51
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Wagenbauer KF, Engelhardt FAS, Stahl E, Hechtl VK, Stömmer P, Seebacher F, Meregalli L, Ketterer P, Gerling T, Dietz H. How We Make DNA Origami. Chembiochem 2017; 18:1873-1885. [PMID: 28714559 DOI: 10.1002/cbic.201700377] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Indexed: 12/14/2022]
Abstract
DNA origami has attracted substantial attention since its invention ten years ago, due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. Although the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know-how for designing and producing the particles with sufficient quality and for preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know-how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge. To foster faster progress, we share in this article the experience in making and preparing DNA origami that we have accumulated over recent years. We discuss design solutions for creating advanced structural motifs including corners and various types of hinges that expand the design space for the more rigid multilayer DNA origami and provide guidelines for preventing undesired aggregation and on how to induce specific oligomerization of multiple DNA origami building blocks. In addition, we provide detailed protocols and discuss the expected results for five key methods that allow efficient and damage-free preparation of DNA origami. These methods are agarose-gel purification, filtration through molecular cut-off membranes, PEG precipitation, size-exclusion chromatography, and ultracentrifugation-based sedimentation. The guide for creating advanced design motifs and the detailed protocols with their experimental characterization that we describe here should lower the barrier for researchers to accomplish the full DNA origami production workflow.
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Affiliation(s)
- Klaus F Wagenbauer
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Floris A S Engelhardt
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Evi Stahl
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Vera K Hechtl
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Pierre Stömmer
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Fabian Seebacher
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Letizia Meregalli
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Philip Ketterer
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Thomas Gerling
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Hendrik Dietz
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
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52
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Kou BB, Chai YQ, Yuan YL, Yuan R. PtNPs as Scaffolds to Regulate Interenzyme Distance for Construction of Efficient Enzyme Cascade Amplification for Ultrasensitive Electrochemical Detection of MMP-2. Anal Chem 2017; 89:9383-9387. [PMID: 28726378 DOI: 10.1021/acs.analchem.7b02210] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The high catalytic efficiency of enzyme cascade reaction mainly depends on optimal interenzyme distance regulated by the special scaffolds. In this work, the rigid PtNPs with different sizes were employed as scaffolds to regulate interenzyme distance for efficient enzyme cascade amplification to construct electrochemical biosensor for sensitive detection of matrix metalloproteinases-2 (MMP-2), which overcame the drawbacks of instable construction and sophisticated preparation induced by conventional scaffolds such as metal-organic frameworks (MOFs), DNA nanostructures. Here, cucurbit[7]uril functionalized PtNPs (CB[7]@PtNPs) was utilized to load ferrocene (Fc)-labeled horseradish peroxidase (HRP) and glucose oxidase (GOx) via host-guest interaction between Fc and CB[7], respectively, resulting in the formation of a stable three-dimensional netlike structure containing amounts of enzymes. Interestingly, the enzyme cascade reaction regulated by 10 nm PtNPs as scaffold showed highly catalytic efficiency. Meanwhile, the PtNPs could also serve as catalyst to accelerate the enzyme cascade reaction with further enhanced catalytic efficiency. As a result, the proposed biosensor exhibited excellent sensitivity with a wide linear range of 0.1 pg·mL-1 to 20 ng·mL-1 and a detection limit of 0.03 pg·mL-1 for MMP-2. Such a strategy opened a new avenue for adopting metal nanoparticles to regulate interenzyme distance for efficient enzyme cascade amplification, thus providing a universal and easy operating method for sensitively detecting various targets such as DNA, metal ion, and protein.
