1
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Liao H, Cao Y, Hu C, Shen S, Zhang Z, Li D, Du Y. Oxygen-producing and pH-responsive targeted DNA nanoflowers for enhanced chemo-sonodynamic therapy of lung cancer. Mater Today Bio 2024; 25:101005. [PMID: 38445013 PMCID: PMC10912725 DOI: 10.1016/j.mtbio.2024.101005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Lung cancer is the deadliest kind of cancer in the world, and the hypoxic tumor microenvironment can significantly lower the sensitivity of chemotherapeutic drugs and limit the efficacy of different therapeutic approaches. In order to overcome these problems, we have designed a drug-loaded targeted DNA nanoflowers encoding AS1411 aptamer and encapsulating chemotherapeutic drug doxorubicin and oxygen-producing drug horseradish peroxidase (DOX/HRP-DFs). These nanoflowers can release drugs in response to acidic tumor microenvironment and alleviate tumor tissue hypoxia, enhancing the therapeutic effects of chemotherapy synergistic with sonodynamic therapy. Owing to the encoded drug-loading sequence, the doxorubicin loading rate of DNA nanoflowers reached 73.24 ± 3.45%, and the drug could be released quickly by disintegrating in an acidic environment. Furthermore, the AS1411 aptamer endowed DNA nanoflowers with exceptional tumor targeting properties, which increased the concentration of chemotherapeutic drug doxorubicin in tumor cells. It is noteworthy that both in vitro and in vivo experiments demonstrated DNA nanoflowers could considerably improve the hypoxia of tumor cells, which enabled the generation of sufficient reactive oxygen species in combination with ultrasound, significantly enhancing the therapeutic effect of sonodynamic therapy and evidently inhibiting tumor growth and metastasis. Overall, this DNA nanoflowers delivery system offers a promising approach for treating lung cancer.
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Affiliation(s)
- Hongjian Liao
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Yuchao Cao
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Can Hu
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Shangfeng Shen
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Zhifei Zhang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
| | - Dairong Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Yonghong Du
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
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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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Cao X, Buryska T, Yang T, Wang J, Fischer P, Streets A, Stavrakis S, deMello A. Towards an active droplet-based microfluidic platform for programmable fluid handling. LAB ON A CHIP 2023; 23:2029-2038. [PMID: 37000567 PMCID: PMC10091362 DOI: 10.1039/d3lc00015j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Droplet-based microfluidic systems have emerged as powerful alternatives to conventional high throughput screening platforms, due to their operational flexibility, high-throughput nature and ability to efficiently process small fluid volumes. However, the challenges associated with performing bespoke operations on user-defined droplets often limit their utility in screening applications that involve complex workflows. To this end, the marriage of droplet- and valve-based microfluidic technologies offers the prospect of balancing the controllability of droplet manipulations and analytical throughput. In this spirit, we present a microfluidic platform that combines the capabilities of integrated microvalve technology with droplet-based sample compartmentalization to realize a highly adaptable programmable fluid handling functionality. The microfluidic device consists of a programmable formulator linked to an automated droplet generation device and storage array. The formulator leverages multiple inputs coupled to a mixing ring to produce combinatorial solution mixtures, with a peristaltic pump enabling titration of reagents into the ring with picoliter resolution. The platform allows for the execution of user-defined reaction protocols within an array of storage chambers by consecutively merging programmable sequences of pL-volume droplets containing specified reagents. The precision in formulating solutions with small differences in concentration is perfectly suited for the accurate estimation of kinetic parameters. The utility of our platform is showcased through the performance of enzymatic kinetic measurements of beta-galactosidase and horseradish peroxidase with fluorogenic substrates. The presented platform provides for a range of automated manipulations and paves the way for a more diverse range of droplet-based biological experiments.
