H, Nakata E, Morii T. Dynamic Shape Transformation of a DNA Scaffold Applied for an Enzyme Nanocarrier. Front Chem 2021; 9:697857. [PMID: 34249866 PMCID: PMC8263910 DOI: 10.3389/fchem.2021.697857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Structural programmability and accurate addressability of DNA nanostructures are ideal characteristics for the platform of arranging enzymes with the nanoscale precision. In this study, a three-dimensional DNA scaffold was designed to enable a dynamic shape transition from an open plate-like structure to its closed state of a hexagonal prism structure. The two domains in the open state were folded together to transform into the closed state by hybridization of complementary short DNA closing keys at both of the facing edges in over 90% yield. The shape transformation of the DNA scaffold was extensively studied by means of the fluorescence energy transfer measurement, atomic force microscope images, and agarose gel electrophoretic analyses. A dimeric enzyme xylitol dehydrogenase was assembled on the DNA scaffold in its open state in a high-loading yield. The enzyme loaded on the scaffold was subsequently transformed to its closed state by the addition of short DNA closing keys. The enzyme encapsulated in the closed state displayed comparable activity to that in the open state, ensuring that the catalytic activity of the enzyme was well maintained in the DNA nanocarrier. The nanocarrier with efficient encapsulation ability is potentially applicable for drug delivery, biosensing, biocatalytic, and diagnostic tools.
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Affiliation(s)
- Peng Lin
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
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18
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Shen H, Zhou Z, He W, Chao H, Su P, Song J, Yang Y. Oligonucleotide-Functionalized Enzymes Chemisorbing on Magnetic Layered Double Hydroxides: A Multimodal Catalytic Platform with Boosted Activity for Ultrasensitive Glucose Detection. ACS APPLIED MATERIALS & INTERFACES 2021; 13:14995-15007. [PMID: 33769803 DOI: 10.1021/acsami.1c01350] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A reasonable design of multifarious chemo- and biocatalytic functions within individual nano/microunits is urgently desired for high-performance cascade reactions but has heretofore remained elusive. Herein, glucose oxidase was functionalized with oligonucleotides and steadily chemisorbed on magnetic layered double hydroxides (mLDHs) to construct a multimodal catalytic platform for realizing divergent reactions with heterogeneous and biocatalytic steps. The flowerlike mLDHs served both as an enzyme support and a peroxidase mimic cooperating with enzymes for tandem catalysis. Oligo-DNA connected the enzymes to mLDHs like a bridge, and a stepwise ligand-exchange-assisted coordination mechanism was proposed to explain the robust interaction between DNA and mLDHs. More importantly, DNA significantly improved the bioactivity of the whole system. The acceleration mechanism was attributed to the diffusion tunnels for the substrate/product and enhanced substrates binding on mLDHs. The multimodal catalytic platform was applied for colorimetric and electrochemical sensing of glucose with a low limit of detection and high selectivity. The practical analysis capability of the ultrasensitive sensor was evaluated by detecting glucose in human serum and sweat, showing reliable results, satisfactory recovery, and excellent stability. The strategy of combining mLDHs and enzymes for cascade catalysis provides a universal approach to prepare chemo-enzyme hybrids with high performance, which holds great promise for applications in biosensors and industrial catalysis.
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Affiliation(s)
- Hao Shen
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Zixin Zhou
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Wenting He
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Hao Chao
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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19
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Abstract
Significant advances in enzyme discovery, protein and reaction engineering have transformed biocatalysis into a viable technology for the industrial scale manufacturing of chemicals. Multi-enzyme catalysis has emerged as a new frontier for the synthesis of complex chemicals. However, the in vitro operation of multiple enzymes simultaneously in one vessel poses challenges that require new strategies for increasing the operational performance of enzymatic cascade reactions. Chief among those strategies is enzyme co-immobilization. This review will explore how advances in synthetic biology and protein engineering have led to bioinspired co-localization strategies for the scaffolding and compartmentalization of enzymes. Emphasis will be placed on genetically encoded co-localization mechanisms as platforms for future autonomously self-organizing biocatalytic systems. Such genetically programmable systems could be produced by cell factories or emerging cell-free systems. Challenges and opportunities towards self-assembling, multifunctional biocatalytic materials will be discussed.