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Affiliation(s)
- Bei-Bei Kou
- Key Labortary of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
| | - Ya-Qin Chai
- Key Labortary of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
| | - Ya-Li Yuan
- Key Labortary of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
| | - Ruo Yuan
- Key Labortary of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, PR China
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53
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Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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54
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Rajendran A, Nakata E, Nakano S, Morii T. Nucleic-Acid-Templated Enzyme Cascades. Chembiochem 2017; 18:696-716. [DOI: 10.1002/cbic.201600703] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Indexed: 11/08/2022]
Affiliation(s)
| | - Eiji Nakata
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Shun Nakano
- 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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55
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Mathur D, Medintz IL. Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community. Anal Chem 2017; 89:2646-2663. [DOI: 10.1021/acs.analchem.6b04033] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Divita Mathur
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, D.C. 20375, United States
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56
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Collins J, Zhang T, Oh SW, Maloney R, Fu J. DNA-crowded enzyme complexes with enhanced activities and stabilities. Chem Commun (Camb) 2017; 53:13059-13062. [DOI: 10.1039/c7cc07361e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We present a robust and simple method to prepare DNA-crowded enzyme complexes by directly assembling long DNA duplexes on the enzyme surface.
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Affiliation(s)
- John Collins
- Department of Chemistry
- Rutgers University – Camden
- Camden
- USA
| | - Ting Zhang
- Department of Chemistry
- Rutgers University – Camden
- Camden
- USA
| | - Sung Won Oh
- Center for Computational and Integrative Biology
- Rutgers University – Camden
- Camden
- USA
| | - Robert Maloney
- Department of Chemistry
- Rutgers University – Camden
- Camden
- USA
| | - Jinglin Fu
- Department of Chemistry
- Rutgers University – Camden
- Camden
- USA
- Center for Computational and Integrative Biology
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57
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Quin MB, Wallin KK, Zhang G, Schmidt-Dannert C. Spatial organization of multi-enzyme biocatalytic cascades. Org Biomol Chem 2017; 15:4260-4271. [DOI: 10.1039/c7ob00391a] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-enzyme cascades provide a wealth of valuable chemicals. Efficiency of reaction schemes can be improved by spatial organization of biocatalysts. This review will highlight various methods of spatial organization of biocatalysts: fusion, immobilization, scaffolding and encapsulation.
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Affiliation(s)
- M. B. Quin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - K. K. Wallin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - G. Zhang
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - C. Schmidt-Dannert
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
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58
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Abstract
Separation of self-assembled three-dimensional nanostructures from excess staple strands, misfolded structures, or unattached functional elements is critical for downstream applications. Numerous purification techniques exist, with varying yields, purities, and hetero-element compatibilities. In this chapter, we focus on three such techniques-agarose gel electrophoresis, ultrafiltration, and polymeric bead pull-down-which together satisfy requirements for a range of applications.
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59
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Zhang Y, Tsitkov S, Hess H. Proximity does not contribute to activity enhancement in the glucose oxidase-horseradish peroxidase cascade. Nat Commun 2016; 7:13982. [PMID: 28004753 PMCID: PMC5196434 DOI: 10.1038/ncomms13982] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/14/2016] [Indexed: 12/23/2022] Open
Abstract
A proximity effect has been invoked to explain the enhanced activity of enzyme cascades on DNA scaffolds. Using the cascade reaction carried out by glucose oxidase and horseradish peroxidase as a model system, here we study the kinetics of the cascade reaction when the enzymes are free in solution, when they are conjugated to each other and when a competing enzyme is present. No proximity effect is found, which is in agreement with models predicting that the rapidly diffusing hydrogen peroxide intermediate is well mixed. We suggest that the reason for the activity enhancement of enzymes localized by DNA scaffolds is that the pH near the surface of the negatively charged DNA nanostructures is lower than that in the bulk solution, creating a more optimal pH environment for the anchored enzymes. Our findings challenge the notion of a proximity effect and provide new insights into the role of DNA scaffolds.
