1
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Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
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Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
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2
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Liu S, Xiang K, Wang C, Zhang Y, Fan GC, Wang W, Han H. DNA Nanotweezers for Biosensing Applications: Recent Advances and Future Prospects. ACS Sens 2022; 7:3-20. [PMID: 34989231 DOI: 10.1021/acssensors.1c01647] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA nanotweezers (DTs) are reversible DNA nanodevices that can optionally switch between opened and closed states. Due to their excellent flexibility and high programmability, they have been recognized as a promising platform for constructing a diversity of biosensors and logic gates, as well as a versatile tool for molecular biology studies. In this review, we provide an overview of biosensing applications using DTs. First, the design and working principle of DTs are introduced. Next, the signal producing principles of DTs are summarized. Furthermore, biosensing applications of DTs for varying targets and purposes, both in buffers and complex biological environments, are highlighted. Finally, we provide potential opportunities and challenges for the further development of DTs.
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Affiliation(s)
- Shanshan Liu
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Kaikai Xiang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Chunyan Wang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Yutian Zhang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Gao-Chao Fan
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, Shandong, People’s Republic of China
| | - Wenjing Wang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, People’s Republic of China
| | - Heyou Han
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
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3
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Kosinski R, Perez JM, Schöneweiß EC, Ruiz-Blanco YB, Ponzo I, Bravo-Rodriguez K, Erkelenz M, Schlücker S, Uhlenbrock G, Sanchez-Garcia E, Saccà B. The role of DNA nanostructures in the catalytic properties of an allosterically regulated protease. SCIENCE ADVANCES 2022; 8:eabk0425. [PMID: 34985948 PMCID: PMC8730604 DOI: 10.1126/sciadv.abk0425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/10/2021] [Indexed: 06/04/2023]
Abstract
DNA-scaffolded enzymes typically show altered kinetic properties; however, the mechanism behind this phenomenon is still poorly understood. We address this question using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features. We compare the hydrolysis of substrates that differ only in their net charge due to a terminal residue far from the cleavage site and presumably involved in the allosteric activation of thrombin. Our data show that the reaction rate is affected by DNA/substrate electrostatic interactions, proportionally to the degree of DNA/enzyme tethering. For substrates of opposite net charge, this leads to an inversion of the catalytic response of the DNA-scaffolded thrombin when compared to its freely diffusing counterpart. Hence, by altering the electrostatic environment nearby the encaged enzyme, DNA nanostructures interfere with charge-dependent mechanisms of enzyme-substrate recognition and may offer an alternative tool to regulate allosteric processes through spatial confinement.
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Affiliation(s)
- Richard Kosinski
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joel Mieres Perez
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elisa-C. Schöneweiß
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Irene Ponzo
- Dynamic Biosensors GmbH, 82152 Martinsried, Germany
| | | | - Michael Erkelenz
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Elsa Sanchez-Garcia
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Barbara Saccà
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
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4
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Bernal-Chanchavac J, Al-Amin M, Stephanopoulos N. Nanoscale structures and materials from the self-assembly of polypeptides and DNA. Curr Top Med Chem 2021; 22:699-712. [PMID: 34911426 DOI: 10.2174/1568026621666211215142916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/22/2022]
Abstract
The use of biological molecules with programmable self-assembly properties is an attractive route to functional nanomaterials. Proteins and peptides have been used extensively for these systems due to their biological relevance and large number of supramolecular motifs, but it is still difficult to build highly anisotropic and programmable nanostructures due to their high complexity. Oligonucleotides, by contrast, have the advantage of programmability and reliable assembly, but lack biological and chemical diversity. In this review, we discuss systems that merge protein or peptide self-assembly with the addressability of DNA. We outline the various self-assembly motifs used, the chemistry for linking polypeptides with DNA, and the resulting nanostructures that can be formed by the interplay of these two molecules. Finally, we close by suggesting some interesting future directions in hybrid polypeptide-DNA nanomaterials, and potential applications for these exciting hybrids.