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Affiliation(s)
- Xiaobao Cao
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong Province, China
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Tomas Buryska
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Jing Wang
- Institute of Environmental Engineering, ETH Zürich, 8093, Zürich, Switzerland
| | - Peter Fischer
- IFNH Food Process Engineering Group, ETH Zürich, 8092, Zürich, Switzerland
| | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
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4
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Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
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Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
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5
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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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6
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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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7
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Kosinski R, Perez JM, Schöneweiß EC, Ruiz-Blanco YB, Ponzo I, Bravo-Rodriguez K, Erkelenz M, Schlücker S, Uhlenbrock G, Sanchez-Garcia E, Saccà B. The role of DNA nanostructures in the catalytic properties of an allosterically regulated protease. SCIENCE ADVANCES 2022; 8:eabk0425. [PMID: 34985948 PMCID: PMC8730604 DOI: 10.1126/sciadv.abk0425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/10/2021] [Indexed: 06/04/2023]
Abstract
DNA-scaffolded enzymes typically show altered kinetic properties; however, the mechanism behind this phenomenon is still poorly understood. We address this question using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features. We compare the hydrolysis of substrates that differ only in their net charge due to a terminal residue far from the cleavage site and presumably involved in the allosteric activation of thrombin. Our data show that the reaction rate is affected by DNA/substrate electrostatic interactions, proportionally to the degree of DNA/enzyme tethering. For substrates of opposite net charge, this leads to an inversion of the catalytic response of the DNA-scaffolded thrombin when compared to its freely diffusing counterpart. Hence, by altering the electrostatic environment nearby the encaged enzyme, DNA nanostructures interfere with charge-dependent mechanisms of enzyme-substrate recognition and may offer an alternative tool to regulate allosteric processes through spatial confinement.
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Affiliation(s)
- Richard Kosinski
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joel Mieres Perez
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elisa-C. Schöneweiß
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Irene Ponzo
- Dynamic Biosensors GmbH, 82152 Martinsried, Germany
| | | | - Michael Erkelenz
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Elsa Sanchez-Garcia
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Barbara Saccà
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
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8
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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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9
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Mariconti M, Morel M, Baigl D, Rudiuk S. Enzymatically Active DNA-Protein Nanogels with Tunable Cross-Linking Density. Biomacromolecules 2021; 22:3431-3439. [PMID: 34260203 DOI: 10.1021/acs.biomac.1c00501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Hybrid DNA-protein nanogels represent potential protein vectors and enzymatic nanoreactors for modern biotechnology. Here, we describe a new, easy, and robust method for preparation of tunable DNA-protein nanogels with controllable size and density. For this purpose, polymerase chain reaction is used to prepare highly biotinylated DNA as a soft biopolymeric backbone, which can be efficiently cross-linked via streptavidin-biotin binding. This approach enables us to control both the density and size of the resulting nanogels not only by adjusting the amount of the cross-linking streptavidin but also by using different rates of DNA biotinylation. This gives DNA-streptavidin nanogels with the size ranging from 80 nm, for the most compact state, to up to 200 nm. Furthermore, using streptavidin-enzyme conjugates allows the straightforward one-pot incorporation of enzymes during the preparation of the nanogels. Monoenzymatic and multienzymatic nanogels have been obtained in this manner, and their catalytic activities have been characterized. All tested enzymes (alkaline phosphatase (AP), horseradish peroxidase (HRP), and β-galactosidase (βGal)), incorporated individually or in a coupled manner (glucose oxidase (GOx)-HRP cascade), were shown to remain functional. The activities of AP and βGal were unchanged while that of HRP was slightly improved inside the nanogels. We demonstrate that, for HRP, it is not the DNA-to-enzyme ratio but the physical density of the functionalized DNA nanogels that is responsible for the improvement of its enzymatic activity.
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Affiliation(s)
- Marina Mariconti
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
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10
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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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11
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Jaekel A, Stegemann P, Saccà B. Manipulating Enzymes Properties with DNA Nanostructures. Molecules 2019; 24:molecules24203694. [PMID: 31615123 PMCID: PMC6832416 DOI: 10.3390/molecules24203694] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology-and indeed its initial motivation-is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.
