201
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Yu Y, Jin B, Li Y, Deng Z. Stimuli-Responsive DNA Self-Assembly: From Principles to Applications. Chemistry 2019; 25:9785-9798. [PMID: 30931536 DOI: 10.1002/chem.201900491] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Indexed: 01/01/2023]
Abstract
Stimuli-responsive DNA self-assembly shares the advantages of both designed stimuli-responsiveness and the molecular programmability of DNA structures, offering great opportunities for basic and applied research in dynamic DNA nanotechnology. In this minireview, we summarize the most recent progress in this rapidly developing field. The trigger mechanisms of the responsive DNA systems are first divided into six categories, which are then explained with illustrative examples following this classification. Subsequently, proof-of-concept applications in terms of biosensing, in vivo pH-mapping, drug delivery, and therapy are discussed. Finally, we provide some remarks on the challenges and opportunities of this highly promising research direction in DNA nanotechnology.
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Affiliation(s)
- Yang Yu
- Anhui Province Key Laboratory of Advanced Catalytic Materials, and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Bang Jin
- Anhui Province Key Laboratory of Advanced Catalytic Materials, and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials, and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, China
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202
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Kim J, Narayana A, Patel S, Sahay G. Advances in intracellular delivery through supramolecular self-assembly of oligonucleotides and peptides. Theranostics 2019; 9:3191-3212. [PMID: 31244949 PMCID: PMC6567962 DOI: 10.7150/thno.33921] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
Cells utilize natural supramolecular assemblies to maintain homeostasis and biological functions. Naturally inspired modular assembly of biomaterials are now being exploited for understanding or manipulating cell biology for treatment, diagnosis, and detection of diseases. Supramolecular biomaterials, in particular peptides and oligonucleotides, can be precisely tuned to have diverse structural, mechanical, physicochemical and biological properties. These merits of oligonucleotides and peptides as building blocks have given rise to the evolution of numerous nucleic acid- and peptide-based self-assembling nanomaterials for various medical applications, including drug delivery, tissue engineering, regenerative medicine, and immunotherapy. In this review, we provide an extensive overview of the intracellular delivery approaches using supramolecular self-assembly of DNA, RNA, and peptides. Furthermore, we discuss the current challenges related to subcellular delivery and provide future perspectives of the application of supramolecular biomaterials for intracellular delivery in theranostics.
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Affiliation(s)
- Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
| | - Ashwanikumar Narayana
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
| | - Siddharth Patel
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
- Department of Biomedical Engineering, Robertson Life Sciences Building, Oregon Health Science University, Portland, OR
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203
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Abstract
Many biochemical events of importance are complex and dynamic. Fluorescence microscopy offers a versatile solution to study the dynamics of biology at the mesoscale. An important challenge in the field is the simultaneous study of several objects of interest, referred to as optical multiplexing. For improved multiplexing, some prior techniques used repeated reporter washing or the geometry of nanostructures; however, these techniques require complex nanostructure assembly, multiple reporters, or advanced multistep drift correction. Here we propose a time-based approach, for improved optical multiplexing, that uses readily available inexpensive reporters and requires minimal preparation efforts. We program short DNA strands, referred hereby as DNA devices, such that they undergo unique conformation changes in the presence of the dye-labeled reporters. The universal fluorescent reporter transiently binds with the devices to report their activity. Since each device is programmed to exhibit different hybridization kinetics, their fluorescent time trace, referred to as the temporal barcode, will be unique. We model our devices using continuous-time Markov chains and use stochastic simulation algorithm to generate their temporal patterns. We first ran simulation experiments with a small number of DNA devices, demonstrating several distinct temporal barcodes, all of which use a single dye color. Later, using nanostructure-based devices, we designed a much larger pool of temporal barcodes and used machine learning for classification of these barcodes. Our simulation experiments and design principles can aid in the experimental demonstration of the DNA devices.