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Affiliation(s)
- Julio Bernal-Chanchavac
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
| | - Md Al-Amin
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
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5
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Strategies to Build Hybrid Protein-DNA Nanostructures. NANOMATERIALS 2021; 11:nano11051332. [PMID: 34070149 PMCID: PMC8158336 DOI: 10.3390/nano11051332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/24/2021] [Accepted: 05/14/2021] [Indexed: 12/15/2022]
Abstract
Proteins and DNA exhibit key physical chemical properties that make them advantageous for building nanostructures with outstanding features. Both DNA and protein nanotechnology have growth notably and proved to be fertile disciplines. The combination of both types of nanotechnologies is helpful to overcome the individual weaknesses and limitations of each one, paving the way for the continuing diversification of structural nanotechnologies. Recent studies have implemented a synergistic combination of both biomolecules to assemble unique and sophisticate protein-DNA nanostructures. These hybrid nanostructures are highly programmable and display remarkable features that create new opportunities to build on the nanoscale. This review focuses on the strategies deployed to create hybrid protein-DNA nanostructures. Here, we discuss strategies such as polymerization, spatial directing and organizing, coating, and rigidizing or folding DNA into particular shapes or moving parts. The enrichment of structural DNA nanotechnology by incorporating protein nanotechnology has been clearly demonstrated and still shows a large potential to create useful and advanced materials with cell-like properties or dynamic systems. It can be expected that structural protein-DNA nanotechnology will open new avenues in the fabrication of nanoassemblies with unique functional applications and enrich the toolbox of bionanotechnology.
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6
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DNA Nanodevices as Mechanical Probes of Protein Structure and Function. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has reported a wide range of structurally tunable scaffolds with precise control over their size, shape and mechanical properties. One promising application of these nanodevices is as probes for protein function or determination of protein structure. In this perspective we cover several recent examples in this field, including determining the effect of ligand spacing and multivalency on cell activation, applying forces at the nanoscale, and helping to solve protein structure by cryo-EM. We also highlight some future directions in the chemistry necessary for integrating proteins with DNA nanoscaffolds, as well as opportunities for computational modeling of hybrid protein-DNA nanomaterials.
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7
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Zhao D, Kong Y, Zhao S, Xing H. Engineering Functional DNA–Protein Conjugates for Biosensing, Biomedical, and Nanoassembly Applications. Top Curr Chem (Cham) 2020; 378:41. [DOI: 10.1007/s41061-020-00305-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 12/31/2022]
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8
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9
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Ge Z, Fu J, Liu M, Jiang S, Andreoni A, Zuo X, Liu Y, Yan H, Fan C. Constructing Submonolayer DNA Origami Scaffold on Gold Electrode for Wiring of Redox Enzymatic Cascade Pathways. ACS APPLIED MATERIALS & INTERFACES 2019; 11:13881-13887. [PMID: 30379533 DOI: 10.1021/acsami.8b12374] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Advances in biomimetic microelectronics offer a range of patterned assemblies of proteins and cells for in vitro metabolic engineering where coordinated biochemical pathways allow cell metabolism to be characterized and potentially controlled on a chip. To achieve these goals, developing new methods for interfacing biological systems to microelectronic devices has been in urgent demand. Here, we report the assembly of a DNA origami-templated enzymatic cascade (glucose oxidase and horseradish peroxidase) on gold electrodes, where a monolayer of DNA origami is anchored on gold electrodes via Au-S chemistry, to create programmable, electrochemically driven biomimetic device containing both biochemical and electronic components. Upon the posing of a specific electrical potential, substrates/products flow through the enzyme pair and the end product transfers electrons to the electrode. The steady state flux of the distance-dependent enzymatic cascade reactions is translated into a steady state current signal that records the overall enzyme activity. This biological system can be finely tuned by varying the distance between the enzyme pair, which opens new routes to interface microelectronic devices to biological functions.
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Affiliation(s)
- Zhilei Ge
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Jinglin Fu
- Department of Chemistry, and Center for Computational and Integrative Biology , Rutgers University-Camden , Camden , New Jersey 08102 , United States
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Alessio Andreoni
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Yan Liu
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China
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10
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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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11
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Earl E, Calabrese Barton S. Simulation of intermediate transport in nanoscale scaffolds for multistep catalytic reactions. Phys Chem Chem Phys 2018; 19:15463-15470. [PMID: 28580995 DOI: 10.1039/c7cp00239d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient catalytic cascades that involve several sequential reactions are found frequently in nature. The efficiency of multi-step biochemical pathways is enhanced by substrate channelling, wherein the product of one reaction is directed toward and acts as substrate to the next sequential reaction. Such mechanisms can partially overcome diffusion, which is often fast compared to reaction rates, and promotes loss of intermediates. Biochemical substrate channelling is achieved by the architecture and scaffolding of enzymes, and mimicking these natural structures could lead to innovative catalyst designs. We investigate the efficiency of two channelling approaches - electrostatic interactions and surface adsorption - through continuum modelling, to identify the limits of these modes and the extent to which they can interact. The model considers transport between two active sites where an intermediate is produced at the first active site and consumed at the second. The system includes mass transport through diffusion and migration, and reaction kinetics at the active sites. The effectiveness of this model is quantified by yield of the second reaction relative to the first. Channelling via proximity between active sites and via surface adsorption are found to be inefficient, requiring high values of the rate constant at the second active site to obtain significant yields. The introduction of electrostatic interactions, however, leads to yields of over 90% at much lower values of the rate constant.