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Affiliation(s)
- Andreas Jaekel
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| | - Pierre Stegemann
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| | - Barbara Saccà
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
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12
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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: 28] [Impact Index Per Article: 4.7] [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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Akhtar MK, Vijay D, Umbreen S, McLean CJ, Cai Y, Campopiano DJ, Loake GJ. Hydrogen Peroxide-Based Fluorometric Assay for Real-Time Monitoring of SAM-Dependent Methyltransferases. Front Bioeng Biotechnol 2018; 6:146. [PMID: 30406092 PMCID: PMC6200863 DOI: 10.3389/fbioe.2018.00146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/24/2018] [Indexed: 11/26/2022] Open
Abstract
Methylated chemicals are widely used as key intermediates for the syntheses of pharmaceuticals, fragrances, flavors, biofuels and plastics. In nature, the process of methylation is commonly undertaken by a super-family of S-adenosyl methionine-dependent enzymes known as methyltransferases. Herein, we describe a novel high throughput enzyme-coupled assay for determining methyltransferase activites. Adenosylhomocysteine nucleosidase, xanthine oxidase, and horseradish peroxidase enzymes were shown to function in tandem to generate a fluorescence signal in the presence of S-adenosyl-L-homocysteine and Amplex Red (10-acetyl-3,7-dihydroxyphenoxazine). Since S-adenosyl-L-homocysteine is a key by-product of reactions catalyzed by S-adenosyl methionine-dependent methyltransferases, the coupling enzymes were used to assess the activities of EcoRI methyltransferase and a salicylic acid methyltransferase from Clarkia breweri in the presence of S-adenosyl methionine. For the EcoRI methyltransferase, the assay was sensitive enough to allow the monitoring of DNA methylation in the nanomolar range. In the case of the salicylic acid methyltransferase, detectable activity was observed for several substrates including salicylic acid, benzoic acid, 3-hydroxybenzoic acid, and vanillic acid. Additionally, the de novo synthesis of the relatively expensive and unstable cosubstrate, S-adenosyl methionine, catalyzed by methionine adenosyltransferase could be incorporated within the assay. Overall, the assay offers an excellent level of sensitivity that permits continuous and reliable monitoring of methyltransferase activities. We anticipate this assay will serve as a useful bioanalytical tool for the rapid screening of S-adenosyl methionine-dependent methyltransferase activities.
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Affiliation(s)
- M Kalim Akhtar
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates.,Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Dhanya Vijay
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Saima Umbreen
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chris J McLean
- EastChem School of Chemistry, Joseph Black Building, University of Edinburgh, Edinburgh, United Kingdom
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Dominic J Campopiano
- EastChem School of Chemistry, Joseph Black Building, University of Edinburgh, Edinburgh, United Kingdom
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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14
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Al-Kaidy H, Kuthan K, Hering T, Tippkötter N. Aqueous Droplets Used as Enzymatic Microreactors and Their Electromagnetic Actuation. J Vis Exp 2017. [PMID: 28872132 DOI: 10.3791/54643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
For the successful implementation of microfluidic reaction systems, such as PCR and electrophoresis, the movement of small liquid volumes is essential. In conventional lab-on-a-chip-platforms, solvents and samples are passed through defined microfluidic channels with complex flow control installations. The droplet actuation platform presented here is a promising alternative. With it, it is possible to move a liquid drop (microreactor) on a planar surface of a reaction platform (lab-in-a-drop). The actuation of microreactors on the hydrophobic surface of the platform is based on the use of magnetic forces acting on the outer shell of the liquid drops which is made of a thin layer of superhydrophobic magnetite particles. The hydrophobic surface of the platform is needed to avoid any contact between the liquid core and the surface to allow a smooth movement of the microreactor. On the platform, one or more microreactors with volumes of 10 µL can be positioned and moved simultaneously. The platform itself consists of a 3 x 3 matrix of electrical double coils which accommodate either neodymium or iron cores. The magnetic field gradients are automatically controlled. By variation of the magnetic field gradients, the microreactors' magnetic hydrophobic shell can be manipulated automatically to move the microreactor or open the shell reversibly. Reactions of substrates and corresponding enzymes can be initiated by merging the microreactors or bringing them into contact with surface immobilized catalysts.