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Affiliation(s)
- Shalin Shah
- Department of Electrical & Computer Engineering, Duke University, Durham, North Carolina 27701, United States
| | - Abhishek K. Dubey
- Department of Computer Science, Duke University, Durham, North Carolina 27701, United States
- Computational Sciences and Engineering Division, Health Data Sciences Institute, Oak Ridge National Lab, Oak Ridge, Tennessee 37831, United States
| | - John Reif
- Department of Electrical & Computer Engineering, Duke University, Durham, North Carolina 27701, United States
- Department of Computer Science, Duke University, Durham, North Carolina 27701, United States
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204
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Liu S, Jiang Q, Wang Y, Ding B. Biomedical Applications of DNA-Based Molecular Devices. Adv Healthc Mater 2019; 8:e1801658. [PMID: 30938489 DOI: 10.1002/adhm.201801658] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/01/2019] [Indexed: 11/11/2022]
Abstract
Strict Watson-Crick base pairing and availability by automated synthesis have allowed deoxyribonucleic acid (DNA) molecules to be used as engineerable building blocks for constructing versatile nanostructures. In recent decades, with the development of DNA nanotechnology, a range of DNA-based dynamic molecular devices with sophisticated nanostructures have been designed and constructed. Featuring programmability and biocompatibility, the applications of DNA-based nanodevices have been extensively focused on the interfaces of biological systems. This review summarizes the recent progress in the design of DNA devices exhibiting programmable functions for biomedical applications. In vitro and in vivo applications of DNA-based nanodevices in cellular imaging and systemic drug delivery are highlighted. The challenges and open opportunities are also discussed.
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Affiliation(s)
- Shaoli Liu
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationCAS Center for Excellence in NanoscienceNational Center for NanoScience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationCAS Center for Excellence in NanoscienceNational Center for NanoScience and Technology Beijing 100190 China
| | - Yuanning Wang
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationCAS Center for Excellence in NanoscienceNational Center for NanoScience and Technology Beijing 100190 China
- Northeast Electric Power University Jilin 132012 China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical FabricationCAS Center for Excellence in NanoscienceNational Center for NanoScience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- School of Materials Science and EngineeringZhengzhou University Zhengzhou 450001 China
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205
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Jeon I, Peeks MD, Savagatrup S, Zeininger L, Chang S, Thomas G, Wang W, Swager TM. Janus Graphene: Scalable Self-Assembly and Solution-Phase Orthogonal Functionalization. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1900438. [PMID: 30968473 DOI: 10.1002/adma.201900438] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/11/2019] [Indexed: 06/09/2023]
Abstract
Orthogonal functionalization of 2D materials by selective assembly at interfaces provides opportunities to create new materials with transformative properties. Challenges remain in realizing controllable, scalable surface-selective, and orthogonal functionalization. Herein, dynamic covalent assembly is reported that directs the functionalization of graphene surfaces at liquid-liquid interfaces. This process allows facile addition and segregation of chemical functionalities to impart Janus characteristics to graphenes. Specifically, dynamic covalent functionalization is accomplished via Meisenheimer complexes produced by reactions of primary amines with pendant dinitroaromatics attached to graphenes. Janus graphenes are demonstrated to be powerful surfactants that organize at water/organic, water/fluorocarbon, and organic/fluorocarbon liquid interfaces. This approach provides general access to the creation of diverse surfactant materials and promising building blocks for 2D materials.