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Affiliation(s)
- Yifei Zhang
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA
| | - Stanislav Tsitkov
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, USA
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60
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Wagner HJ, Sprenger A, Rebmann B, Weber W. Upgrading biomaterials with synthetic biological modules for advanced medical applications. Adv Drug Deliv Rev 2016; 105:77-95. [PMID: 27179764 DOI: 10.1016/j.addr.2016.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/02/2016] [Accepted: 05/04/2016] [Indexed: 02/04/2023]
Abstract
One key aspect of synthetic biology is the development and characterization of modular biological building blocks that can be assembled to construct integrated cell-based circuits performing computational functions. Likewise, the idea of extracting biological modules from the cellular context has led to the development of in vitro operating systems. This principle has attracted substantial interest to extend the repertoire of functional materials by connecting them with modules derived from synthetic biology. In this respect, synthetic biological switches and sensors, as well as biological targeting or structure modules, have been employed to upgrade functions of polymers and solid inorganic material. The resulting systems hold great promise for a variety of applications in diagnosis, tissue engineering, and drug delivery. This review reflects on the most recent developments and critically discusses challenges concerning in vivo functionality and tolerance that must be addressed to allow the future translation of such synthetic biology-upgraded materials from the bench to the bedside.
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61
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Sommese RF, Hariadi RF, Kim K, Liu M, Tyska MJ, Sivaramakrishnan S. Patterning protein complexes on DNA nanostructures using a GFP nanobody. Protein Sci 2016; 25:2089-2094. [PMID: 27538185 DOI: 10.1002/pro.3020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 08/15/2016] [Accepted: 08/15/2016] [Indexed: 11/06/2022]
Abstract
DNA nanostructures have become an important and powerful tool for studying protein function over the last 5 years. One of the challenges, though, has been the development of universal methods for patterning protein complexes on DNA nanostructures. Herein, we present a new approach for labeling DNA nanostructures by functionalizing them with a GFP nanobody. We demonstrate the ability to precisely control protein attachment via our nanobody linker using two enzymatic model systems, namely adenylyl cyclase activity and myosin motility. Finally, we test the power of this attachment method by patterning unpurified, endogenously expressed Arp2/3 protein complex from cell lysate. By bridging DNA nanostructures with a fluorescent protein ubiquitous throughout cell and developmental biology and protein biochemistry, this approach significantly streamlines the application of DNA nanostructures as a programmable scaffold in biological studies.
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Affiliation(s)
- R F Sommese
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, 55455
| | - R F Hariadi
- Department of Physics, Arizona State University, Tempe, Arizona, 85287.,Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona, 85287
| | - K Kim
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, 55455
| | - M Liu
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona, 85287.,School of Molecular Sciences, Arizona State University, Tempe, Arizona, 85287
| | - M J Tyska
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, 37232
| | - S Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, 55455.
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62
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Ke G, Liu M, Jiang S, Qi X, Yang YR, Wootten S, Zhang F, Zhu Z, Liu Y, Yang CJ, Yan H. Directional Regulation of Enzyme Pathways through the Control of Substrate Channeling on a DNA Origami Scaffold. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603183] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guoliang Ke
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation State Key Laboratory of Physical Chemistry of Solid Surfaces Collaborative Innovation Center of Chemistry for Energy Materials 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 School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Xiaodong Qi
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Yuhe Renee Yang
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Shaun Wootten
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Fei Zhang
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation State Key Laboratory of Physical Chemistry of Solid Surfaces Collaborative Innovation Center of Chemistry for Energy Materials Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Yan Liu
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Chaoyong James Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation State Key Laboratory of Physical Chemistry of Solid Surfaces Collaborative Innovation Center of Chemistry for Energy Materials Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Hao Yan
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
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63
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Ke G, Liu M, Jiang S, Qi X, Yang YR, Wootten S, Zhang F, Zhu Z, Liu Y, Yang CJ, Yan H. Directional Regulation of Enzyme Pathways through the Control of Substrate Channeling on a DNA Origami Scaffold. Angew Chem Int Ed Engl 2016; 55:7483-6. [PMID: 27159899 DOI: 10.1002/anie.201603183] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/11/2022]
Abstract
Artificial multi-enzyme systems with precise and dynamic control over the enzyme pathway activity are of great significance in bionanotechnology and synthetic biology. Herein, we exploit a spatially addressable DNA nanoplatform for the directional regulation of two enzyme pathways (G6pDH-MDH and G6pDH-LDH) through the control of NAD(+) substrate channeling by specifically shifting NAD(+) between the two enzyme pairs. We believe that this concept will be useful for the design of regulatory biological circuits for synthetic biology and biomedicine.