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Affiliation(s)
| | - Kai Kuthan
- Institute of Bioprocess Engineering, University of Kaiserslautern
| | - Thomas Hering
- Institute of Bioprocess Engineering, University of Kaiserslautern
| | - Nils Tippkötter
- Institute of Bioprocess Engineering, University of Kaiserslautern; Bioprocess Engineering, University of Applied Sciences, FH Aachen;
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15
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Zhou L, Morel M, Rudiuk S, Baigl D. Intramolecularly Protein-Crosslinked DNA Gels: New Biohybrid Nanomaterials with Controllable Size and Catalytic Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700706. [PMID: 28561941 DOI: 10.1002/smll.201700706] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/11/2017] [Indexed: 06/07/2023]
Abstract
DNA micro- and nanogels-small-sized hydrogels made of a crosslinked DNA backbone-constitute new promising materials, but their functions have mainly been limited to those brought by DNA. Here a new way is described to prepare sub-micrometer-sized DNA gels of controllable crosslinking density that are able to embed novel functions, such as an enzymatic activity. It consists of using proteins, instead of traditional base-pairing assembly or covalent approaches, to form crosslinks inside individual DNA molecules, resulting in structures referred to as intramolecularly protein-crosslinked DNA gels (IPDGs). It is first shown that the addition of streptavidin to biotinylated T4DNA results in the successful formation of thermally stable IPDGs with a controllable crosslinking density, forming structures ranging from elongated to raspberry-shaped and pearl-necklace-like morphologies. Using reversible DNA condensation strategies, this paper shows that the gels can be reversibly actuated at a low crosslinking density, or further stabilized when they are highly crosslinked. Finally, by using streptavidin-protein conjugates, IPDGs with various enzymes are successfully functionalized. It is demonstrated that the enzymes keep their catalytic activity upon their incorporation into the gels, opening perspectives ranging from biotechnologies (e.g., enzyme manipulation) to nanomedicine (e.g., vectorization).
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Affiliation(s)
- Li Zhou
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005, Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, Ecole normale supérieure, CNRS, PASTEUR, 75005, Paris, France
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16
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Baumann P, Spulber M, Fischer O, Car A, Meier W. Investigation of Horseradish Peroxidase Kinetics in an "Organelle-Like" Environment. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1603943. [PMID: 28244215 DOI: 10.1002/smll.201603943] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/19/2017] [Indexed: 06/06/2023]
Abstract
In order to mimic cell organelles, artificial nanoreactors have been investigated based on polymeric vesicles with reconstituted channel proteins (outer membrane protein F) and coencapsulated enzymes horseradish peroxidase (HRP) along with a crowding agent (Ficoll or polyethylene glycol) inside the cavity. Importantly, the presence of macromolecules has a strong impact on the enzyme kinetics, but no influence on the integrity of vesicles up to certain concentrations. This particular design allows for the first time the determination of HRP kinetics inside nanoreactors with crowded milieu. The values of the Michaelis-Menten constant (K m ) measured for HRP in a confined space (encapsulated in nanoreactors) in the absence of macromolecules are ≈50% lower than in free conditions, and the presence of a crowding agent results in a further pronounced decrease. These results clearly suggest that activities of enzymes in confined spaces can be tuned by varying the concentrations of crowding compounds. The present investigation represents an advance in nanoreactor design by considering the influence of environmental factors on enzymatic performance, and it demonstrates that both encapsulation and the presence of a crowding environment increase the enzyme-substrate affinity.