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Affiliation(s)
- Erica Earl
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA.
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12
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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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13
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Sato Y, Hiratsuka Y, Kawamata I, Murata S, Nomura SIM. Micrometer-sized molecular robot changes its shape in response to signal molecules. Sci Robot 2017; 2:2/4/eaal3735. [DOI: 10.1126/scirobotics.aal3735] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/03/2017] [Indexed: 11/02/2022]
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14
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Wakabayashi R, Yahiro K, Hayashi K, Goto M, Kamiya N. Protein-Grafted Polymers Prepared Through a Site-Specific Conjugation by Microbial Transglutaminase for an Immunosorbent Assay. Biomacromolecules 2016; 18:422-430. [DOI: 10.1021/acs.biomac.6b01538] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rie Wakabayashi
- Department
of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kensuke Yahiro
- Department
of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kounosuke Hayashi
- Department
of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Hitachi Aloka
Medical, Ltd., 3-7-19 Imai, Ome-shi, Tokyo 198-8577, Japan
| | - Masahiro Goto
- Department
of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Division
of Biotechnology, Center for Future Chemistry, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395 Japan
| | - Noriho Kamiya
- Department
of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Division
of Biotechnology, Center for Future Chemistry, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395 Japan
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15
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Hirano Y, Ikegami M, Kowata K, Komatsu Y. Bienzyme reactions on cross-linked DNA scaffolds for electrochemical analysis. Bioelectrochemistry 2016; 113:15-19. [PMID: 27611764 DOI: 10.1016/j.bioelechem.2016.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 08/16/2016] [Accepted: 08/31/2016] [Indexed: 10/21/2022]
Abstract
Enzymes play an essential role in various detection technologies. We show here that interstrand cross-linked oligodeoxynucleotides (CL-ODNs) can provide stable scaffolds for efficiently coupling two types of enzymatic reactions on an electrode. Glucose can be electrochemically detected using glucose oxidase (GOx) and horseradish peroxidase (HRP). When both GOx and HRP were immobilized on an electrode surface by attachment at the termini of CL-ODNs, the current value was markedly increased compared with that obtained on a standard ODN scaffold. The relative orientation of the enzymes on the electrode strongly affected the current intensities. The CL-ODN also allowed GOx-HRP to form a complex on the tiny surface of a microelectrode, resulting in the imaging of local glucose distribution. These results suggest that CL-ODNs have potential utility in other sensing technologies.
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Affiliation(s)
- Yu Hirano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo, Japan
| | - Masiki Ikegami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo, Japan
| | - Keiko Kowata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo, Japan.
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16
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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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17
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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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18
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Affiliation(s)
- Sundus Erbas-Cakmak
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Charlie T. McTernan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alina
L. Nussbaumer
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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19
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Abstract
The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.
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20
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Lan J, Wen F, Fu F, Zhang X, Cai S, Liu Z, Wu D, Li C, Chen J, Wang C. A photoluminescent biosensor based on long-range self-assembled DNA cascades and upconversion nanoparticles for the detection of breast cancer-associated circulating microRNA in serum samples. RSC Adv 2015. [DOI: 10.1039/c5ra01288k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A photoluminescent biosensor was developed for the detection of microRNA (miRNA) combined signal amplification of long-range self-assembled DNA cascades with upconversion nanoparticles.
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21
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Humenik M, Scheibel T. Self-assembly of nucleic acids, silk and hybrid materials thereof. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:503102. [PMID: 25419786 DOI: 10.1088/0953-8984/26/50/503102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Top-down approaches based on etching techniques have almost reached their limits in terms of dimension. Therefore, novel assembly strategies and types of nanomaterials are required to allow technological advances. Self-assembly processes independent of external energy sources and unlimited in dimensional scaling have become a very promising approach. Here,we highlight recent developments in self-assembled DNA-polymer, silk-polymer and silk-DNA hybrids as promising materials with biotic and abiotic moieties for constructing complex hierarchical materials in ‘bottom-up’ approaches. DNA block copolymers assemble into nanostructures typically exposing a DNA corona which allows functionalization, labeling and higher levels of organization due to its specific addressable recognition properties. In contrast, self-assembly of natural silk proteins as well as their recombinant variants yields mechanically stable β-sheet rich nanostructures. The combination of silk with abiotic polymers gains hybrid materials with new functionalities. Together, the precision of DNA hybridization and robustness of silk fibrillar structures combine in novel conjugates enable processing of higher-order structures with nanoscale architecture and programmable functions.