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Affiliation(s)
- Intak Jeon
- Department of Chemistry, Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Martin D Peeks
- Department of Chemistry, Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Suchol Savagatrup
- Department of Chemistry, Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lukas Zeininger
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sehoon Chang
- Aramco Services Company, Aramco Research Center-Boston, Cambridge, MA, 02139, USA
| | - Gawain Thomas
- Aramco Services Company, Aramco Research Center-Boston, Cambridge, MA, 02139, USA
| | - Wei Wang
- Aramco Services Company, Aramco Research Center-Boston, Cambridge, MA, 02139, USA
| | - Timothy M Swager
- Department of Chemistry, Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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206
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Yu J, Wang Y, Zhao C, Chen S, Zhang S. A 3D molecular cantilever based on interfacial self-assembly and the cobra-like actuation of long-chain imidazolium ionic liquids. NANOSCALE 2019; 11:7277-7286. [PMID: 30932116 DOI: 10.1039/c8nr08824a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cantilever structures usually function as a key building block in the construction of supramolecular systems. In this work, based on the controllable interfacial self-assembly of monolayer long-chain imidazolium ionic liquids (ILs) on multi-walled carbon nanotubes, we design a 3D molecular cantilever with advantages including facile assembly, multi-mechanism actuation and high scalability. Molecular dynamics simulations predict that the lifting of the cation alkyl chain as a cantilever possesses a cobra-like actuation mechanism, including structure-induced and environmental response effects, which is further verified via experimental observations. On one hand, regulating the internal alkyl chain units results in the regular variation of the cantilever tilt angle with respect to the surface; on the other hand, applying external electric fields with various strengths/directions can also drive the cantilever to rise or fall. As expected, the interfacial self-assembly structure of the molecular cantilever directionally induces a change in the phase transition behaviour, delivering significantly enhanced thermal stability for immobilized ILs compared with the bulk state.
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Affiliation(s)
- Jia Yu
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China.
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207
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Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetische DNA‐Nanoröhren: Gezielte Synthese und Anwendung nanoskopischer Kanäle. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
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208
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Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetic DNA Nanotubes: Nanoscale Channel Design and Applications. Angew Chem Int Ed Engl 2019; 58:8996-9011. [PMID: 30290046 DOI: 10.1002/anie.201807779] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/25/2018] [Indexed: 01/04/2023]
Abstract
Biomacromolecular nanotubes play important physiological roles in transmembrane ion/molecule channeling, intracellular transport, and inter-cellular communications. While genetically encoded protein nanotubes are prevalent in vivo, the in vitro construction of biomimetic DNA nanotubes has attracted intense interest with the rise of structural DNA nanotechnology. The abiotic use of DNA assembly provides a powerful bottom-up approach for the rational construction of complex materials with arbitrary size and shape at the nanoscale. More specifically, a typical DNA nanotube can be assembled either with parallel-aligned DNA duplexes or by closing DNA tile lattices. These artificial DNA nanotubes can be tailored and site-specifically modified to realize biomimetic functions including ionic or molecular channeling, bioreactors, drug delivery, and biomolecular sensing. In this Minireview, we aim to summarize recent advances in design strategies, including the characterization and applications of biomimetic DNA nanotubes.
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Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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209
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Wang SS, Ellington AD. Pattern Generation with Nucleic Acid Chemical Reaction Networks. Chem Rev 2019; 119:6370-6383. [DOI: 10.1021/acs.chemrev.8b00625] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Siyuan S. Wang
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
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210
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Kim YY, Bang Y, Lee AH, Song YK. Multivalent Traptavidin-DNA Conjugates for the Programmable Assembly of Nanostructures. ACS NANO 2019; 13:1183-1194. [PMID: 30654610 DOI: 10.1021/acsnano.8b06170] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Here, we explore the extended utility of two important functional biomolecules, DNA and protein, by hybridizing them through avidin-biotin conjugation. We report a simple yet scalable technique of successive magnetic separations to synthesize traptavidin-DNA conjugates with four distinct DNA binding sites that can be used as a supramolecular building block for programmable assembly of nanostructures. Using this nanoassembly platform, we fabricate several different plasmonic nanostructures with various metallic as well as semiconductor nanoparticles in predetermined ways. We also use the platform to construct dendrimer nanostructures using valency-controlled traptavidin-DNA conjugates in a programmable manner. These results suggest that our protein-DNA supramolecular building blocks would make a significant contribution to the assembly of multicomponent and complex nanostructures for numerous contemporary and future applications from molecular imaging to drug delivery.