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Affiliation(s)
- Guoliang Ke
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA.,The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, 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, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Xiaodong Qi
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Yuhe Renee Yang
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Shaun Wootten
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Fei Zhang
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yan Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA.
| | - Chaoyong James Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Hao Yan
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA.
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64
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Koßmann KJ, Ziegler C, Angelin A, Meyer R, Skoupi M, Rabe KS, Niemeyer CM. A Rationally Designed Connector for Assembly of Protein-Functionalized DNA Nanostructures. Chembiochem 2016; 17:1102-6. [PMID: 26972311 DOI: 10.1002/cbic.201600039] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 11/12/2022]
Abstract
We report on the rational engineering of the binding interface of the self-ligating HaloTag protein to generate an optimized linker for DNA nanostructures. Five amino acids positioned around the active-site entry channel for the chlorohexyl ligand (CH) of the HaloTag protein were exchanged for positively charged lysine amino acids to produce the HOB (halo-based oligonucleotide binder) protein. HOB was genetically fused with the enzyme cytochrome P450 BM3, as well as with BMR, the separated reductase domain of BM3. The resulting HOB-fusion proteins revealed significantly improved rates in ligation with CH-modified oligonucleotides and DNA origami nanostructures. These results suggest that the efficient self-assembly of protein-decorated DNA structures can be greatly improved by fine-tuning of the electrostatic interactions between proteins and the negatively charged nucleic acid nanostructures.
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Affiliation(s)
- Katja J Koßmann
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Cornelia Ziegler
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Alessandro Angelin
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Rebecca Meyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Marc Skoupi
- 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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65
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Ngo TA, Nakata E, Saimura M, Morii T. Spatially Organized Enzymes Drive Cofactor-Coupled Cascade Reactions. J Am Chem Soc 2016; 138:3012-21. [PMID: 26881296 DOI: 10.1021/jacs.5b10198] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report the construction of an artificial enzyme cascade based on the xylose metabolic pathway. Two enzymes, xylose reductase and xylitol dehydrogenase, were assembled at specific locations on DNA origami by using DNA-binding protein adaptors with systematic variations in the interenzyme distances and defined numbers of enzyme molecules. The reaction system, which localized the two enzymes in close proximity to facilitate transport of reaction intermediates, resulted in significantly higher yields of the conversion of xylose into xylulose through the intermediate xylitol with recycling of the cofactor NADH. Analysis of the initial reaction rate, regenerated amount of NADH, and simulation of the intermediates' diffusion indicated that the intermediates diffused to the second enzyme by Brownian motion. The efficiency of the cascade reaction with the bimolecular transport of xylitol and NAD(+) likely depends more on the interenzyme distance than that of the cascade reaction with unimolecular transport between two enzymes.
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Affiliation(s)
- Tien Anh Ngo
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Masayuki Saimura
- 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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66
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Zhao Z, Fu J, Dhakal S, Johnson-Buck A, Liu M, Zhang T, Woodbury NW, Liu Y, Walter NG, Yan H. Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion. Nat Commun 2016; 7:10619. [PMID: 26861509 PMCID: PMC4749968 DOI: 10.1038/ncomms10619] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/05/2016] [Indexed: 01/06/2023] Open
Abstract
Cells routinely compartmentalize enzymes for enhanced efficiency of their metabolic pathways. Here we report a general approach to construct DNA nanocaged enzymes for enhancing catalytic activity and stability. Nanocaged enzymes are realized by self-assembly into DNA nanocages with well-controlled stoichiometry and architecture that enabled a systematic study of the impact of both encapsulation and proximal polyanionic surfaces on a set of common metabolic enzymes. Activity assays at both bulk and single-molecule levels demonstrate increased substrate turnover numbers for DNA nanocage-encapsulated enzymes. Unexpectedly, we observe a significant inverse correlation between the size of a protein and its activity enhancement. This effect is consistent with a model wherein distal polyanionic surfaces of the nanocage enhance the stability of active enzyme conformations through the action of a strongly bound hydration layer. We further show that DNA nanocages protect encapsulated enzymes against proteases, demonstrating their practical utility in functional biomaterials and biotechnology.