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20
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Lin P, Dinh H, Morita Y, Zhang Z, Nakata E, Kinoshita M, Morii T. Evaluation of the role of the DNA surface for enhancing the activity of scaffolded enzymes. Chem Commun (Camb) 2021; 57:3925-3928. [PMID: 33871490 DOI: 10.1039/d1cc00276g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The catalytic enhancements of enzymes loaded on DNA nanostructures have been attributed to the characteristics provided by highly negative charges on the surface of the DNA scaffold, such as the modulation of the local pH near enzymes. In this study, two types of enzymes with optimal activity at pH 6 and 8 equally displayed significant catalytic enhancements on the DNA scaffold surface. By using a ratiometric pH indicator, a lower local pH shift of 0.8 was observed near the DNA scaffold surface. The postulated local pH change near the DNA scaffold surface is unlikely to play a general role in enhancing the activity of the scaffolded enzymes.
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Affiliation(s)
- Peng Lin
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Yuki Morita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Zhengxiao Zhang
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
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21
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Weinhold E, Chakraborty B. DNA modification and visualization on an origami-based enzyme nano-factory. NANOSCALE 2021; 13:2465-2471. [PMID: 33471009 DOI: 10.1039/d0nr07618j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The past decade has seen enormous progress in DNA nanotechnology through the advent of DNA origami. Functionalizing the DNA origami for multiple applications is the recent focus of this field. Here we have constructed a novel DNA enzyme nano-factory, which modifies target DNA embedded on a DNA origami platform. The enzyme is programmed to reside in close proximity to the target DNA which enhances significantly the local concentration compared to solution-based DNA modification. To demonstrate this we have immobilized DNA methyltransferase M·TaqI next to the target DNA on the DNA origami and used this enzyme to sequence-specifically modify the target DNA with biotin using a cofactor analogue. Streptavidin binding to biotin is applied as a topographic marker to follow the machine cycle of this enzyme nano-factory using atomic force microscopy imaging. The nano-factory is demonstrated to be recyclable and holds the potential to be expanded to a multi-enzyme, multi-substrate operating system controlled by simple to complex molecules made of DNA, RNA or proteins.
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Affiliation(s)
- Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India.
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22
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Rossetti M, Bertucci A, Patiño T, Baranda L, Porchetta A. Programming DNA-Based Systems through Effective Molarity Enforced by Biomolecular Confinement. Chemistry 2020; 26:9826-9834. [PMID: 32428310 DOI: 10.1002/chem.202001660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/12/2020] [Indexed: 12/12/2022]
Abstract
The fundamental concept of effective molarity is observed in a variety of biological processes, such as protein compartmentalization within organelles, membrane localization and signaling paths. To control molecular encountering and promote effective interactions, nature places biomolecules in specific sites inside the cell in order to generate a high, localized concentration different from the bulk concentration. Inspired by this mechanism, scientists have artificially recreated in the lab the same strategy to actuate and control artificial DNA-based functional systems. Here, it is discussed how harnessing effective molarity has led to the development of a number of proximity-induced strategies, with applications ranging from DNA-templated organic chemistry and catalysis, to biosensing and protein-supported DNA assembly.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Bertucci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Tania Patiño
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Lorena Baranda
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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23
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Surface charge-controlled electron transfer and catalytic behavior of immobilized cytochrome P450 BM3 inside dendritic mesoporous silica nanoparticles. Anal Bioanal Chem 2020; 412:4703-4712. [PMID: 32483647 DOI: 10.1007/s00216-020-02727-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