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22
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Heger Z, Kominkova M, Cernei N, Krejcova L, Kopel P, Zitka O, Adam V, Kizek R. Fluorescence resonance energy transfer between green fluorescent protein and doxorubicin enabled by DNA nanotechnology. Electrophoresis 2014; 35:3290-301. [DOI: 10.1002/elps.201400166] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 05/23/2014] [Accepted: 08/11/2014] [Indexed: 01/15/2023]
Affiliation(s)
- Zbynek Heger
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
| | - Marketa Kominkova
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
| | - Natalia Cernei
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Ludmila Krejcova
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
| | - Pavel Kopel
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
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23
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Fu J, Yang YR, Johnson-Buck A, Liu M, Liu Y, Walter NG, Woodbury NW, Yan H. Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm. NATURE NANOTECHNOLOGY 2014; 9:531-6. [PMID: 24859813 DOI: 10.1038/nnano.2014.100] [Citation(s) in RCA: 348] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 04/14/2014] [Indexed: 05/20/2023]
Abstract
Swinging arms are a key functional component of multistep catalytic transformations in many naturally occurring multi-enzyme complexes. This arm is typically a prosthetic chemical group that is covalently attached to the enzyme complex via a flexible linker, allowing the direct transfer of substrate molecules between multiple active sites within the complex. Mimicking this method of substrate channelling outside the cellular environment requires precise control over the spatial parameters of the individual components within the assembled complex. DNA nanostructures can be used to organize functional molecules with nanoscale precision and can also provide nanomechanical control. Until now, protein-DNA assemblies have been used to organize cascades of enzymatic reactions by controlling the relative distance and orientation of enzymatic components or by facilitating the interface between enzymes/cofactors and electrode surfaces. Here, we show that a DNA nanostructure can be used to create a multi-enzyme complex in which an artificial swinging arm facilitates hydride transfer between two coupled dehydrogenases. By exploiting the programmability of DNA nanostructures, key parameters including position, stoichiometry and inter-enzyme distance can be manipulated for optimal activity.
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Affiliation(s)
- Jinglin Fu
- 1] Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Center for Innovations in Medicine, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [3] [4]
| | - Yuhe Renee Yang
- 1] Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA [3]
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan at Ann Arbor, Ann Arbor, Michigan 48109, USA
| | - Minghui Liu
- 1] Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Yan Liu
- 1] Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan at Ann Arbor, Ann Arbor, Michigan 48109, USA
| | - Neal W Woodbury
- 1] Center for Innovations in Medicine, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Hao Yan
- 1] Center for Molecular Design and Biomimicry, Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA [2] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
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24
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Liu X, Lu CH, Willner I. Switchable reconfiguration of nucleic acid nanostructures by stimuli-responsive DNA machines. Acc Chem Res 2014; 47:1673-80. [PMID: 24654959 DOI: 10.1021/ar400316h] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CONSPECTUS: The base sequence in DNA dictates structural and reactivity features of the biopolymer. These properties are implemented to use DNA as a unique material for developing the area of DNA nanotechnology. The design of DNA machines represents a rapidly developing research field in the area of DNA nanotechnology. The present Account discusses the switchable reconfiguration of nucleic acid nanostructures by stimuli-responsive DNA machines, and it highlights potential applications and future perspectives of the area. Programmed switchable DNA machines driven by various fuels and antifuels, such as pH, Hg(2+) ions/cysteine, or nucleic acid strands/antistrands, are described. These include the assembly of DNA tweezers, walkers, a rotor, a pendulum, and more. Using a pH-oscillatory system, the oscillatory mechanical operation of a DNA pendulum is presented. Specifically, the synthesis and "mechanical" properties of interlocked DNA rings are described. This is exemplified with the preparation of interlocked DNA catenanes and a DNA rotaxane. The dynamic fuel-driven reconfiguration of the catenane/rotaxane structures is followed by fluorescence spectroscopy. The use of DNA machines as functional scaffolds to reconfigurate Au nanoparticle assemblies and to switch the fluorescence features within fluorophore/Au nanoparticle conjugates between quenching and surface-enhanced fluorescence states are addressed. Specifically, the fluorescence features of the different DNA machines are characterized as a function of the spatial separation between the fluorophore and Au nanoparticles. The experimental results are supported by theoretical calculations. The future development of reconfigurable stimuli-responsive DNA machines involves fundamental challenges, such as the synthesis of molecular devices exhibiting enhanced complexities, the introduction of new fuels and antifuels, and the integration of new payloads being reconfigured by the molecular devices, such as enzymes or catalytic nanoparticles. Exciting applications of these systems are ahead of us, and switchable catalytic nanoparticle systems, switchable enzyme cascades, and spatially programmed nanoparticles for innovative nanomedicine may be envisaged. Also, the intracellular reconfiguration of nucleic acids by stimuli-responsive DNA machines holds great promise as a means to silence genes or inhibit metabolic pathways.