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Affiliation(s)
- Zhao Zhao
- Center for Molecular Design and Biomimetics, the Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Jinglin Fu
- Department of Chemistry, Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey 08102, USA
| | - Soma Dhakal
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Alexander Johnson-Buck
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, the Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
| | - Ting Zhang
- Department of Chemistry, Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey 08102, USA
| | - Neal W. Woodbury
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
- Center for Innovations in Medicine, the Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
| | - Yan Liu
- Center for Molecular Design and Biomimetics, the Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics, the Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
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67
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Wang Y, Zou L, Xiao J, Qiao Y, Lu Z. Oligonucleotide length- and probe number-dependent assembly of gold nanoparticle on triangular DNA origami. RSC Adv 2016. [DOI: 10.1039/c6ra03700c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Effects of oligonucleotide length and probe number on assembly of gold nanoparticles with DNA origami were investigated.
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Affiliation(s)
- Ying Wang
- Chongqing Key Laboratory for Advanced Materials & Technologies of Clean Energies
- Southwest University
- Chongqing 400715
- P. R. China
- Institute for Clean Energy & Advanced Materials
| | - Long Zou
- Chongqing Key Laboratory for Advanced Materials & Technologies of Clean Energies
- Southwest University
- Chongqing 400715
- P. R. China
- Institute for Clean Energy & Advanced Materials
| | - Jing Xiao
- Chongqing Key Laboratory for Advanced Materials & Technologies of Clean Energies
- Southwest University
- Chongqing 400715
- P. R. China
- Institute for Clean Energy & Advanced Materials
| | - Yan Qiao
- Chongqing Key Laboratory for Advanced Materials & Technologies of Clean Energies
- Southwest University
- Chongqing 400715
- P. R. China
- Institute for Clean Energy & Advanced Materials
| | - Zhisong Lu
- Chongqing Key Laboratory for Advanced Materials & Technologies of Clean Energies
- Southwest University
- Chongqing 400715
- P. R. China
- Institute for Clean Energy & Advanced Materials
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68
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Campos R, Zhang S, Majikes JM, Ferraz LCC, LaBean TH, Dong MD, Ferapontova EE. Electronically addressable nanomechanical switching of i-motif DNA origami assembled on basal plane HOPG. Chem Commun (Camb) 2015; 51:14111-4. [DOI: 10.1039/c5cc04678e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Here, a pH-induced nanomechanical switching of i-motif structures incorporated into DNA origami bound onto cysteamine-modified basal plane HOPG was electronically addressed, demonstrating for the first time the electrochemical read-out of the nanomechanics of DNA origami.
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Affiliation(s)
- R. Campos
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- 8000 Aarhus C
- Denmark
| | - S. Zhang
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- 8000 Aarhus C
- Denmark
| | - J. M. Majikes
- Department of Materials Science and Engineering
- North Carolina State University
- Raleigh
- USA
| | - L. C. C. Ferraz
- Department of Materials Science and Engineering
- North Carolina State University
- Raleigh
- USA
| | - T. H. LaBean
- Department of Materials Science and Engineering
- North Carolina State University
- Raleigh
- USA
| | - M. D. Dong
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- 8000 Aarhus C
- Denmark
| | - E. E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO)
- Science and Technology
- Aarhus University
- 8000 Aarhus C
- Denmark
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