Understanding the influencing factors on the reaction kinetics of P450 BM3 within confined spaces is essential for developing efficient P450 BM3 bioreactors. Herein, two dendritic mesoporous silica nanoparticles (OH-DMSNs and NH2-DMSNs) with similar pore size but opposite surface charge have been prepared and served as the vehicle to immobilize P450 BM3. With the help of the film-forming material of chitosan, P450 BM3/OH-DMSN and P450 BM3/NH2-DMSN composites were immobilized on GC electrode and characterized with electrochemical measurements. Compared with P450 BM3/OH-DMSNs/GCE, P450 BM3/NH2-DMSNs/GCE showed higher electron transfer efficiency with higher current charge and lower ks value. Besides, the generated catalytic current towards testosterone on P450 BM3/NH2-DMSNs/GCE was 1.81 times larger than P450 BM3/OH-DMSNs/GCE. Furthermore, P450 BM3 inside NH2-DMSNs displayed higher affinity towards testosterone with the lower Kmapp value of 244.82 μM. These results are attributed to the positively charged internal walls of NH2-DMSNs so that P450 BM3 adapts to an orientation favorable for electron exchange with electrodes and substrate binding with the active sites. The present study provides fundamentals for regulating the surface charge to optimize redox process and catalytic behavior in CYP bioreactors through electrostatic interactions.
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24
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Shang Y, Li N, Liu S, Wang L, Wang ZG, Zhang Z, Ding B. Site-Specific Synthesis of Silica Nanostructures on DNA Origami Templates. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2000294. [PMID: 32301202 DOI: 10.1002/adma.202000294] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/20/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
DNA origami has been widely investigated as a template for the organization of various functional elements, leading to potential applications in many fields such as biosensing, nanoelectronics, and nanophotonics. However, the synthesis of inorganic nonmetallic nanomaterials with predesigned patterns using DNA origami templates has seldom been explored. Here, a novel method is reported to site-specifically synthesize silica nanostructures with designed patterns on DNA origami templates. The molecular dynamic simulation confirms that the positively charged silica precursors have a stronger electrostatic affinity to protruding double-stranded DNA (dsDNA) than DNA origami surfaces. The work describes a novel strategy to fabricate silica nanostructures with nanoscale precision. Moreover, the site-specific silicification of DNA nanoarchitectures expands the scope of customized synthesis of inorganic nonmetallic nanomaterials.
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Affiliation(s)
- Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun, Beijing, 100190, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun, Beijing, 100190, China
| | - Shengbo Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun, Beijing, 100190, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun, Beijing, 100190, China
| | - Zhong Zhang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun, Beijing, 100190, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun, Beijing, 100190, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
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25
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Rosier BJHM, Markvoort AJ, Gumí Audenis B, Roodhuizen JAL, den Hamer A, Brunsveld L, de Greef TFA. Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome. Nat Catal 2020; 3:295-306. [PMID: 32190819 PMCID: PMC7080557 DOI: 10.1038/s41929-019-0403-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Living cells regulate key cellular processes by spatial organisation of catalytically active proteins in higher-order signalling complexes. These act as organising centres to facilitate proximity-induced activation and inhibition of multiple intrinsically weakly associating signalling components, which makes elucidation of the underlying protein-protein interactions challenging. Here we show that DNA origami nanostructures provide a programmable molecular platform for the systematic analysis of signalling proteins by engineering a synthetic DNA origami-based version of the apoptosome, a multi-protein complex that regulates apoptosis by co-localizing multiple caspase-9 monomers. Tethering of both wildtype and inactive caspase-9 variants to a DNA origami platform demonstrates that enzymatic activity is induced by proximity-driven dimerization with half-of-sites reactivity, and additionally, reveals a multivalent activity enhancement in oligomers of three and four enzymes. Our results offer fundamental insights in caspase-9 activity regulation and demonstrate that DNA origami-based protein assembly platforms have the potential to inform the function of other multi-enzyme complexes involved in inflammation, innate immunity and cell death.