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Affiliation(s)
- Xiaoqing Liu
- Institute of Chemistry, Center
for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Chun-Hua Lu
- Institute of Chemistry, Center
for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center
for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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25
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A protein adaptor to locate a functional protein dimer on molecular switchboard. Methods 2014; 67:142-50. [DOI: 10.1016/j.ymeth.2013.10.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 01/25/2023] Open
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26
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Zhou Z, Xiang Y, Tong A, Lu Y. Simple and efficient method to purify DNA-protein conjugates and its sensing applications. Anal Chem 2014; 86:3869-75. [PMID: 24605905 PMCID: PMC4004194 DOI: 10.1021/ac4040554] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 03/08/2014] [Indexed: 11/28/2022]
Abstract
DNA-protein conjugates are very useful in analytical chemistry for target recognition and signal amplification. While a number of methods for conjugating DNA with proteins are known, methods for purification of DNA-protein conjugates from reaction mixture containing unreacted proteins are much less investigated. In this work, a simple and efficient approach to purify DNA-invertase conjugates from reaction mixture via a biotin displacement strategy to release desthiobiotinylated DNA-invertase conjugates from streptavidin-coated magnetic beads was developed. The conjugates purified by this approach were utilized for quantitative detection of cocaine and DNA using a personal glucose meter through structure-switching DNA aptamer sensors and competitive DNA hybridization assays, respectively. In both cases, the purified DNA-invertase conjugates showed better performance compared to the same assays using unpurified conjugates. The approach demonstrated here can be further expanded to other DNA and proteins to generate purified DNA-protein conjugates for analytical and other applications.
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Affiliation(s)
- Zhaojuan Zhou
- Department of Chemistry, Key Laboratory
of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry
of Education), Beijing Key Laboratory for Microanalytical Methods
and Instrumentation, Tsinghua University, Beijing 100084, China
- Department of Chemistry and Beckman Institute
for Advanced Science and Technology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yu Xiang
- Department of Chemistry, Key Laboratory
of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry
of Education), Beijing Key Laboratory for Microanalytical Methods
and Instrumentation, Tsinghua University, Beijing 100084, China
- Department of Chemistry and Beckman Institute
for Advanced Science and Technology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Aijun Tong
- Department of Chemistry, Key Laboratory
of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry
of Education), Beijing Key Laboratory for Microanalytical Methods
and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Yi Lu
- Department of Chemistry and Beckman Institute
for Advanced Science and Technology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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27
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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28
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Humenik M, Scheibel T. Nanomaterial building blocks based on spider silk-oligonucleotide conjugates. ACS NANO 2014; 8:1342-1349. [PMID: 24405063 DOI: 10.1021/nn404916f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Self-assembling protein nanofibrils are promising structures for the "bottom-up" fabrication of bionanomaterials. Here, the recombinant protein eADF4(C16), a variant of Araneus diadematus dragline silk ADF4, which self-assembles into nanofibrils, and short oligonucleotides were modified for site-specific azide-alkyne coupling. Corresponding oligonuleotide-eADF4(C16) "click" conjugates were hybridized in linear or branched fashion according to the designed complementarities of the DNA moieties. Self-assembly properties of higher ordered structures of the spider silk-DNA conjugates were dominated by the silk component. Assembled β-sheet rich conjugate fibrils were similar in appearance to fibrils of unmodified eADF4(C16) but enabled the specific attachment of neutravidin-modified gold nanoparticles on their surface directed by complementary biotin-oligonucleotides, providing the basis for functionalization of such conjugates.
