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Zhou L, Liu Y, Shi H, Yang X, Huang J, Liu S, Chen Q, Liu J, Wang K. Flexible Assembly of an Enzyme Cascade on a DNA Triangle Prism Nanostructure for the Controlled Biomimetic Generation of Nitric Oxide. Chembiochem 2018; 19:2099-2106. [DOI: 10.1002/cbic.201800337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Li Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Yu Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Songyang Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Qiaoshu Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province; Hunan University; Changsha 410082 China
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Loescher S, Groeer S, Walther A. 3D DNA Origami Nanoparticles: From Basic Design Principles to Emerging Applications in Soft Matter and (Bio‐)Nanosciences. Angew Chem Int Ed Engl 2018; 57:10436-10448. [DOI: 10.1002/anie.201801700] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/11/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Sebastian Loescher
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31University of Freiburg 79104 Freiburg Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21University of Freiburg 79104 Freiburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105University of Freiburg 79110 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albertstrasse 19University of Freiburg 79104 Freiburg Germany
| | - Saskia Groeer
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31University of Freiburg 79104 Freiburg Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21University of Freiburg 79104 Freiburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105University of Freiburg 79110 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albertstrasse 19University of Freiburg 79104 Freiburg Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31University of Freiburg 79104 Freiburg Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21University of Freiburg 79104 Freiburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105University of Freiburg 79110 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albertstrasse 19University of Freiburg 79104 Freiburg Germany
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Loescher S, Groeer S, Walther A. 3D‐DNA‐Origami‐Nanopartikel: von grundlegenden Designprinzipien hin zu neuartigen Anwendungen in der weichen Materie und den (Bio‐)Nanowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sebastian Loescher
- Institut für Makromolekulare Chemie, Stefan-Meier-Straße 31Albert-Ludwigs-Universität Freiburg 79104 Freiburg Deutschland
- Freiburger MaterialforschungszentrumAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte TechnologienAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburg Institute for Advanced Studies (FRIAS)Albert-Ludwigs-Universität Freiburg Deutschland
| | - Saskia Groeer
- Institut für Makromolekulare Chemie, Stefan-Meier-Straße 31Albert-Ludwigs-Universität Freiburg 79104 Freiburg Deutschland
- Freiburger MaterialforschungszentrumAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte TechnologienAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburg Institute for Advanced Studies (FRIAS)Albert-Ludwigs-Universität Freiburg Deutschland
| | - Andreas Walther
- Institut für Makromolekulare Chemie, Stefan-Meier-Straße 31Albert-Ludwigs-Universität Freiburg 79104 Freiburg Deutschland
- Freiburger MaterialforschungszentrumAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte TechnologienAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburg Institute for Advanced Studies (FRIAS)Albert-Ludwigs-Universität Freiburg Deutschland
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104
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Ijäs H, Nummelin S, Shen B, Kostiainen MA, Linko V. Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems. Int J Mol Sci 2018; 19:E2114. [PMID: 30037005 PMCID: PMC6073283 DOI: 10.3390/ijms19072114] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022] Open
Abstract
DNA nanotechnology provides an excellent foundation for diverse nanoscale structures that can be used in various bioapplications and materials research. Among all existing DNA assembly techniques, DNA origami proves to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA advanced drastically, and therefore, more and more complex DNA-based systems became accessible. So far, the vast majority of the demonstrated DNA origami frameworks are static by nature; however, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that exhibit controlled translational or rotational movement when triggered by predefined DNA sequences, various molecular interactions, and/or external stimuli such as light, pH, temperature, and electromagnetic fields. The rapid evolution of such dynamic DNA origami tools will undoubtedly have a significant impact on molecular-scale precision measurements, targeted drug delivery and diagnostics; however, they can also play a role in the development of optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.
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Affiliation(s)
- Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland.
| | - Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
- HYBER Center of Excellence, Department of Applied Physics, Aalto University, 00076 Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
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105
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106
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Nummelin S, Kommeri J, Kostiainen MA, Linko V. Evolution of Structural DNA Nanotechnology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703721. [PMID: 29363798 DOI: 10.1002/adma.201703721] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/17/2017] [Indexed: 05/24/2023]
Abstract
The research field entitled structural DNA nanotechnology emerged in the beginning of the 1980s as the first immobile synthetic nucleic acid junctions were postulated and demonstrated. Since then, the field has taken huge leaps toward advanced applications, especially during the past decade. This Progress Report summarizes how the controllable, custom, and accurate nanostructures have recently evolved together with powerful design and simulation software. Simultaneously they have provided a significant expansion of the shape space of the nanostructures. Today, researchers can select the most suitable fabrication methods, and design paradigms and software from a variety of options when creating unique DNA nanoobjects and shapes for a plethora of implementations in materials science, optics, plasmonics, molecular patterning, and nanomedicine.
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Affiliation(s)
- Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Juhana Kommeri
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
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107
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Ahmadi Y, De Llano E, Barišić I. (Poly)cation-induced protection of conventional and wireframe DNA origami nanostructures. NANOSCALE 2018; 10:7494-7504. [PMID: 29637957 DOI: 10.1039/c7nr09461b] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA nanostructures hold immense potential to be used for biological and medical applications. However, they are extremely vulnerable towards salt depletion and nucleases, which are common under physiological conditions. In this contribution, we used chitosan and linear polyethyleneimine for coating and long-term stabilization of several three-dimensional DNA origami nanostructures. The impact of the degree of polymerization and the charge density of the polymer together with the N/P charge ratio (ratio of the amines in polycations to the phosphates in DNA) on the stability of encapsulated DNA origami nanostructures in the presence of nucleases and in low-salt media was examined. The polycation shells were compatible with enzyme- and aptamer-based functionalization of the DNA nanostructures. Additionally, we showed that despite being highly vulnerable to salt depletion and nucleolytic digestion, self-assembled DNA nanostructures are stable in cell culture media up to a week. This was contrary to unassembled DNA scaffolds that degraded in one hour, showing that placing DNA strands into a spatially designed configuration crucially affect the structural integrity. The stability of naked DNA nanostructures in cell culture was shown to be mediated by growth media. DNA origami nanostructures kept in growth media were significantly more resistant towards low-salt denaturation, DNase I and serum-mediated digestion than when in a conventional buffer. Moreover, we confirmed that DNA origami nanostructures remain not only structurally intact but also fully functional after exposure to cell media. Agarose gel electrophoresis and negative stain transmission electron microscopy analysis revealed the hybridization of DNA origami nanostructures to their targets in the presence of serum proteins and nucleases. The structural integrity and functionality of DNA nanostructures in physiological fluids validate their use particularly for short-time biological applications in which the shape and structural details of DNA nanodevices are functionally critical.