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Affiliation(s)
- Bas J H M Rosier
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Albert J Markvoort
- Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands
| | - Berta Gumí Audenis
- Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Laboratory of Self-Organising Soft Matter and Laboratory of Macromolecular and Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, The Netherlands
| | - Job A L Roodhuizen
- Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands
| | - Anniek den Hamer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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26
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Ellis GA, Klein WP, Lasarte-Aragonés G, Thakur M, Walper SA, Medintz IL. Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02413] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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Li X, Wang X, Li H, Shi X, Zheng P. A Programming 20-30nm Rectangular DNA Origami for Loading Doxorubicin to Penetrate Ovarian Cancer Cells. IEEE Trans Nanobioscience 2019; 19:152-157. [PMID: 31581088 DOI: 10.1109/tnb.2019.2943923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In DNA nanotechnology, the aim in folding DNA origami is to find a good piece of rectangular DNA origami with desired sizes, which could be larger or smaller for different application purposes. In recent three years, the technique of folding smaller ones is paid heavily attentions. In this work, we design a programming rectangular DNA origami in size 20*30nm with M13p18, which is smallest and cheapest to the best acknowledge of the authors. Since it is not hard to prepare with 30 staple strands and short annealing time, the cost of folding our designed rectangular DNA origami is less than 100 dollars. Although the large origami give more space, the smaller ones are cheaper and has the potential applications in penetrating cancer cells. It is obtained by cell penetrating experiments that our designed rectangular DNA origami can penetrate ovarian cancer cells efficiently even loading doxorubicin, but the thermodynamic stability needs further improved. Our designed programming 20 30nm triangular DNA origami shows potential applications in precision control of nanoscale particles and anti-tumor drug delivery in vivo.
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28
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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29
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Wang W, Yu S, Huang S, Bi S, Han H, Zhang JR, Lu Y, Zhu JJ. Bioapplications of DNA nanotechnology at the solid-liquid interface. Chem Soc Rev 2019; 48:4892-4920. [PMID: 31402369 PMCID: PMC6746594 DOI: 10.1039/c8cs00402a] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.
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Affiliation(s)
- Wenjing Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.
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30
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Hu Y, Niemeyer CM. From DNA Nanotechnology to Material Systems Engineering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806294. [PMID: 30767279 DOI: 10.1002/adma.201806294] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/29/2018] [Indexed: 05/25/2023]
Abstract
In the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure "structural DNA nanotechnology" over protein-DNA assemblies, nanoparticle-based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine-based approaches in microfluidics, robotics, and data-driven science, DNA-material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.
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Affiliation(s)
- Yong Hu
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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31
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Wamhoff EC, Banal JL, Bricker WP, Shepherd TR, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M. Programming Structured DNA Assemblies to Probe Biophysical Processes. Annu Rev Biophys 2019; 48:395-419. [PMID: 31084582 PMCID: PMC7035826 DOI: 10.1146/annurev-biophys-052118-115259] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Rémi Veneziano
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew B Stone
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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Chao J, Wang J, Wang F, Ouyang X, Kopperger E, Liu H, Li Q, Shi J, Wang L, Hu J, Wang L, Huang W, Simmel FC, Fan C. Solving mazes with single-molecule DNA navigators. NATURE MATERIALS 2019; 18:273-279. [PMID: 30397311 DOI: 10.1038/s41563-018-0205-3] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 09/24/2018] [Indexed: 05/22/2023]
Abstract
Molecular devices with information-processing capabilities hold great promise for developing intelligent nanorobotics. Here we demonstrate a DNA navigator system that can perform single-molecule parallel depth-first search on a ten-vertex rooted tree defined on a two-dimensional DNA origami platform. Pathfinding by the DNA navigators exploits a localized strand exchange cascade, which is initiated at a unique trigger site on the origami with subsequent automatic progression along paths defined by DNA hairpins containing a universal traversal sequence. Each single-molecule navigator autonomously explores one of the possible paths through the tree. A specific solution path connecting a given pair of start and end vertices can then be easily extracted from the set of all paths taken by the navigators collectively. The solution path laid out on origami is illustrated with single-molecule imaging. Our approach points towards the realization of molecular materials with embedded computational functions operating at the single-molecule level.