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Affiliation(s)
- Martin Humenik
- Lehrstuhl Biomaterialien, Fakultät für Ingenieurwissenschaften, Universität Bayreuth , Universitätsstraße 30, 95440 Bayreuth, Germany
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29
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Liu T, Chen X, Hong CY, Xu XP, Yang HH. Label-free and ultrasensitive electrochemiluminescence detection of microRNA based on long-range self-assembled DNA nanostructures. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1113-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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30
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Lu CH, Willner B, Willner I. DNA nanotechnology: from sensing and DNA machines to drug-delivery systems. ACS NANO 2013; 7:8320-8332. [PMID: 24070191 DOI: 10.1021/nn404613v] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
DNA/nanoparticle hybrid systems combine the unique electronic and optical properties of nanomaterials with the recognition and catalytic properties of nucleic acids. These materials hold great promise for the development of new sensing platforms, the programmed organization of nanoparticles, the switchable control of plasmonic phenomena in the nanostructures, and the controlled delivery of drugs. In this Perspective, we summarize recent advances in the application of DNA/nanoparticle (NP) hybrids in these different disciplines. Nucleic acid-semiconductor quantum dot hybrids are implemented to develop multiplexed sensing platforms for targeted DNA. The chemiluminescence resonance energy transfer mechanism is introduced as a new transduction signal, and the amplified detection of DNA targets through the biocatalytic regeneration of analytes is demonstrated. DNA machines consisting of catenanes or tweezers, and modified with fluorophore/Au NP pairs are used as functional devices for the switchable "mechanical" control of the fluorescence properties of the fluorophore. Also, nucleic acid nanostructures act as stimuli-responsive caps for trapping drugs in the pores of mesoporous SiO2 nanoparticles. In the presence of appropriate biomarker triggers, the pores are unlocked, leading to the controlled release of anticancer drugs. Selective cancer-cell death is demonstrated with the stimuli-responsive SiO2 nanoparticles.
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Affiliation(s)
- Chun-Hua Lu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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31
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Muscat RA, Strauss K, Ceze L, Seelig G. DNA-based molecular architecture with spatially localized components. ACTA ACUST UNITED AC 2013. [DOI: 10.1145/2508148.2485938] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Performing computation inside living cells offers life-changing applications, from improved medical diagnostics to better cancer therapy to intelligent drugs. Due to its bio-compatibility and ease of engineering, one promising approach for performing in-vivo computation is DNA strand displacement. This paper introduces computer architects to DNA strand displacement "circuits", discusses associated architectural challenges, and proposes a new organization that provides practical composability. In particular, prior approaches rely mostly on stochastic interaction of freely diffusing components. This paper proposes practical
spatial
isolation of components, leading to more easily designed DNA-based circuits. DNA nanotechnology is currently at a turning point, with many proposed applications being realized [20, 9]. We believe that it is time for the computer architecture community to take notice and contribute.
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32
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Hirakawa H, Kakitani A, Nagamune T. Introduction of selective intersubunit disulfide bonds into self-assembly protein scaffold to enhance an artificial multienzyme complex's activity. Biotechnol Bioeng 2013; 110:1858-64. [DOI: 10.1002/bit.24861] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/24/2013] [Accepted: 01/28/2013] [Indexed: 11/09/2022]
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33
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Abstract
The folding of various intra- and intermolecular i-motif DNAs is systematically studied to expand the toolbox for the control of mechanical operations in DNA nanoarchitectures. We analyzed i-motif DNAs with two C-tracts under acidic conditions by gel electrophoresis, circular dichroism, and thermal denaturation and show that their intra- versus intermolecular folding primarily depends on the length of the C-tracts. Two stretches of six or fewer C-residues favor the intermolecular folding of i-motifs, whereas longer C-tracts promote the formation of intramolecular i-motif structures with unusually high thermal stability. We then introduced intra- and intermolecular i-motifs formed by DNAs containing two C-tracts into single-stranded regions within otherwise double-stranded DNA nanocircles. By adjusting the length of C-tracts we can control the intra- and intermolecular folding of i-motif DNAs and achieve programmable functionalization of dsDNA nanocircles. Single-stranded gaps in the nanocircle that are functionalized with an intramolecular i-motif enable the reversible contraction and extension of the DNA circle, as monitored by fluorescence quenching. Thereby, the nanocircle behaves as a proton-fueled DNA prototype machine. In contrast, nanorings containing intermolecular i-motifs induce the assembly of defined multicomponent DNA architectures in response to proton-triggered predicted structural changes, such as dimerization, "kiss", and cyclization. The resulting DNA nanostructures are verified by gel electrophoresis and visualized by atomic force microscopy, including different folding topologies of an intermolecular i-motif. The i-motif-functionalized DNA nanocircles may serve as a versatile tool for the formation of larger interlocked dsDNA nanostructures, like rotaxanes and catenanes, to achieve diverse mechanical operations.