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Affiliation(s)
- Yasaman Ahmadi
- Molecular Diagnostics, Centre for Health and Bioresources, AIT Austrian Institute of Technology GmbH, 1190 Vienna, Austria.
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108
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Wenz NL, Piasecka S, Kalinowski M, Schneider A, Richert C, Wege C. Building expanded structures from tetrahedral DNA branching elements, RNA and TMV protein. NANOSCALE 2018; 10:6496-6510. [PMID: 29569670 DOI: 10.1039/c7nr07743b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
By combining both chemical and enzymatic ligation with procedures guiding the self-assembly of nanotubular tobacco mosaic virus (TMV)-like particles (TLPs), novel nucleoprotein structures based on DNA-terminated branching elements, RNA scaffolds and TMV coat protein (CP) are made accessible. Tetrahedral tetrakis(hydroxybiphenyl)adamantane cores with four 5'-phosphorylated dinucleotide arms were coupled to DNA linkers by chemical ligation. The resulting three-dimensional (3D) branching elements were enzymatically ligated to the 3' termini of RNA scaffolds either prior to or after the RNAs' incorporation into TLPs. Thus, architectures with interconnected nanotube domains in two different length classes were generated, each containing 70 CP subunits per 10 nm length. Short TMV origin-of-assembly-containing RNA scaffolds ligated to the DNA allowed the growth of protein-coated 34 nm tubes on the terminal RNA strands in situ. Alternatively, 290 nm pre-fabricated tubes with accessible RNA 3' termini, attained by DNA blocking elements hybridized to the RNAs, were ligated with the branched cores. Both approaches resulted in four-armed nanoobjects, demonstrating a so far unique combination of organic synthesis of branching elements, enzymatic modifications, nucleic acid-based scaffolding and RNA-guided and DNA-controlled assembly of tubular RNA-encapsidating protein domains, yielding a novel class of 3D nucleoprotein architectures with polyvalent protein elements. In the long term, the production route might give rise to supramolecular systems with complex functionalities, installed via the orthogonal coupling of effector molecules to TLP domains.
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Affiliation(s)
- Nana L Wenz
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Sylwia Piasecka
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Matthäus Kalinowski
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Angela Schneider
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
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109
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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110
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Ora A, Järvihaavisto E, Zhang H, Auvinen H, Santos HA, Kostiainen MA, Linko V. Cellular delivery of enzyme-loaded DNA origami. Chem Commun (Camb) 2018; 52:14161-14164. [PMID: 27869278 DOI: 10.1039/c6cc08197e] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In this communication, we show that active enzymes can be delivered into HEK293 cells in vitro when they are attached to tubular DNA origami nanostructures. We use bioluminescent enzymes as a cargo and monitor their activity from a cell lysate. The results show that the enzymes stay intact and retain their activity in the transfection process. The method is highly modular, which makes it a compelling candidate for a great variety of delivery applications.
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Affiliation(s)
- Ari Ora
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Erika Järvihaavisto
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Hongbo Zhang
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00790 Helsinki, Finland
| | - Henni Auvinen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Hélder A Santos
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00790 Helsinki, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
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111
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Tang MSL, Shiu SCC, Godonoga M, Cheung YW, Liang S, Dirkzwager RM, Kinghorn AB, Fraser LA, Heddle JG, Tanner JA. An aptamer-enabled DNA nanobox for protein sensing. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:1161-1168. [PMID: 29410111 DOI: 10.1016/j.nano.2018.01.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
Abstract
DNA nanostructures can show dynamic responses to molecular triggers for a wide variety of applications. While DNA sequence signal triggers are now well-established, there is a critical need for a broader diversity of molecular triggers to drive dynamic responses in DNA nanostructures. DNA aptamers are ideal; they can both seamlessly integrate into DNA nanostructure scaffolds and transduce molecular recognition into functional responses. Here, we report construction and optimization of a DNA origami nanobox locked by a pair of DNA double strands where one strand is a DNA aptamer targeting the malaria biomarker protein Plasmodium falciparum lactate dehydrogenase. The protein acts as the key which enables box opening. We observe highly specific protein-mediated box opening by both transmission electron microscopy and fluorescence. Aptamer-enabled DNA boxes have significant potential for enabling direct responses to proteins and other biomolecules in nanoscale diagnostics, drug delivery and sensing devices.
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Affiliation(s)
- Marco S L Tang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Maia Godonoga
- Heddle Initiative Research Unit, RIKEN, Saitama, Japan
| | - Yee-Wai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shaolin Liang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Roderick M Dirkzwager
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lewis A Fraser
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jonathan G Heddle
- Heddle Initiative Research Unit, RIKEN, Saitama, Japan; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Julian A Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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112
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Abstract
The DNA origami technique is a widely used method to create customized, complex, spatially well-defined two-dimensional (2D) and three-dimensional (3D) DNA nanostructures. These structures have huge potential to serve as smart drug-delivery vehicles and molecular devices in various nanomedical and biotechnological applications. However, so far only little is known about the behavior of these novel structures in living organisms or in cell culture/tissue models. Moreover, enhancing pharmacokinetic bioavailability and transfection properties of such structures still remains a challenge. One intriguing approach to overcome these issues is to coat DNA origami nanostructures with proteins or lipid membranes. Here, we show how cowpea chlorotic mottle virus (CCMV) capsid proteins (CPs) can be used for coating DNA origami nanostructures. We present a method for disassembling native CCMV particles and isolating the pure CP dimers, which can further bind and encapsulate a rectangular DNA origami shape. Owing to the highly programmable nature of DNA origami, packaging of DNA nanostructures into viral protein cages could find imminent uses in enhanced targeting and cellular delivery of various active nano-objects, such as enzymes and drug molecules.