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Affiliation(s)
- Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, China
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Jianbang Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital South Campus, Shanghai Fengxian Central Hospital, Shanghai, China
| | - Xiangyuan Ouyang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Enzo Kopperger
- Physics of Synthetic Biological Systems (E14), Physics Department, Technische Universität München, Garching, Germany
| | - Huajie Liu
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
- School of Chemical Science and Engineering, Tongji Univeristy, Shanghai, China.
| | - Qian Li
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiye Shi
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Lihua Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Jun Hu
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, China
| | - Wei Huang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing, China
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems (E14), Physics Department, Technische Universität München, Garching, Germany.
| | - Chunhai Fan
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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33
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Li T, Li J, Pang Q, Ma L, Tong W, Gao C. Construction of Microreactors for Cascade Reaction and Their Potential Applications as Antibacterial Agents. ACS APPLIED MATERIALS & INTERFACES 2019; 11:6789-6795. [PMID: 30702277 DOI: 10.1021/acsami.8b20069] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Enzymatic cascade reactions in confined microenvironments play important roles in cellular chemical transformation. They also have important biotechnological and therapeutic applications. Here, enzymatic cascade microreactors (MRs) coupling glucose oxidase (GOx) and hemoglobin (Hb) (GOx-Hb MRs) were successfully fabricated by co-precipitation of GOx and Hb into a MnCO3 template, followed by the assembly of a multilayer film on a template surface, slight cross-linking, and final removal of MnCO3. In the presence of glucose with blood-relevant concentration, the GOx-Hb MRs exhibited a higher cascade reaction activity under mild acidic conditions than that under neutral conditions at physiological temperature. The GOx-Hb MRs effectively consumed glucose to generate HO· at pH = 5, which significantly inhibited bacterial growth and biofilm formation. This kind of enzymatic cascade microreactors might be useful for applications in biomedical fields.
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Affiliation(s)
- Tong Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Jiawei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Qian Pang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Lie Ma
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Weijun Tong
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
| | - Changyou Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , China
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34
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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35
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Burgahn T, Garrecht R, Rabe KS, Niemeyer CM. Solid-Phase Synthesis and Purification of Protein-DNA Origami Nanostructures. Chemistry 2019; 25:3483-3488. [PMID: 30609150 DOI: 10.1002/chem.201805506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/07/2018] [Indexed: 12/13/2022]
Abstract
We present a facile method for the combined synthesis and purification of protein-decorated DNA origami nanostructures (DONs). DONs bearing reductively cleavable biotin groups in addition to ligands for ligation of recombinant proteins are bound to magnetic beads. Protein immobilization is conducted with a large protein excess to achieve high ligation yields. Subsequent to cleavage from the solid support, pure sample solutions are obtained which are suitable for direct AFM analysis of occupation patterns. We demonstrate the method's utility using three different orthogonal ligation methods, the "halo-based oligonucleotide binder" (HOB), a variant of Halo-tag, the "SpyTag/SpyCatcher" (ST/SC) system, and the enzymatic "ybbR tag" coupling. We find surprisingly low efficiency for ST/SC ligation, presumably due to electrostatic repulsion and steric hindrance, whereas the ybbR method, despite its ternary nature, shows good ligation yields. Our method is particularly useful for the development of novel ligation methods and the synthesis of mechanically fragile DONs that present protein patterns for surface-based cell assays.
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Affiliation(s)
- Teresa Burgahn
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ruben Garrecht
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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36
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Song J, He W, Shen H, Zhou Z, Li M, Su P, Yang Y. Self-assembly of a magnetic DNA hydrogel as a new biomaterial for enzyme encapsulation with enhanced activity and stability. Chem Commun (Camb) 2019; 55:2449-2452. [DOI: 10.1039/c8cc09717h] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A rationally designed strategy has been established to construct a magnetic DNA hydrogel for enzyme encapsulation through a programmable one-pot self-assembly approach.