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Affiliation(s)
- Patric Baumann
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland
| | - Mariana Spulber
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland
| | - Ozana Fischer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland
| | - Anja Car
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland
| | - Wolfgang Meier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland
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17
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Gao Y, Roberts CC, Toop A, Chang CEA, Wheeldon I. Mechanisms of Enhanced Catalysis in Enzyme-DNA Nanostructures Revealed through Molecular Simulations and Experimental Analysis. Chembiochem 2016; 17:1430-6. [PMID: 27173175 DOI: 10.1002/cbic.201600224] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Indexed: 12/12/2022]
Abstract
Understanding and controlling the molecular interactions between enzyme substrates and DNA nanostructures has important implications in the advancement of enzyme-DNA technologies as solutions in biocatalysis. Such hybrid nanostructures can be used to create enzyme systems with enhanced catalysis by controlling the local chemical and physical environments and the spatial organization of enzymes. Here we have used molecular simulations with corresponding experiments to describe a mechanism of enhanced catalysis due to locally increased substrate concentrations. With a series of DNA nanostructures conjugated to horseradish peroxidase, we show that binding interactions between substrates and the DNA structures can increase local substrate concentrations. Increased local substrate concentrations in HRP(DNA) nanostructures resulted in 2.9- and 2.4-fold decreases in the apparent Michaelis constants of tetramethylbenzidine and 4-aminophenol, substrates of HRP with tunable binding interactions to DNA nanostructures with dissociation constants in the micromolar range. Molecular simulations and kinetic analysis also revealed that increased local substrate concentrations enhanced the rates of substrate association. Identification of the mechanism of increased local concentration of substrates in close proximity to enzymes and their active sites adds to our understanding of nanostructured biocatalysis from which we can develop guidelines for enhancing catalysis in rationally designed systems.
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Affiliation(s)
- Yingning Gao
- The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Christopher C Roberts
- The Department of Chemistry, University of Californi-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Aaron Toop
- The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Chia-En A Chang
- The Department of Chemistry, University of Californi-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ian Wheeldon
- The Department of Chemical and Environmental Engineering, University of California-Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
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18
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Bauer DM, Ahmed I, Vigovskaya A, Fruk L. Clickable Tyrosine Binding Bifunctional Linkers for Preparation of DNA–Protein Conjugates. Bioconjug Chem 2013; 24:1094-101. [DOI: 10.1021/bc4001799] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dennis M. Bauer
- Karlsruher
Institute of Technology (KIT), DFG-Center for Functional Nanostructures (CFN), Wolfgang-Gaede-Str.
1a, 76131 Karlsruhe, Germany
| | - Ishtiaq Ahmed
- Karlsruher
Institute of Technology (KIT), DFG-Center for Functional Nanostructures (CFN), Wolfgang-Gaede-Str.
1a, 76131 Karlsruhe, Germany
| | - Antonina Vigovskaya
- Karlsruher
Institute of Technology (KIT), DFG-Center for Functional Nanostructures (CFN), Wolfgang-Gaede-Str.
1a, 76131 Karlsruhe, Germany
| | - Ljiljana Fruk
- Karlsruher
Institute of Technology (KIT), DFG-Center for Functional Nanostructures (CFN), Wolfgang-Gaede-Str.