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113
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Control of enzyme reactions by a reconfigurable DNA nanovault. Nat Commun 2017; 8:992. [PMID: 29051565 PMCID: PMC5648847 DOI: 10.1038/s41467-017-01072-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/16/2017] [Indexed: 12/21/2022] Open
Abstract
Biological systems use compartmentalisation as a general strategy to control enzymatic reactions by precisely regulating enzyme–substrate interactions. With the advent of DNA nanotechnology, it has become possible to rationally design DNA-based nano-containers with programmable structural and dynamic properties. These DNA nanostructures have been used to cage enzymes, but control over enzyme–substrate interactions using a dynamic DNA nanostructure has not been achieved yet. Here we introduce a DNA origami device that functions as a nanoscale vault: an enzyme is loaded in an isolated cavity and the access to free substrate molecules is controlled by a multi-lock mechanism. The DNA vault is characterised for features such as reversible opening/closing, cargo loading and wall porosity, and is shown to control the enzymatic reaction catalysed by an encapsulated protease. The DNA vault represents a general concept to control enzyme–substrate interactions by inducing conformational changes in a rationally designed DNA nanodevice. DNA nanostructures can cage enzymes but currently fall short of controlling their reactions with substrates. Here, the authors enclose an enzyme inside a dynamic DNA vault, which regulates its access to substrate molecules—and thus its enzymatic activity—through a multi-lock mechanism.
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114
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Komiyama M, Yoshimoto K, Sisido M, Ariga K. Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170156] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8577
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902
| | - Masahiko Sisido
- Professor Emeritus, Research Core for Interdisciplinary Sciences, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0827
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115
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Hou C, Guan S, Wang R, Zhang W, Meng F, Zhao L, Xu J, Liu J. Supramolecular Protein Assemblies Based on DNA Templates. J Phys Chem Lett 2017; 8:3970-3979. [PMID: 28792224 DOI: 10.1021/acs.jpclett.7b01564] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA plays an important role in the process of protein assembly. DNA viruses such as the M13 virus are typical examples in which single DNA genomes behave as templates to induce the assembly of multiple major coat protein (PVIII) monomers. Thus, the design of protein assemblies based on DNA templates attracts much interest in the construction of supramolecular structures and materials. With the development of DNA nanotechnology, precise 1D and 3D protein nanostructures have been designed and constructed by using DNA templates through DNA-protein interactions, protein-ligand interactions, and protein-adapter interactions. These DNA-templated protein assemblies show great potential in catalysis, medicine, light-responsive systems, drug delivery, and signal transduction. Herein, we review the progress on DNA-based protein nanostructures that possess sophisticated nanometer-sized structures with programmable shapes and stimuli-responsive parameters, and we present their great potential in the design of biomaterials and biodevices in the future.
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Affiliation(s)
| | | | - Ruidi Wang
- Department of Chemistry, University of British Columbia , Vancouver, British Columbia V6T 1Z1, Canada
| | - Wei Zhang
- Zhuhai United Laboratories Co., Ltd. , Nation High & New Technology Industry Development Zone, Zhuhai 519040, China
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116
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Ross JF, Bridges A, Fletcher JM, Shoemark D, Alibhai D, Bray HEV, Beesley JL, Dawson WM, Hodgson LR, Mantell J, Verkade P, Edge CM, Sessions RB, Tew D, Woolfson DN. Decorating Self-Assembled Peptide Cages with Proteins. ACS NANO 2017; 11:7901-7914. [PMID: 28686416 DOI: 10.1021/acsnano.7b02368] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
An ability to organize and encapsulate multiple active proteins into defined objects and spaces at the nanoscale has potential applications in biotechnology, nanotechnology, and synthetic biology. Previously, we have described the design, assembly, and characterization of peptide-based self-assembled cages (SAGEs). These ≈100 nm particles comprise thousands of copies of de novo designed peptide-based hubs that array into a hexagonal network and close to give caged structures. Here, we show that, when fused to the designed peptides, various natural proteins can be co-assembled into SAGE particles. We call these constructs pSAGE for protein-SAGE. These particles tolerate the incorporation of multiple copies of folded proteins fused to either the N or the C termini of the hubs, which modeling indicates form the external and internal surfaces of the particles, respectively. Up to 15% of the hubs can be functionalized without compromising the integrity of the pSAGEs. This corresponds to hundreds of copies giving mM local concentrations of protein in the particles. Moreover, and illustrating the modularity of the SAGE system, we show that multiple different proteins can be assembled simultaneously into the same particle. As the peptide-protein fusions are made via recombinant expression of synthetic genes, we envisage that pSAGE systems could be developed modularly to actively encapsulate or to present a wide variety of functional proteins, allowing them to be developed as nanoreactors through the immobilization of enzyme cascades or as vehicles for presenting whole antigenic proteins as synthetic vaccine platforms.