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Affiliation(s)
- Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Wenting He
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Hao Shen
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Zixin Zhou
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Mengqi Li
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
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37
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Yan Y, Li J, Li W, Wang Y, Song W, Bi S. DNA flower-encapsulated horseradish peroxidase with enhanced biocatalytic activity synthesized by an isothermal one-pot method based on rolling circle amplification. NANOSCALE 2018; 10:22456-22465. [PMID: 30478460 DOI: 10.1039/c8nr07294a] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA nanotechnology has been developed to construct a variety of functional two- and three-dimensional structures for versatile applications. Rolling circle amplification (RCA) has become prominent in the assembly of DNA-inorganic composites with hierarchical structures and attractive properties. Here, we demonstrate a one-pot method to directly encapsulate horseradish peroxidase (HRP) in DNA flowers (DFs) during RCA. The growing DNA strands and Mg2PPi crystals lead to the construction of porous DFs, which provide sufficient interaction sites for spontaneously incorporating HRP molecules into DFs with high loading capacity and good stability. Furthermore, in comparison with free HRP, the DNA flower-encapsulated HRP (termed HRP-DFs) demonstrate enhanced enzymatic activity, which can efficiently biocatalyze the H2O2-mediated etching of gold nanorods (AuNRs) to generate distinct color changes since the longitudinal localized surface plasmon resonance (LSPR) frequency of AuNRs is highly sensitive to the changes in the AuNR aspect ratio. Through rationally incorporating the complementary thrombin aptamer sequence into the circular template, the synthesized HRP-DF composites are readily used as amplified labels for visual and colorimetric detection of thrombin with ultrahigh sensitivity and excellent selectivity. Therefore, our proposed strategy for direct encapsulation of enzyme molecules into DNA structures shows considerable potential applications in biosensing, biocatalysis, and point-of-care diagnostics.
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Affiliation(s)
- Yongcun Yan
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, P. R. China.
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Affiliation(s)
- Simona Ranallo
- Department of Chemical Sciences and Technologies , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
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39
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Krerowicz SJ, Hernandez-Ortiz JP, Schwartz DC. Microscale Objects via Restructuring of Large, Double-Stranded DNA Molecules. ACS APPLIED MATERIALS & INTERFACES 2018; 10:41215-41223. [PMID: 30403478 PMCID: PMC6453721 DOI: 10.1021/acsami.8b18157] [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] [Indexed: 06/08/2023]
Abstract
As the interest in DNA nanotechnology increases, so does the need for larger and more complex DNA structures. In this work, we describe two methods of using large, double-stranded (ds) DNA to self-assemble sequence-specific, nonrepetitive microscale structures. A model system restructures T7 DNA (40 kb) through sequence-specific biotinylation followed by intramolecular binding to a 40 nm diameter neutravidin bead to create T7 "rosettes". This model system informed the creation of "nodal DNA" where "nodes" with single-stranded DNA flaps are attached to a large dsDNA insert so that a complementary oligonucleotide "strap" bridges the two nodes for restructuring to form a DNA "bolo". To do this in high yield, several methodologies were developed, including a protection/deprotection scheme using RNA/RNase H and dialysis chambers, which remove excess straps while retaining large DNA molecules. To assess these restructuring processes, the DNA was adsorbed onto supported lipid bilayers, allowing for a visual assay of their structure using single-molecule fluorescence microscopy. Good agreement between the expected and observed fluorescence intensity measurements of the individual features of restructured DNA for both the DNA rosettes and bolos gives us a high degree of confidence that both processes give sequence-specific restructuring of large, dsDNA molecules to create microscale objects.