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Affiliation(s)
- Young-Youb Kim
- Graduate School of Convergence Science and Technology , Seoul National University , Seoul 08826 , South Korea
| | - Yongbin Bang
- Graduate School of Convergence Science and Technology , Seoul National University , Seoul 08826 , South Korea
| | - Ah-Hyoung Lee
- Graduate School of Convergence Science and Technology , Seoul National University , Seoul 08826 , South Korea
| | - Yoon-Kyu Song
- Graduate School of Convergence Science and Technology , Seoul National University , Seoul 08826 , South Korea
- Advanced Institutes of Convergence Technology , Suwon , Gyeonggi-do 16229 , South Korea
- Inter-university Semiconductor Research Center (ISRC) , Seoul National University , Seoul 08826 , South Korea
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211
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Özkale B, Parreira R, Bekdemir A, Pancaldi L, Özelçi E, Amadio C, Kaynak M, Stellacci F, Mooney DJ, Sakar MS. Modular soft robotic microdevices for dexterous biomanipulation. LAB ON A CHIP 2019; 19:778-788. [PMID: 30714604 PMCID: PMC6394202 DOI: 10.1039/c8lc01200h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/18/2019] [Indexed: 05/20/2023]
Abstract
We present a methodology for building biologically inspired, soft microelectromechanical systems (MEMS) devices. Our strategy combines several advanced techniques including programmable colloidal self-assembly, light-harvesting with plasmonic nanotransducers, and in situ polymerization of compliant hydrogel mechanisms. We synthesize optomechanical microactuators using a template-assisted microfluidic approach in which gold nanorods coated with thermoresponsive poly(N-isopropylmethacrylamide) (pNIPMAM) polymer function as nanoscale building blocks. The resulting microactuators exhibit mechanical properties (4.8 ± 2.1 kPa stiffness) and performance metrics (relative stroke up to 0.3 and stress up to 10 kPa) that are comparable to that of bioengineered muscular constructs. Near-infrared (NIR) laser illumination provides effective spatiotemporal control over actuation (sub-micron spatial resolution at millisecond temporal resolution). Spatially modulated hydrogel photolithography guided by an experimentally validated finite element-based design methodology allows construction of compliant poly(ethylene glycol) diacrylate (PEGDA) mechanisms around the microactuators. We demonstrate the versatility of our approach by manufacturing a diverse array of microdevices including lever arms, continuum microrobots, and dexterous microgrippers. We present a microscale compression device that is developed for mechanical testing of three-dimensional biological samples such as spheroids under physiological conditions.
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Affiliation(s)
- Berna Özkale
- Institute of Mechanical Engineering and Institute of Bioengineering
, Ecole Polytechnique Federale de Lausanne (EPFL)
,
CH-1015 Lausanne
, Switzerland
.
- Wyss Institute of Biologically Inspired Engineering
, School of Engineering and Applied Sciences
, Harvard University
,
Massachusetts 02138
, USA
| | - Raquel Parreira
- Institute of Mechanical Engineering and Institute of Bioengineering
, Ecole Polytechnique Federale de Lausanne (EPFL)
,
CH-1015 Lausanne
, Switzerland
.
| | - Ahmet Bekdemir
- Institute of Materials Science and Engineering
, EPFL
,
CH-1015 Lausanne
, Switzerland
| | - Lucio Pancaldi
- Institute of Mechanical Engineering and Institute of Bioengineering
, Ecole Polytechnique Federale de Lausanne (EPFL)
,
CH-1015 Lausanne
, Switzerland
.
| | - Ece Özelçi
- Institute of Mechanical Engineering and Institute of Bioengineering
, Ecole Polytechnique Federale de Lausanne (EPFL)
,
CH-1015 Lausanne
, Switzerland
.
| | - Claire Amadio
- Institute of Mechanical Engineering and Institute of Bioengineering
, Ecole Polytechnique Federale de Lausanne (EPFL)
,
CH-1015 Lausanne
, Switzerland
.