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Affiliation(s)
- James F Ross
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Angela Bridges
- GlaxoSmithKline (GSK) , Gunnels Wood Rd, Stevenage SG21 2NY, United Kingdom
| | - Jordan M Fletcher
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Deborah Shoemark
- BrisSynBio, Life Sciences Building, University of Bristol , Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | | | - Harriet E V Bray
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Joseph L Beesley
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - William M Dawson
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | | | | | | | - Colin M Edge
- GlaxoSmithKline (GSK) , Gunnels Wood Rd, Stevenage SG21 2NY, United Kingdom
| | - Richard B Sessions
- BrisSynBio, Life Sciences Building, University of Bristol , Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - David Tew
- GlaxoSmithKline (GSK) , Gunnels Wood Rd, Stevenage SG21 2NY, United Kingdom
| | - Derek N Woolfson
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol , Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
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117
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Affiliation(s)
- Yifei Zhang
- Department of Biomedical
Engineering, Columbia University, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical
Engineering, Columbia University, New York, New York 10027, United States
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118
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Zhou X, Guo S, Gao J, Zhao J, Xue S, Xu W. Glucose oxidase-initiated cascade catalysis for sensitive impedimetric aptasensor based on metal-organic frameworks functionalized with Pt nanoparticles and hemin/G-quadruplex as mimicking peroxidases. Biosens Bioelectron 2017; 98:83-90. [PMID: 28654887 DOI: 10.1016/j.bios.2017.06.039] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 12/21/2022]
Abstract
Based on cascade catalysis amplification driven by glucose oxidase (GOx), a sensitive electrochemical impedimetric aptasensor for protein (carcinoembryonic antigen, CEA as tested model) was proposed by using Cu-based metal-organic frameworks functionalized with Pt nanoparticles, aptamer, hemin and GOx (Pt@CuMOFs-hGq-GOx). CEA aptamer loaded onto Pt@CuMOFs was bound with hemin to form hemin@G-quadruplex (hGq) with mimicking peroxidase activity. Through sandwich-type reaction of target CEA and CEA aptamers (Apt1 and Apt2), the obtained Pt@CuMOFs-hGq-GOx as signal transduction probes (STPs) was captured to the modified electrode interface. When 3,3-diaminobenzidine (DAB) and glucose were introduced, the cascade reaction was initiated by GOx to catalyze the oxidation of glucose, in situ generating H2O2. Simultaneously, the decomposition of the generated H2O2 was greatly promoted by Pt@CuMOFs and hGq as synergistic peroxide catalysts, accompanying with the significant oxidation process of DAB and the formation of nonconductive insoluble precipitates (IPs). As a result, the electron transfer in the resultant sensing interface was effectively hindered and the electrochemical impedimetric signal (EIS) was efficiently amplified. Thus, the high sensitivity of the proposed CEA aptasensor was successfully improved with 0.023pgmL-1, which may be promising and potential in assaying certain clinical disease related to CEA.
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Affiliation(s)
- Xingxing Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Shijing Guo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jiaxi Gao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jianmin Zhao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Shuyan Xue
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wenju Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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119
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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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120
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Nagamune T. Biomolecular engineering for nanobio/bionanotechnology. NANO CONVERGENCE 2017; 4:9. [PMID: 28491487 PMCID: PMC5401866 DOI: 10.1186/s40580-017-0103-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/29/2017] [Indexed: 05/02/2023]
Abstract
Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.
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Affiliation(s)
- Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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121
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Vranish JN, Ancona MG, Oh E, Susumu K, Medintz IL. Enhancing coupled enzymatic activity by conjugating one enzyme to a nanoparticle. NANOSCALE 2017; 9:5172-5187. [PMID: 28393943 DOI: 10.1039/c7nr00200a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Enzymes have long been a prime research target for the commercial production of commodity and specialty chemicals, design of sensing devices, and the development of therapeutics and new chemical processes. Industrial applications for enzymes can potentially be enhanced by enzyme immobilization which often allows for increased enzyme stability, facile product purification, and minimized substrate diffusion times in multienzymatic cascades, but this is usually at the cost of a significant decrease in catalytic rates. Recently, enzyme immobilization has been advanced by the discovery that nanoparticle surfaces are frequently able to enhance the activity of the bound enzyme. Here we extend this observation to a multienzymatic coupled system using semiconductor quantum dots (QDs) as a model nanoparticle material and the prototypical enzyme pair of glucose oxidase (GOX) and horseradish peroxidase (HRP). We first demonstrate that HRP binding to QDs has a significant beneficial effect on enzymatic activity, producing a >2-fold improvement in kcat. We argue that this enhancement is due to affinity of the QD surface for the substrate. Furthermore, we demonstrate that when the ratio of GOX to HRP is adjusted to allow HRP to be the rate-limiting step of the pathway, the QD-induced rate enhancement of HRP can be maintained in a multi-enzyme cascade. Kinetic analysis shows that the underlying processes can be simulated numerically and provide insight into the governing mechanisms. The potential of nanoparticle-based catalytic enhancement is then discussed in the context of multienzyme cascades and synthetic biology.
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122
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Abstract
Transmembrane proteins are mostly nanochannels playing a highly important role in metabolism. Understanding their structures and functions is vital for revealing life processes. It is of fundamental interest to develop chemical devices to mimic biological channels. Structural DNA nanotechnology has been proven to be a promising method for the preparation of fine DNA nanochannels as a result of the excellent properties of DNA molecules. This review presents the development history and current situation of three different types of DNA nanochannel: tile-based nanotube, DNA origami nanochannel, and DNA bundle nanochannel.
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Affiliation(s)
- Dianming Wang
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Yiyang Zhang
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Dongsheng Liu
- Department of Chemistry, Tsinghua University, Beijing, China
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123
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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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124
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Balasubramanian V, Correia A, Zhang H, Fontana F, Mäkilä E, Salonen J, Hirvonen J, Santos HA. Biomimetic Engineering Using Cancer Cell Membranes for Designing Compartmentalized Nanoreactors with Organelle-Like Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1605375. [PMID: 28112838 DOI: 10.1002/adma.201605375] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/08/2016] [Indexed: 05/18/2023]
Abstract
A new biomimetic nanoreactor design is presented based on cancer cell membrane material in combination with porous silicon nanoparticles. This cellular nanoreactor features a biocompartment enclosed by a cell membrane and readily integrated with cells and supplementing the cellular functions under oxidative stress. The study demonstrates the impact of the nanoreactors on improving cellular functions with a potential to serve as artificial organelles.