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Affiliation(s)
- Samuel J.W. Krerowicz
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Juan P. Hernandez-Ortiz
- UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Departamento de Materiales y Nanotecnología, Universidad Nacional de Colombia- Medellín, Medellín 050034, Colombia
- Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia- Medellín, Medellín 050034, Colombia
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia- Medellín, Medellín 050034, Colombia
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40
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Jäger VD, Lamm R, Kloß R, Kaganovitch E, Grünberger A, Pohl M, Büchs J, Jaeger KE, Krauss U. A Synthetic Reaction Cascade Implemented by Colocalization of Two Proteins within Catalytically Active Inclusion Bodies. ACS Synth Biol 2018; 7:2282-2295. [PMID: 30053372 DOI: 10.1021/acssynbio.8b00274] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In nature, enzymatic reaction cascades, i.e., realized in metabolic networks, operate with unprecedented efficacy, with the reactions often being spatially and temporally orchestrated. The principle of "learning from nature" has in recent years inspired the setup of synthetic reaction cascades combining biocatalytic reaction steps to artificial cascades. Hereby, the spatial organization of multiple enzymes, e.g., by coimmobilization, remains a challenging task, as currently no generic principles are available that work for every enzyme. We here present a tunable, genetically programmed coimmobilization strategy that relies on the fusion of a coiled-coil domain as aggregation inducing-tag, resulting in the formation of catalytically active inclusion body coimmobilizates (Co-CatIBs). Coexpression and coimmobilization was proven using two fluorescent proteins, and the strategy was subsequently extended to two enzymes, which enabled the realization of an integrated enzymatic two-step cascade for the production of (1 R,2 R)-1-phenylpropane-1,2-diol (PPD), a precursor of the calicum channel blocker diltiazem. In particular, the easy production and preparation of Co-CatIBs, readily yielding a biologically produced enzyme immobilizate renders the here presented strategy an interesting alternative to existing cascade immobilization techniques.
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Affiliation(s)
- Vera D. Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Robin Lamm
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, D-52074 Aachen, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Ramona Kloß
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Eugen Kaganovitch
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Multiscale Bioengineering group, Bielefeld University, D-33615 Bielefeld, Germany
| | - Martina Pohl
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Jochen Büchs
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, D-52074 Aachen, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
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Furst A, Smith MJ, Lee MC, Francis MB. DNA Hybridization To Interface Current-Producing Cells with Electrode Surfaces. ACS CENTRAL SCIENCE 2018; 4:880-884. [PMID: 30062116 PMCID: PMC6062829 DOI: 10.1021/acscentsci.8b00255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Indexed: 05/23/2023]
Abstract
As fossil fuels are increasingly linked to environmental damage, the development of renewable, affordable biological alternative fuels is vital. Shewanella oneidensis is often suggested as a potential component of bioelectrochemical cells because of its ability to act as an electron donor to metal surfaces. These microbes remain challenging to implement, though, due to inconsistency in biofilm formation on electrodes and therefore current generation. We have applied DNA hybridization-based cell adhesion to immobilize S. oneidensis on electrodes. High levels of current are reproducibly generated from these cell layers following only 30 min of immobilization without the need for the formation of a biofilm. Upon incorporation of DNA mismatches in the microbe immobilization sequence, significant attenuation in current production is observed, suggesting that at least part of the electron transfer to the electrode is DNA-mediated. This method of microbe assembly is rapid, reproducible, and facile for the production of anodes for biofuel cells.