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Affiliation(s)
- Tao Li
- Life and Medical Science (LIMES) Institute, Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
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34
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Chen X, Hong CY, Lin YH, Chen JH, Chen GN, Yang HH. Enzyme-Free and Label-Free Ultrasensitive Electrochemical Detection of Human Immunodeficiency Virus DNA in Biological Samples Based on Long-Range Self-Assembled DNA Nanostructures. Anal Chem 2012; 84:8277-83. [DOI: 10.1021/ac3017828] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Xian Chen
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Cheng-Yi Hong
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Ya-Hui Lin
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Jing-Hua Chen
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350004, China
| | - Guo-Nan Chen
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Huang-Hao Yang
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
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35
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Fu J, Liu M, Liu Y, Yan H. Spatially-interactive biomolecular networks organized by nucleic acid nanostructures. Acc Chem Res 2012; 45:1215-26. [PMID: 22642503 DOI: 10.1021/ar200295q] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Living systems have evolved a variety of nanostructures to control the molecular interactions that mediate many functions including the recognition of targets by receptors, the binding of enzymes to substrates, and the regulation of enzymatic activity. Mimicking these structures outside of the cell requires methods that offer nanoscale control over the organization of individual network components. Advances in DNA nanotechnology have enabled the design and fabrication of sophisticated one-, two- and three-dimensional (1D, 2D, and 3D) nanostructures that utilize spontaneous and sequence-specific DNA hybridization. Compared with other self-assembling biopolymers, DNA nanostructures offer predictable and programmable interactions and surface features to which other nanoparticles and biomolecules can be precisely positioned. The ability to control the spatial arrangement of the components while constructing highly organized networks will lead to various applications of these systems. For example, DNA nanoarrays with surface displays of molecular probes can sense noncovalent hybridization interactions with DNA, RNA, and proteins and covalent chemical reactions. DNA nanostructures can also align external molecules into well-defined arrays, which may improve the resolution of many structural determination methods, such as X-ray diffraction, cryo-EM, NMR, and super-resolution fluorescence. Moreover, by constraint of target entities to specific conformations, self-assembled DNA nanostructures can serve as molecular rulers to evaluate conformation-dependent activities. This Account describes the most recent advances in the DNA nanostructure directed assembly of biomolecular networks and explores the possibility of applying this technology to other fields of study. Recently, several reports have demonstrated the DNA nanostructure directed assembly of spatially interactive biomolecular networks. For example, researchers have constructed synthetic multienzyme cascades by organizing the position of the components using DNA nanoscaffolds in vitro or by utilizing RNA matrices in vivo. These structures display enhanced efficiency compared with the corresponding unstructured enzyme mixtures. Such systems are designed to mimic cellular function, where substrate diffusion between enzymes is facilitated and reactions are catalyzed with high efficiency and specificity. In addition, researchers have assembled multiple choromophores into arrays using a DNA nanoscaffold that optimizes the relative distance between the dyes and their spatial organization. The resulting artificial light-harvesting system exhibits efficient cascading energy transfers. Finally, DNA nanostructures have been used as assembly templates to construct nanodevices that execute rationally designed behaviors, including cargo loading, transportation, and route control.
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Affiliation(s)
- Jinglin Fu
- Center for Single Molecule Biophysics, ‡Center for Innovations in Medicine at the Biodesign Institute, and §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Minghui Liu
- Center for Single Molecule Biophysics, ‡Center for Innovations in Medicine at the Biodesign Institute, and §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Single Molecule Biophysics, ‡Center for Innovations in Medicine at the Biodesign Institute, and §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Single Molecule Biophysics, ‡Center for Innovations in Medicine at the Biodesign Institute, and §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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36
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Hötzer B, Medintz IL, Hildebrandt N. Fluorescence in nanobiotechnology: sophisticated fluorophores for novel applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:2297-326. [PMID: 22678833 DOI: 10.1002/smll.201200109] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 02/22/2012] [Indexed: 05/26/2023]
Abstract
Nanobiotechnology is one of the fastest growing and broadest-ranged interdisciplinary subfields of the nanosciences. Countless hybrid bio-inorganic composites are currently being pursued for various uses, including sensors for medical and diagnostic applications, light- and energy-harvesting devices, along with multifunctional architectures for electronics and advanced drug-delivery. Although many disparate biological and nanoscale materials will ultimately be utilized as the functional building blocks to create these devices, a common element found among a large proportion is that they exert or interact with light. Clearly continuing development will rely heavily on incorporating many different types of fluorophores into these composite materials. This review covers the growing utility of different classes of fluorophores in nanobiotechnology, from both a photophysical and a chemical perspective. For each major structural or functional class of fluorescent probe, several representative applications are provided, and the necessary technological background for acquiring the desired nano-bioanalytical information are presented.