| | - Murat Kaynak
- Institute of Mechanical Engineering and Institute of Bioengineering
, Ecole Polytechnique Federale de Lausanne (EPFL)
,
CH-1015 Lausanne
, Switzerland
.
| | - Francesco Stellacci
- Institute of Materials Science and Engineering
, EPFL
,
CH-1015 Lausanne
, Switzerland
| | - David J. Mooney
- Wyss Institute of Biologically Inspired Engineering
, School of Engineering and Applied Sciences
, Harvard University
,
Massachusetts 02138
, USA
| | - Mahmut Selman Sakar
- Institute of Mechanical Engineering and Institute of Bioengineering
, Ecole Polytechnique Federale de Lausanne (EPFL)
,
CH-1015 Lausanne
, Switzerland
.
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212
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Smith KB, Tisserant J, Assenza S, Arcari M, Nyström G, Mezzenga R. Confinement-Induced Ordering and Self-Folding of Cellulose Nanofibrils. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1801540. [PMID: 30828528 PMCID: PMC6382315 DOI: 10.1002/advs.201801540] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/02/2018] [Indexed: 05/19/2023]
Abstract
Cellulose is a pervasive polymer, displaying hierarchical lengthscales and exceptional strength and stiffness. Cellulose's complex organization, however, also hinders the detailed understanding of the assembly, mesoscopic properties, and structure of individual cellulose building blocks. This study combines nanolithography with atomic force microscopy to unveil the properties and structure of single cellulose nanofibrils under weak geometrical confinement. By statistical analysis of the fibril morphology, it emerges that confinement induces both orientational ordering and self-folding of the fibrils. Excluded volume simulations reveal that this effect does not arise from a fibril population bias applied by the confining slit, but rather that the fibril conformation itself changes under confinement, with self-folding favoring fibril's free volume entropy. Moreover, a nonstochastics angular bending probability of the fibril kinks is measured, ruling out alternating amorphous-crystalline regions. These findings push forward the understanding of cellulose nanofibrils and may inspire the design of functional materials based on fibrous templates.
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Affiliation(s)
- Kathleen Beth Smith
- Department of Health Sciences and TechnologySwiss Federal Institute of Technology in Zurich8092ZurichSwitzerland
| | - Jean‐Nicolas Tisserant
- Nanotechnology GroupSwiss Federal Institute of Technology in Zurich8803RüschlikonSwitzerland
- Institute for High Frequency TechnologyBraunschweig University of Technology38106BraunschweigGermany
| | - Salvatore Assenza
- Department of Health Sciences and TechnologySwiss Federal Institute of Technology in Zurich8092ZurichSwitzerland
| | - Mario Arcari
- Department of Health Sciences and TechnologySwiss Federal Institute of Technology in Zurich8092ZurichSwitzerland
| | - Gustav Nyström
- Department of Health Sciences and TechnologySwiss Federal Institute of Technology in Zurich8092ZurichSwitzerland
- Laboratory for Applied Wood MaterialsEmpa8600DuebendorfSwitzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and TechnologySwiss Federal Institute of Technology in Zurich8092ZurichSwitzerland
- Department of MaterialsSwiss Federal Institute of Technology8093ZurichSwitzerland
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213
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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214
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Yang GZ, Full RJ, Jacobstein N, Fischer P, Bellingham J, Choset H, Christensen H, Dario P, Nelson BJ, Taylor R. Ten robotics technologies of the year. Sci Robot 2019; 4:4/26/eaaw1826. [DOI: 10.1126/scirobotics.aaw1826] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 12/21/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Guang-Zhong Yang
- James Bellingham is the Director of the Center for Marine Robotics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Howie Choset is a Professor at Carnegie Mellon University and the Robotics Institute, Pittsburgh, PA, USA
| | - Robert J. Full
- James Bellingham is the Director of the Center for Marine Robotics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Howie Choset is a Professor at Carnegie Mellon University and the Robotics Institute, Pittsburgh, PA, USA
| | - Neil Jacobstein
- James Bellingham is the Director of the Center for Marine Robotics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Howie Choset is a Professor at Carnegie Mellon University and the Robotics Institute, Pittsburgh, PA, USA
| | - Peer Fischer
- James Bellingham is the Director of the Center for Marine Robotics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Howie Choset is a Professor at Carnegie Mellon University and the Robotics Institute, Pittsburgh, PA, USA