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Affiliation(s)
- Vimalkumar Balasubramanian
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI, 00014, Helsinki, Finland
| | - Alexandra Correia
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI, 00014, Helsinki, Finland
| | - Hongbo Zhang
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI, 00014, Helsinki, Finland
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Flavia Fontana
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI, 00014, Helsinki, Finland
| | - Ermei Mäkilä
- Laboratory of Industrial Physics, University of Turku, FI, 20014, Turku, Finland
| | - Jarno Salonen
- Laboratory of Industrial Physics, University of Turku, FI, 20014, Turku, Finland
| | - Jouni Hirvonen
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI, 00014, Helsinki, Finland
| | - Hélder A Santos
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI, 00014, Helsinki, Finland
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125
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Chen H, Li R, Li S, Andréasson J, Choi JH. Conformational Effects of UV Light on DNA Origami. J Am Chem Soc 2017; 139:1380-1383. [DOI: 10.1021/jacs.6b10821] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haorong Chen
- School
of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ruixin Li
- School
of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Shiming Li
- Department
of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Joakim Andréasson
- Department
of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jong Hyun Choi
- School
of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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126
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Lu S, Hu T, Wang S, Sun J, Yang X. Ultra-Sensitive Colorimetric Assay System Based on the Hybridization Chain Reaction-Triggered Enzyme Cascade Amplification. ACS APPLIED MATERIALS & INTERFACES 2017; 9:167-175. [PMID: 27996245 DOI: 10.1021/acsami.6b13201] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A versatile and ultrasensitive colorimetric detection platform has been developed based on the hybridization chain reaction (HCR)-triggered enzyme cascade amplification in this work. The proposal involves the preparation of two different hairpin DNA strands consisting of the H1, modified with glucose oxidase (GOx-H1) and H2, modified with horseradish peroxidase (HRP-H2). The H1 and H2 were composed of complementary sequence of nucleic acid target (T) and interlaced complementary stem-loop sequences. In the nucleic acid detection, the hybridization of T and its complementary sequence induces the autonomous assembly of GOx-H1 and HRP-H2 through the predictable HCR, accompanied by the formation of GOx/HRP enzyme pairs with a multiple enzymatic cascade. In contrast to the crude mixture of free GOx-H1 and HRP-H2, the catalytic performance of enzyme cascade reaction has been significantly enhanced, which can be determined by monitoring the absorbance change of 2, 2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS2-), a typical substrate with hydrogen peroxide for the HRP. Furthermore, this platform can be utilized in the assay of biological substances by the introduction of corresponding aptamer (Apt), complementary strands (Com), and an assistant hairpin DNA strand (HAssist). In view of the signal amplification of HCR and the enhanced catalytic performance of cascaded enzymes, our colorimetric assay system exhibits excellent sensitivity, and the detection limits have been calculated to be 5.2 fM and 0.8 pM for the nucleic acid target (T as a model) and biological substances (ATP as a model), respectively.
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Affiliation(s)
- Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Tao Hu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
- University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Jian Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China
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127
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Abstract
Self-assembled DNA nanostructures hold great promise to organize multi-enzyme systems with the precise control of the geometric arrangements. Enzymes modified with single-stranded DNA anchors are assembled onto the DNA origami tiles by hybridizing with the corresponding complementary strands displayed on the surface of the DNA nanostructures. Here, we describe a protocol of assembling a two-enzyme cascade on a discrete, rectangular DNA origami tile, where the distance between enzymes is precisely controlled for investigating the distance-dependent cascade activities.
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Affiliation(s)
- Jinglin Fu
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA.
- Department of Chemistry, Rutgers University, Camden, NJ, 08102, USA.
| | - Tianran Li
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA
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128
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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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129
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Chen S, Wen L, Svec F, Tan T, Lv Y. Magnetic metal–organic frameworks as scaffolds for spatial co-location and positional assembly of multi-enzyme systems enabling enhanced cascade biocatalysis. RSC Adv 2017. [DOI: 10.1039/c7ra02291c] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Magnetic metal–organic frameworks have been prepared as scaffolds for spatial co-location and positional assembly of multi-enzymes enabling enhanced cascade biocatalysis.
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Affiliation(s)
- Sijia Chen
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Liyin Wen
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Frantisek Svec
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Tianwei Tan
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Yongqin Lv
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
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130
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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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131
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Tigges T, Heuser T, Tiwari R, Walther A. 3D DNA Origami Cuboids as Monodisperse Patchy Nanoparticles for Switchable Hierarchical Self-Assembly. NANO LETTERS 2016; 16:7870-7874. [PMID: 27802042 DOI: 10.1021/acs.nanolett.6b04146] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The rational design of anisotropic interaction patterns is a key step for programming colloid and nanoparticle self-assembly and emergent functions. Herein, we demonstrate a concept for harnessing the capabilities of 3D DNA origami for extensive supracolloidal self-assembly and showcase its use for making truly monodisperse, patchy, divalent nanocuboids that can self-assemble into supracolloidal fibrils via programmable DNA hybridization. A change in the number of connector duplexes at the patches reveals that multivalency and cooperativity play crucial roles to enhance superstructure formation. We further show thermal and chemical switching of the superstructures as the first steps toward reconfigurable self-assemblies. This concept lays the groundwork for merging monodisperse 3D DNA origami, featuring programmable patchiness and interactions, with nanoparticle self-assembly.
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Affiliation(s)
- Thomas Tigges
- DWI-Leibniz-Institute for Interactive Materials , Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Thomas Heuser
- DWI-Leibniz-Institute for Interactive Materials , Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Rahul Tiwari
- DWI-Leibniz-Institute for Interactive Materials , Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Andreas Walther
- Institute of Macromolecular Chemistry, Albert-Ludwigs-University of Freiburg , Stefan-Meier-Str. 31, 79104 Freiburg, Germany
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132
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Simoncelli S, Roller EM, Urban P, Schreiber R, Turberfield AJ, Liedl T, Lohmüller T. Quantitative Single-Molecule Surface-Enhanced Raman Scattering by Optothermal Tuning of DNA Origami-Assembled Plasmonic Nanoantennas. ACS NANO 2016; 10:9809-9815. [PMID: 27649370 DOI: 10.1021/acsnano.6b05276] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA origami is a powerful approach for assembling plasmonic nanoparticle dimers and Raman dyes with high yields and excellent positioning control. Here we show how optothermal-induced shrinking of a DNA origami template can be employed to control the gap sizes between two 40 nm gold nanoparticles in a range from 1 to 2 nm. The high field confinement achieved with this optothermal approach was demonstrated by detection of surface-enhanced Raman spectroscopy (SERS) signals from single molecules that are precisely placed within the DNA origami template that spans the nanoparticle gap. By comparing the SERS intensity with respect to the field enhancement in the plasmonic hot-spot region, we found good agreement between measurement and theory. Our straightforward approach for the fabrication of addressable plasmonic nanosensors by DNA origami demonstrates a path toward future sensing applications with single-molecule resolution.