1a, 76131 Karlsruhe, Germany
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19
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Lin JL, Wheeldon I. Kinetic Enhancements in DNA–Enzyme Nanostructures Mimic the Sabatier Principle. ACS Catal 2013. [DOI: 10.1021/cs300766d] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jyun-Liang Lin
- Department of Chemical and Environmental Engineering, University of California, Riverside, Bourns Hall, 900
University Avenue,
Riverside, CA 92521, United States
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, Bourns Hall, 900
University Avenue,
Riverside, CA 92521, United States
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20
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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21
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Bauer DM, Rogge A, Stolzer L, Barner-Kowollik C, Fruk L. Light induced DNA–protein conjugation. Chem Commun (Camb) 2013; 49:8626-8. [DOI: 10.1039/c3cc43291b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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22
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Rudiuk S, Venancio-Marques A, Baigl D. Enhancement and modulation of enzymatic activity through higher-order structural changes of giant DNA-protein multibranch conjugates. Angew Chem Int Ed Engl 2012; 51:12694-8. [PMID: 23143988 DOI: 10.1002/anie.201206962] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/02/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Sergii Rudiuk
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
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23
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Rudiuk S, Venancio-Marques A, Baigl D. Enhancement and Modulation of Enzymatic Activity through Higher-Order Structural Changes of Giant DNA-Protein Multibranch Conjugates. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206962] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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24
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Averick SE, Paredes E, Grahacharya D, Woodman BF, Miyake-Stoner SJ, Mehl RA, Matyjaszewski K, Das SR. A protein-polymer hybrid mediated by DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:1954-8. [PMID: 22224833 DOI: 10.1021/la204077v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Protein-polymer hybrids (PPHs) represent an important and rapidly expanding class of biomaterials. Typically in these hybrids the linkage between the protein and the polymer is covalent. Here we describe a straightforward approach to a noncovalent PPH that is mediated by DNA. Although noncovalent, the DNA-mediated approach affords the highly specific pairing and assembly properties of DNA. To obtain the protein-DNA conjugate for assembly of the PPH, we report here the first direct copper catalyzed azide-alkyne cycloaddition-based protein-DNA conjugation. This significantly simplifies access to protein-DNA conjugates. The protein-DNA conjugate and partner polymer-DNA conjugate are readily assembled through annealing of the cDNA strands to obtain the PPH, the assembly of which was confirmed via dynamic light scattering and fluorescence spectroscopy.
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Affiliation(s)
- Saadyah E Averick
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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25
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Chemical modification in the creation of novel biocatalysts. Curr Opin Chem Biol 2011; 15:211-9. [DOI: 10.1016/j.cbpa.2010.12.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 12/04/2010] [Indexed: 01/22/2023]
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26
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Saccà B, Niemeyer CM. Functionalization of DNA nanostructures with proteins. Chem Soc Rev 2011; 40:5910-21. [DOI: 10.1039/c1cs15212b] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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27
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Köhler V, Wilson YM, Lo C, Sardo A, Ward TR. Protein-based hybrid catalysts—design and evolution. Curr Opin Biotechnol 2010; 21:744-52. [DOI: 10.1016/j.copbio.2010.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 09/07/2010] [Accepted: 09/08/2010] [Indexed: 10/19/2022]
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28
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Niemeyer CM. Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew Chem Int Ed Engl 2010; 49:1200-16. [PMID: 20091721 DOI: 10.1002/anie.200904930] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Conjugation with artificial nucleic acids allows proteins to be modified with a synthetically accessible, robust tag. This attachment is addressable in a highly specific manner by means of molecular recognition events, such as Watson-Crick hybridization. Such DNA-protein conjugates, with their combined properties, have a broad range of applications, such as in high-performance biomedical diagnostic assays, fundamental research on molecular recognition, and the synthesis of DNA nanostructures. This Review surveys current approaches to generate DNA-protein conjugates as well as recent advances in their applications. For example, DNA-protein conjugates have been assembled into model systems for the investigation of catalytic cascade reactions and light-harvesting devices. Such hybrid conjugates are also used for the biofunctionalization of planar surfaces for micro- and nanoarrays, and for decorating inorganic nanoparticles to enable applications in sensing, materials science, and catalysis.
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Affiliation(s)
- Christof M Niemeyer
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany.
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29
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Niemeyer C. Halbsynthetische DNA-Protein-Konjugate für Biosensorik und Nanofabrikation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904930] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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