| | - James Bellingham
- James Bellingham is the Director of the Center for Marine Robotics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Howie Choset is a Professor at Carnegie Mellon University and the Robotics Institute, Pittsburgh, PA, USA
| | - Howie Choset
- James Bellingham is the Director of the Center for Marine Robotics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Howie Choset is a Professor at Carnegie Mellon University and the Robotics Institute, Pittsburgh, PA, USA
| | - Henrik Christensen
- James Bellingham is the Director of the Center for Marine Robotics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Howie Choset is a Professor at Carnegie Mellon University and the Robotics Institute, Pittsburgh, PA, USA
| | - Paolo Dario
- James Bellingham is the Director of the Center for Marine Robotics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Howie Choset is a Professor at Carnegie Mellon University and the Robotics Institute, Pittsburgh, PA, USA
| | - Bradley J. Nelson
- James Bellingham is the Director of the Center for Marine Robotics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Howie Choset is a Professor at Carnegie Mellon University and the Robotics Institute, Pittsburgh, PA, USA
| | - Russell Taylor
- James Bellingham is the Director of the Center for Marine Robotics, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Howie Choset is a Professor at Carnegie Mellon University and the Robotics Institute, Pittsburgh, PA, USA
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215
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Kroener F, Traxler L, Heerwig A, Rant U, Mertig M. Magnesium-Dependent Electrical Actuation and Stability of DNA Origami Rods. ACS APPLIED MATERIALS & INTERFACES 2019; 11:2295-2301. [PMID: 30584763 DOI: 10.1021/acsami.8b18611] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Dynamic methods of biosensing based on electrical actuation of surface-tethered nanolevers require the use of levers whose movement in ionic liquids is well controllable and stable. In particular, mechanical integrity of the nanolevers in a wide range of ionic strengths will enable to meet the chemical conditions of a large variety of applications where the specific binding of biomolecular analytes is analyzed. Herein, we study the electrically induced switching behavior of different rodlike DNA origami nanolevers and compare to the actuation of simply double-stranded DNA nanolevers. Our measurements reveal a significantly stronger response of the DNA origami to switching of electrode potential, leading to a smaller potential change necessary to actuate the origami and subsequently to a long-term stable movement. Dynamic measurements in buffer solutions with different Mg2+ contents show that the levers do not disintegrate even at very low ion concentrations and constant switching stress and thus provide stable actuation performance. The latter will pave the way for many new applications without largely restricting application-specific environments.
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Affiliation(s)
- Felix Kroener
- Professur für Physikalische Chemie, Mess- und Sensortechnik , Technische Universität Dresden , 01062 Dresden , Germany
- Dynamic Biosensors GmbH , 82152 Planegg , Germany
| | | | - Andreas Heerwig
- Kurt-Schwabe-Institut für Mess- und Sensortechnik e.V. Meinsberg , 04736 Waldheim , Germany
| | - Ulrich Rant
- Dynamic Biosensors GmbH , 82152 Planegg , Germany
| | - Michael Mertig
- Professur für Physikalische Chemie, Mess- und Sensortechnik , Technische Universität Dresden , 01062 Dresden , Germany
- Kurt-Schwabe-Institut für Mess- und Sensortechnik e.V. Meinsberg , 04736 Waldheim , Germany
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216
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Jun H, Zhang F, Shepherd T, Ratanalert S, Qi X, Yan H, Bathe M. Autonomously designed free-form 2D DNA origami. SCIENCE ADVANCES 2019; 5:eaav0655. [PMID: 30613779 PMCID: PMC6314877 DOI: 10.1126/sciadv.aav0655] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/21/2018] [Indexed: 05/20/2023]
Abstract
Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands needed to fold the long scaffold strand to the target geometry is typically performed manually, limiting the broad application of this materials design paradigm. Here, we present a fully autonomous procedure to design all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami wireframe object. Our algorithm uses wireframe edges consisting of two parallel DNA duplexes and enables the full autonomy of scaffold routing and staple sequence design with arbitrary network edge lengths and vertex angles. The application of our procedure to geometries with both regular and irregular external boundaries and variable internal structures demonstrates its broad utility for nanoscale materials science and nanotechnology.