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Affiliation(s)
- Sabrina Simoncelli
- Photonics and Optoelectronics Group, Department of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München , Amalienstraße 54, Munich 80799, Germany
| | - Eva-Maria Roller
- Department of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München , Geschwister-Scholl-Platz 1, Munich 80539, Germany
| | - Patrick Urban
- Photonics and Optoelectronics Group, Department of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München , Amalienstraße 54, Munich 80799, Germany
| | - Robert Schreiber
- Clarendon Laboratory, Department of Physics, University of Oxford , Parks Road, Oxford OX1 3PU, United Kingdom
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics, University of Oxford , Parks Road, Oxford OX1 3PU, United Kingdom
| | - Tim Liedl
- Department of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München , Geschwister-Scholl-Platz 1, Munich 80539, Germany
- Nanosystems Initiative Munich (NIM) , Schellingstraße 4, Munich 80539, Germany
| | - Theobald Lohmüller
- Photonics and Optoelectronics Group, Department of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München , Amalienstraße 54, Munich 80799, Germany
- Nanosystems Initiative Munich (NIM) , Schellingstraße 4, Munich 80539, Germany
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133
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Tapio K, Leppiniemi J, Shen B, Hytönen VP, Fritzsche W, Toppari JJ. Toward Single Electron Nanoelectronics Using Self-Assembled DNA Structure. NANO LETTERS 2016; 16:6780-6786. [PMID: 27700108 DOI: 10.1021/acs.nanolett.6b02378] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA based structures offer an adaptable and robust way to develop customized nanostructures for various purposes in bionanotechnology. One main aim in this field is to develop a DNA nanobreadboard for a controllable attachment of nanoparticles or biomolecules to form specific nanoelectronic devices. Here we conjugate three gold nanoparticles on a defined size TX-tile assembly into a linear pattern to form nanometer scale isolated islands that could be utilized in a room temperature single electron transistor. To demonstrate this, conjugated structures were trapped using dielectrophoresis for current-voltage characterization. After trapping only high resistance behavior was observed. However, after extending the islands by chemical growth of gold, several structures exhibited Coulomb blockade behavior from 4.2 K up to room temperature, which gives a good indication that self-assembled DNA structures could be used for nanoelectronic patterning and single electron devices.
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Affiliation(s)
- Kosti Tapio
- University of Jyvaskyla , Department of Physics, Nanoscience Center, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Jenni Leppiniemi
- BioMediTech, University of Tampere , Lääkärinkatu 1, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu 4, FI-33520 Tampere, Finland
| | - Boxuan Shen
- University of Jyvaskyla , Department of Physics, Nanoscience Center, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Vesa P Hytönen
- BioMediTech, University of Tampere , Lääkärinkatu 1, FI-33520 Tampere, Finland
- Fimlab Laboratories, Biokatu 4, FI-33520 Tampere, Finland
| | - Wolfgang Fritzsche
- Leibniz Institute of Photonic Technology (IPHT) , Albert-Einstein-Strasse 9, Jena 07745, Germany
| | - J Jussi Toppari
- University of Jyvaskyla , Department of Physics, Nanoscience Center, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
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134
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Fu J, Yang YR, Dhakal S, Zhao Z, Liu M, Zhang T, Walter NG, Yan H. Assembly of multienzyme complexes on DNA nanostructures. Nat Protoc 2016; 11:2243-2273. [DOI: 10.1038/nprot.2016.139] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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135
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Giessen TW, Silver PA. A Catalytic Nanoreactor Based on in Vivo Encapsulation of Multiple Enzymes in an Engineered Protein Nanocompartment. Chembiochem 2016; 17:1931-1935. [DOI: 10.1002/cbic.201600431] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Tobias W. Giessen
- Department of Systems Biology; Harvard Medical School; 200 Longwood Avenue WAB 536 Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; 3 Blackfan Circle Boston MA 02115 USA
| | - Pamela A. Silver
- Department of Systems Biology; Harvard Medical School; 200 Longwood Avenue WAB 536 Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; 3 Blackfan Circle Boston MA 02115 USA
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136
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Shen B, Tapio K, Linko V, Kostiainen MA, Toppari JJ. Metallic Nanostructures Based on DNA Nanoshapes. NANOMATERIALS 2016; 6:nano6080146. [PMID: 28335274 PMCID: PMC5224615 DOI: 10.3390/nano6080146] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 01/10/2023]
Abstract
Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable development of DNA-based nanostructures has provided many successful methods and realizations for these needs, such as chemical DNA metallization via seeding or ionization, as well as DNA-guided lithography and casting of metallic nanoparticles by DNA molds. These methods offer high resolution, versatility and throughput and could enable the fabrication of arbitrarily-shaped structures with a 10-nm feature size, thus bringing novel applications into view. In this review, we cover the evolution of DNA-based metallic nanostructures, starting from the metallized double-stranded DNA for electronics and progress to sophisticated plasmonic structures based on DNA origami objects.
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Affiliation(s)
- Boxuan Shen
- Nanoscience Center, Department of Physics, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland.
| | - Kosti Tapio
- Nanoscience Center, Department of Physics, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, Aalto 00076, Finland.
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, Aalto 00076, Finland.
| | - Jari Jussi Toppari
- Nanoscience Center, Department of Physics, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland.
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137
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Linko V, Nummelin S, Aarnos L, Tapio K, Toppari JJ, Kostiainen MA. DNA-Based Enzyme Reactors and Systems. NANOMATERIALS 2016; 6:nano6080139. [PMID: 28335267 PMCID: PMC5224616 DOI: 10.3390/nano6080139] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/11/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used in the fabrication of artificial biochemical machinery that is able to mimic the complex reactions found in living cells. Currently, DNA-enzyme hybrids can be used to control (multi-enzyme) cascade reactions and to regulate the enzyme functions and the reaction pathways. Moreover, sophisticated DNA structures can be utilized in encapsulating active enzymes and delivering the molecular cargo into cells. In this review, we focus on the latest enzyme systems based on novel DNA nanostructures: enzyme reactors, regulatory devices and carriers that can find uses in various biotechnological and nanomedical applications.
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Affiliation(s)
- Veikko Linko
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, Aalto 00076, Finland.
| | - Sami Nummelin
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, Aalto 00076, Finland.
| | - Laura Aarnos
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, Aalto 00076, Finland.
| | - Kosti Tapio
- Department of Physics, University of Jyvaskyla, Nanoscience Center, P.O. Box 35, Jyväskylä 40014, Finland.
| | - J Jussi Toppari
- Department of Physics, University of Jyvaskyla, Nanoscience Center, P.O. Box 35, Jyväskylä 40014, Finland.