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Affiliation(s)
- Ariel
L. Furst
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720-1460, United States
| | - Matthew J. Smith
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720-1460, United States
| | - Michael C. Lee
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720-1460, United States
| | - Matthew B. Francis
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720-1460, United States
- Materials
Sciences Division, Lawrence Berkeley National
Laboratories, Berkeley, California 94720-1460, United States
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Chen Y, Ke G, Ma Y, Zhu Z, Liu M, Liu Y, Yan H, Yang CJ. A Synthetic Light-Driven Substrate Channeling System for Precise Regulation of Enzyme Cascade Activity Based on DNA Origami. J Am Chem Soc 2018; 140:8990-8996. [DOI: 10.1021/jacs.8b05429] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yahong Chen
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Guoliang Ke
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yanli Ma
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute and School of Molecular Sciences at Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute and School of Molecular Sciences at Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design and Biomimetics, Biodesign Institute and School of Molecular Sciences at Arizona State University, Tempe, Arizona 85287, United States
| | - Chaoyong James Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200127, China
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44
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From Designing the Molecules of Life to Designing Life: Future Applications Derived from Advances in DNA Technologies. Angew Chem Int Ed Engl 2018; 57:4313-4328. [DOI: 10.1002/anie.201707976] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/14/2017] [Indexed: 12/20/2022]
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Kohman RE, Kunjapur AM, Hysolli E, Wang Y, Church GM. Vom Design der Moleküle des Lebens zum Design von Leben: Zukünftige Anwendungen von DNA-Technologien. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201707976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Richie E. Kohman
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
| | | | - Eriona Hysolli
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
| | - Yu Wang
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
| | - George M. Church
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
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46
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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47
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Tang MSL, Shiu SCC, Godonoga M, Cheung YW, Liang S, Dirkzwager RM, Kinghorn AB, Fraser LA, Heddle JG, Tanner JA. An aptamer-enabled DNA nanobox for protein sensing. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:1161-1168. [PMID: 29410111 DOI: 10.1016/j.nano.2018.01.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
Abstract
DNA nanostructures can show dynamic responses to molecular triggers for a wide variety of applications. While DNA sequence signal triggers are now well-established, there is a critical need for a broader diversity of molecular triggers to drive dynamic responses in DNA nanostructures. DNA aptamers are ideal; they can both seamlessly integrate into DNA nanostructure scaffolds and transduce molecular recognition into functional responses. Here, we report construction and optimization of a DNA origami nanobox locked by a pair of DNA double strands where one strand is a DNA aptamer targeting the malaria biomarker protein Plasmodium falciparum lactate dehydrogenase. The protein acts as the key which enables box opening. We observe highly specific protein-mediated box opening by both transmission electron microscopy and fluorescence. Aptamer-enabled DNA boxes have significant potential for enabling direct responses to proteins and other biomolecules in nanoscale diagnostics, drug delivery and sensing devices.
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Affiliation(s)
- Marco S L Tang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Maia Godonoga
- Heddle Initiative Research Unit, RIKEN, Saitama, Japan
| | - Yee-Wai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shaolin Liang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Roderick M Dirkzwager
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lewis A Fraser
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jonathan G Heddle
- Heddle Initiative Research Unit, RIKEN, Saitama, Japan; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Julian A Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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Rabe KS, Müller J, Skoupi M, Niemeyer CM. Cascades in Compartments: En Route to Machine-Assisted Biotechnology. Angew Chem Int Ed Engl 2017; 56:13574-13589. [DOI: 10.1002/anie.201703806] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Kersten S. Rabe
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Joachim Müller
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Marc Skoupi
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
| | - Christof M. Niemeyer
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologsiche Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Germany
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49
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Rabe KS, Müller J, Skoupi M, Niemeyer CM. Kaskaden in Kompartimenten: auf dem Weg zu maschinengestützter Biotechnologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703806] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kersten S. Rabe
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Joachim Müller
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Marc Skoupi
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
| | - Christof M. Niemeyer
- Chair of Chemical Biology; Karlsruher Institut für Technologie, KIT, Institut für Biologische Grenzflächen 1, IBG-I; Herrmann-von-Helmholtz Platz 1, Campus Nord Eggenstein-Leopoldshafen 76344 Deutschland
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50
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Affiliation(s)
- Yifei Zhang
- Department of Biomedical
Engineering, Columbia University, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical
Engineering, Columbia University, New York, New York 10027, United States
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