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Affiliation(s)
- Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Fei Zhang
- The Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Tyson Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Xiaodong Qi
- The Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Hao Yan
- The Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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217
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Li Y, Wang Q, Zhang L, Hu S, Chen L, He P, Feng H, Zhang J, Ji H, Ma X, Li K, Zhao W. Self-assembly of nickel: from nanoparticles to foils with tunable magnetic properties. CrystEngComm 2019. [DOI: 10.1039/c9ce00940j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Self-assembly of nickel from nanoparticles to nanowires and foils can be achieved by controlling the concentrations of sodium citrate during the electroless deposition process.
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218
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Suo Z, Chen J, Hou X, Hu Z, Xing F, Feng L. Growing prospects of DNA nanomaterials in novel biomedical applications. RSC Adv 2019; 9:16479-16491. [PMID: 35516377 PMCID: PMC9064466 DOI: 10.1039/c9ra01261c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/07/2019] [Indexed: 01/01/2023] Open
Abstract
As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications. Recent progress in DNA-based nanomaterials is summarized, ranging from applications in biosensors, biomedicine/imaging, and molecular logic gates to emerging nanomachines, as well as future perspective discussions.![]()
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Affiliation(s)
- Zhiguang Suo
- Materials Genome Institute
- Shanghai University
- Shanghai 200444
- China
| | - Jingqi Chen
- Materials Genome Institute
- Shanghai University
- Shanghai 200444
- China
| | - Xialing Hou
- Materials Genome Institute
- Shanghai University
- Shanghai 200444
- China
| | - Ziheng Hu
- Materials Genome Institute
- Shanghai University
- Shanghai 200444
- China
| | - Feifei Xing
- Department of Chemistry
- College of Science
- Shanghai University
- Shanghai 200444
- China
| | - Lingyan Feng
- Materials Genome Institute
- Shanghai University
- Shanghai 200444
- China
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219
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Affiliation(s)
- Simona Ranallo
- Department of Chemical Sciences and Technologies , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies , University of Rome Tor Vergata , Via della Ricerca Scientifica 1 , 00133 Rome , Italy
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220
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Jorge AF, Eritja R. Overview of DNA Self-Assembling: Progresses in Biomedical Applications. Pharmaceutics 2018; 10:E268. [PMID: 30544945 PMCID: PMC6320858 DOI: 10.3390/pharmaceutics10040268] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
Molecular self-assembling is ubiquitous in nature providing structural and functional machinery for the cells. In recent decades, material science has been inspired by the nature's assembly principles to create artificially higher-order structures customized with therapeutic and targeting molecules, organic and inorganic fluorescent probes that have opened new perspectives for biomedical applications. Among these novel man-made materials, DNA nanostructures hold great promise for the modular assembly of biocompatible molecules at the nanoscale of multiple shapes and sizes, designed via molecular programming languages. Herein, we summarize the recent advances made in the designing of DNA nanostructures with special emphasis on their application in biomedical research as imaging and diagnostic platforms, drug, gene, and protein vehicles, as well as theranostic agents that are meant to operate in-cell and in-vivo.