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, Aalto 00076, Finland.
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138
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Linko V, Ora A, Kostiainen MA. DNA Nanostructures as Smart Drug-Delivery Vehicles and Molecular Devices. Trends Biotechnol 2016; 33:586-594. [PMID: 26409777 DOI: 10.1016/j.tibtech.2015.08.001] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 11/28/2022]
Abstract
DNA molecules can be assembled into custom predesigned shapes via hybridization of sequence-complementary domains. The folded structures have high spatial addressability and a tremendous potential to serve as platforms and active components in a plethora of bionanotechnological applications. DNA is a truly programmable material, and its nanoscale engineering thus opens up numerous attractive possibilities to develop novel methods for therapeutics. The tailored molecular devices could be used in targeting cells and triggering the cellular actions in the biological environment. In this review we focus on the DNA-based assemblies - primarily DNA origami nanostructures - that could perform complex tasks in cells and serve as smart drug-delivery vehicles in, for example, cancer therapy, prodrug medication, and enzyme replacement therapy.
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Affiliation(s)
- Veikko Linko
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, PO Box 16100, 00076 Aalto, Finland
| | - Ari Ora
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, PO Box 16100, 00076 Aalto, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, PO Box 16100, 00076 Aalto, Finland.
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139
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Kiviaho JK, Linko V, Ora A, Tiainen T, Järvihaavisto E, Mikkilä J, Tenhu H, Kostiainen MA. Cationic polymers for DNA origami coating - examining their binding efficiency and tuning the enzymatic reaction rates. NANOSCALE 2016; 8:11674-80. [PMID: 27219684 DOI: 10.1039/c5nr08355a] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
DNA origamis are fully tailored, programmable, biocompatible and readily functionalizable nanostructures that provide an excellent foundation for the development of sophisticated drug-delivery systems. However, the DNA origami objects suffer from certain drawbacks such as low cell-transfection rates and low stability. A great deal of studies on polymer-based transfection agents, mainly focusing on polyplex formation and toxicity, exists. In this study, the electrostatic binding between a brick-like DNA origami and cationic block-copolymers was explored. The effect of the polymer structure on the binding was investigated and the toxicity of the polymer-origami complexes evaluated. The study shows that all of the analyzed polymers had a suitable binding efficiency irrespective of the block structure. It was also observed that the toxicity of polymer-origami complexes was insignificant at the biologically relevant concentration levels. Besides brick-like DNA origamis, tubular origami carriers equipped with enzymes were also coated with the polymers. By adjusting the amount of cationic polymers that cover the DNA structures, we showed that it is possible to control the enzyme kinetics of the complexes. This work gives a starting point for further development of biocompatible and effective polycation-based block copolymers that can be used in coating different DNA origami nanostructures for various bioapplications.
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Affiliation(s)
- Jenny K Kiviaho
- Biohybrid Materials Group, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials Group, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Ari Ora
- Biohybrid Materials Group, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Tony Tiainen
- Laboratory of Polymer Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, 00014 Helsinki, Finland
| | - Erika Järvihaavisto
- Biohybrid Materials Group, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Joona Mikkilä
- Biohybrid Materials Group, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Heikki Tenhu
- Laboratory of Polymer Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, 00014 Helsinki, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials Group, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
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140
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Chen H, Zhang H, Pan J, Cha TG, Li S, Andréasson J, Choi JH. Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts. ACS NANO 2016; 10:4989-96. [PMID: 27057775 DOI: 10.1021/acsnano.6b01339] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.
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Affiliation(s)
- Haorong Chen
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Hanyu Zhang
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Jing Pan
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Tae-Gon Cha
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Shiming Li
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Joakim Andréasson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
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141
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Küchler A, Yoshimoto M, Luginbühl S, Mavelli F, Walde P. Enzymatic reactions in confined environments. NATURE NANOTECHNOLOGY 2016; 11:409-20. [PMID: 27146955 DOI: 10.1038/nnano.2016.54] [Citation(s) in RCA: 473] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 03/04/2016] [Indexed: 05/17/2023]
Abstract
Within each biological cell, surface- and volume-confined enzymes control a highly complex network of chemical reactions. These reactions are efficient, timely, and spatially defined. Efforts to transfer such appealing features to in vitro systems have led to several successful examples of chemical reactions catalysed by isolated and immobilized enzymes. In most cases, these enzymes are either bound or adsorbed to an insoluble support, physically trapped in a macromolecular network, or encapsulated within compartments. Advanced applications of enzymatic cascade reactions with immobilized enzymes include enzymatic fuel cells and enzymatic nanoreactors, both for in vitro and possible in vivo applications. In this Review, we discuss some of the general principles of enzymatic reactions confined on surfaces, at interfaces, and inside small volumes. We also highlight the similarities and differences between the in vivo and in vitro cases and attempt to critically evaluate some of the necessary future steps to improve our fundamental understanding of these systems.
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Affiliation(s)
- Andreas Küchler
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland
| | - Makoto Yoshimoto
- Department of Applied Molecular Bioscience, Yamaguchi University, Tokiwadai 2-16-1, Ube 755-8611, Japan
| | - Sandra Luginbühl
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland
| | - Fabio Mavelli
- Chemistry Department, University 'Aldo Moro', Via Orabona 4, 70125 Bari, Italy
| | - Peter Walde
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland
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142
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Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X. Beyond the Fold: Emerging Biological Applications of DNA Origami. Chembiochem 2016; 17:1081-9. [PMID: 26928725 DOI: 10.1002/cbic.201600038] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/22/2023]
Abstract
The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.