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Affiliation(s)
- Benjamin Hötzer
- NanoBioPhotonics, Institut d'Electronique Fondamentale, Université Paris-Sud, 91405 Orsay Cedex, France
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Li T, Ackermann D, Hall AM, Famulok M. Input-dependent induction of oligonucleotide structural motifs for performing molecular logic. J Am Chem Soc 2012; 134:3508-16. [PMID: 22296341 PMCID: PMC3284195 DOI: 10.1021/ja2108883] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The K(+)-H(+)-triggered structural conversion of multiple nucleic acid helices involving duplexes, triplexes, G-quadruplexes, and i-motifs is studied by gel electrophoresis, circular dichroism, and thermal denaturation. We employ the structural interconversions for perfoming molecular logic operations, as verified by fluorimetry and colorimetry. Short G-rich and C-rich cDNA and RNA single strands are hybridized to produce four A-form and B-form duplexes. Addition of K(+) triggers the unwinding of the duplexes by inducing the folding of G-rich strands into DNA- or RNA G-quadruplex mono- and multimers, respectively. We found a decrease in pH to have different consequences on the resulting structural output, depending on whether the C-rich strand is DNA or RNA: while the protonated C-rich DNA strand folds into at least two isomers of a stable i-motif structure, the protonated C-rich RNA strand binds a DNA/RNA hybrid duplex to form a Y·RY parallel triplex. When using K(+) and H(+) as external stimuli, or inputs, and the induced G-quadruplexes as reporters, these structural interconversions of nucleic acid helices can be employed for performing logic-gate operations. The signaling mode for detecting these conversions relies on complex formation between DNA or RNA G-quadruplexes (G4) and the cofactor hemin. The G4/hemin complexes catalyze the H(2)O(2)-mediated oxidation of peroxidase substrates, resulting in a fluorescence or color change. Depending on the nature of the respective peroxidase substrate, distinct output signals can be generated, allowing one to operate multiple logic gates such as NOR, INH, or AND.
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Affiliation(s)
- Tao Li
- Life and Medical Science Institute, Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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Nakata E, Liew FF, Uwatoko C, Kiyonaka S, Mori Y, Katsuda Y, Endo M, Sugiyama H, Morii T. Zinc-Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108199] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Nakata E, Liew FF, Uwatoko C, Kiyonaka S, Mori Y, Katsuda Y, Endo M, Sugiyama H, Morii T. Zinc-Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures. Angew Chem Int Ed Engl 2012; 51:2421-4. [DOI: 10.1002/anie.201108199] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/27/2011] [Indexed: 01/22/2023]
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Shimada J, Maruyama T, Kitaoka M, Yoshinaga H, Nakano K, Kamiya N, Goto M. Programmable protein–protein conjugation via DNA-based self-assembly. Chem Commun (Camb) 2012; 48:6226-8. [DOI: 10.1039/c2cc30618b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Laisne A, Ewald M, Ando T, Lesniewska E, Pompon D. Self-Assembly Properties and Dynamics of Synthetic Proteo–Nucleic Building Blocks in Solution and on Surfaces. Bioconjug Chem 2011; 22:1824-34. [DOI: 10.1021/bc2002264] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aude Laisne
- Centre de Génétique Moléculaire, CNRS, UPR3404, Avenue de la Terrasse, F91190 Gif-sur-Yvette, France
| | - Maxime Ewald
- Institut Carnot Bourgogne, UMR CNRS 5209, University of Bourgogne, F21078 Dijon, France
| | - Toshio Ando
- Department of Physics, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Eric Lesniewska
- Institut Carnot Bourgogne, UMR CNRS 5209, University of Bourgogne, F21078 Dijon, France
| | - Denis Pompon
- Centre de Génétique Moléculaire, CNRS, UPR3404, Avenue de la Terrasse, F91190 Gif-sur-Yvette, France
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Szilvay GR, Brocato S, Ivnitski D, Li C, Iglesia PDL, Lau C, Chi E, Werner-Washburne M, Banta S, Atanassov P. Engineering of a redox protein for DNA-directed assembly. Chem Commun (Camb) 2011; 47:7464-6. [DOI: 10.1039/c1cc11951f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Saccà B, Niemeyer CM. Functionalization of DNA nanostructures with proteins. Chem Soc Rev 2011; 40:5910-21. [DOI: 10.1039/c1cs15212b] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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