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Affiliation(s)
| | - Nate Anderson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. , .,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. ,
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143
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Valero J, Lohmann F, Keppner D, Famulok M. Single-Stranded Tile Stoppers for Interlocked DNA Architectures. Chembiochem 2016; 17:1146-9. [DOI: 10.1002/cbic.201500685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Julián Valero
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Finn Lohmann
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Daniel Keppner
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Michael Famulok
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
- Center of Advanced European Studies and Research (CAESAR); Ludwig-Erhard-Allee 2 53175 Bonn Germany
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144
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Zenk J, Tuntivate C, Schulman R. Kinetics and Thermodynamics of Watson–Crick Base Pairing Driven DNA Origami Dimerization. J Am Chem Soc 2016; 138:3346-54. [DOI: 10.1021/jacs.5b10502] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- John Zenk
- Chemical
and Biomolecular Engineering and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chanon Tuntivate
- Chemical
and Biomolecular Engineering and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Chemical
and Biomolecular Engineering and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
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145
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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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146
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Wang L, Sun Y, Li Z, Wu A, Wei G. Bottom-Up Synthesis and Sensor Applications of Biomimetic Nanostructures. MATERIALS (BASEL, SWITZERLAND) 2016; 9:E53. [PMID: 28787853 PMCID: PMC5456561 DOI: 10.3390/ma9010053] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 12/21/2022]
Abstract
The combination of nanotechnology, biology, and bioengineering greatly improved the developments of nanomaterials with unique functions and properties. Biomolecules as the nanoscale building blocks play very important roles for the final formation of functional nanostructures. Many kinds of novel nanostructures have been created by using the bioinspired self-assembly and subsequent binding with various nanoparticles. In this review, we summarized the studies on the fabrications and sensor applications of biomimetic nanostructures. The strategies for creating different bottom-up nanostructures by using biomolecules like DNA, protein, peptide, and virus, as well as microorganisms like bacteria and plant leaf are introduced. In addition, the potential applications of the synthesized biomimetic nanostructures for colorimetry, fluorescence, surface plasmon resonance, surface-enhanced Raman scattering, electrical resistance, electrochemistry, and quartz crystal microbalance sensors are presented. This review will promote the understanding of relationships between biomolecules/microorganisms and functional nanomaterials in one way, and in another way it will guide the design and synthesis of biomimetic nanomaterials with unique properties in the future.
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Affiliation(s)
- Li Wang
- College of Chemistry, Jilin Normal University, Haifeng Street 1301, Siping 136000, China.
| | - Yujing Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Renmin Street 5625, Changchun 130022, China.
| | - Zhuang Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Renmin Street 5625, Changchun 130022, China.
| | - Aiguo Wu
- Key Laboratory of Magnetic Materials and Devices & Division of Functional Materials and Nanodevices, Ningbo Institute of Material Technology and Engineering, Chinese Academy Sciences, Ningbo 315201, China.
| | - Gang Wei
- Faculty of Production Engineering, University of Bremen, Am Fallturm 1, D-28359 Bremen, Germany.
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147
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Linko V, Shen B, Tapio K, Toppari JJ, Kostiainen MA, Tuukkanen S. One-step large-scale deposition of salt-free DNA origami nanostructures. Sci Rep 2015; 5:15634. [PMID: 26492833 PMCID: PMC4616047 DOI: 10.1038/srep15634] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/28/2015] [Indexed: 01/13/2023] Open
Abstract
DNA origami nanostructures have tremendous potential to serve as versatile platforms in self-assembly -based nanofabrication and in highly parallel nanoscale patterning. However, uniform deposition and reliable anchoring of DNA nanostructures often requires specific conditions, such as pre-treatment of the chosen substrate or a fine-tuned salt concentration for the deposition buffer. In addition, currently available deposition techniques are suitable merely for small scales. In this article, we exploit a spray-coating technique in order to resolve the aforementioned issues in the deposition of different 2D and 3D DNA origami nanostructures. We show that purified DNA origamis can be controllably deposited on silicon and glass substrates by the proposed method. The results are verified using either atomic force microscopy or fluorescence microscopy depending on the shape of the DNA origami. DNA origamis are successfully deposited onto untreated substrates with surface coverage of about 4 objects/mm(2). Further, the DNA nanostructures maintain their shape even if the salt residues are removed from the DNA origami fabrication buffer after the folding procedure. We believe that the presented one-step spray-coating method will find use in various fields of material sciences, especially in the development of DNA biochips and in the fabrication of metamaterials and plasmonic devices through DNA metallisation.
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Affiliation(s)
- Veikko Linko
- Aalto University, Department of Biotechnology and Chemical Technology, Biohybrid Materials, Espoo, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Boxuan Shen
- University of Jyvaskyla, Department of Physics, Nanoscience Center, Jyväskylä, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Kosti Tapio
- University of Jyvaskyla, Department of Physics, Nanoscience Center, Jyväskylä, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - J. Jussi Toppari
- University of Jyvaskyla, Department of Physics, Nanoscience Center, Jyväskylä, P.O. Box 35, FI-40014 University of Jyväskylä, Finland
| | - Mauri A. Kostiainen
- Aalto University, Department of Biotechnology and Chemical Technology, Biohybrid Materials, Espoo, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Sampo Tuukkanen
- Tampere University of Technology, Department of Automation Science and Engineering, Tampere, P.O. Box 692, FI-33101, Finland
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Shen B, Linko V, Tapio K, Kostiainen MA, Toppari JJ. Custom-shaped metal nanostructures based on DNA origami silhouettes. NANOSCALE 2015; 7:11267-72. [PMID: 26066528 DOI: 10.1039/c5nr02300a] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The DNA origami technique provides an intriguing possibility to develop customized nanostructures for various bionanotechnological purposes. One target is to create tailored bottom-up-based plasmonic devices and metamaterials based on DNA metallization or controlled attachment of nanoparticles to the DNA designs. In this article, we demonstrate an alternative approach: DNA origami nanoshapes can be utilized in creating accurate, uniform and entirely metallic (e.g. gold, silver and copper) nanostructures on silicon substrates. The technique is based on developing silhouettes of the origamis in the grown silicon dioxide layer, and subsequently using this layer as a mask for further patterning. The proposed method has a high spatial resolution, and the fabrication yields can approach 90%. The approach allows a cost-effective, parallel, large-scale patterning on a chip with fully tailored metallic nanostructures; the DNA origami shape and the applied metal can be specifically chosen for each conceivable implementation.
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Affiliation(s)
- Boxuan Shen
- University of Jyvaskyla, Department of Physics, Nanoscience Center, P.O. Box 35, FI-40014. and University of Jyväskylä, Finland.
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