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Affiliation(s)
- Andreia F Jorge
- Coimbra Chemistry Centre (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain.
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221
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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222
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018; 57:16959-16967. [DOI: 10.1002/anie.201811713] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/15/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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223
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Haydell MW, Centola M, Adam V, Valero J, Famulok M. Temporal and Reversible Control of a DNAzyme by Orthogonal Photoswitching. J Am Chem Soc 2018; 140:16868-16872. [DOI: 10.1021/jacs.8b08738] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Michael W. Haydell
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Mathias Centola
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Volker Adam
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Julián Valero
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Michael Famulok
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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224
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Zhou C, Xin L, Duan X, Urban MJ, Liu N. Dynamic Plasmonic System That Responds to Thermal and Aptamer-Target Regulations. NANO LETTERS 2018; 18:7395-7399. [PMID: 30383969 DOI: 10.1021/acs.nanolett.8b03807] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The DNA origami technique has empowered a new paradigm in plasmonics for manipulating light and matter at the nanoscale. This interdisciplinary field has witnessed vigorous growth, outlining a viable route to construct advanced plasmonic architectures with tailored optical properties. However, so far plasmonic systems templated by DNA origami have been restricted to respond to only single stimuli. Despite broad interest and scientific importance, thermal and aptamer-target regulations have not yet been widely utilized to reconfigure three-dimensional plasmonic architectures. In this Letter, we demonstrate a chiral plasmonic nanosystem integrated with split aptamers, which can respond to both thermal and aptamer-target regulations. We show that our dual-responsive system can be noninvasively tuned in a wide range of temperatures, readily correlating thermal control with optical signal changes. Meanwhile, our system can detect specific targets including adenosine triphosphate and cocaine molecules, which further enhance the optical response modulations and in turn influence the thermal tunability.
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Affiliation(s)
- Chao Zhou
- Max Planck Institute for Intelligent Systems , Heisenbergstrasse 3 , D-70569 Stuttgart , Germany
| | - Ling Xin
- Max Planck Institute for Intelligent Systems , Heisenbergstrasse 3 , D-70569 Stuttgart , Germany
| | - Xiaoyang Duan
- Max Planck Institute for Intelligent Systems , Heisenbergstrasse 3 , D-70569 Stuttgart , Germany
- Kirchhoff Institute for Physics , University of Heidelberg , Im Neuenheimer Feld 227 , D-69120 , Heidelberg , Germany
| | - Maximilian J Urban
- Max Planck Institute for Intelligent Systems , Heisenbergstrasse 3 , D-70569 Stuttgart , Germany
- Kirchhoff Institute for Physics , University of Heidelberg , Im Neuenheimer Feld 227 , D-69120 , Heidelberg , Germany
| | - Na Liu
- Max Planck Institute for Intelligent Systems , Heisenbergstrasse 3 , D-70569 Stuttgart , Germany
- Kirchhoff Institute for Physics , University of Heidelberg , Im Neuenheimer Feld 227 , D-69120 , Heidelberg , Germany
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225
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Kogikoski S, Paschoalino WJ, Kubota LT. Supramolecular DNA origami nanostructures for use in bioanalytical applications. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.08.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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226
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Zhou L, Marras AE, Huang CM, Castro CE, Su HJ. Paper Origami-Inspired Design and Actuation of DNA Nanomachines with Complex Motions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802580. [PMID: 30369060 DOI: 10.1002/smll.201802580] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/19/2018] [Indexed: 05/26/2023]
Abstract
Significant progress in DNA nanotechnology has accelerated the development of molecular machines with functions like macroscale machines. However, the mobility of DNA self-assembled nanorobots is still dramatically limited due to challenges with designing and controlling nanoscale systems with many degrees of freedom. Here, an origami-inspired method to design transformable DNA nanomachines is presented. This approach integrates stiff panels formed by bundles of double-stranded DNA connected with foldable creases formed by single-stranded DNA. To demonstrate the method, a DNA version of the paper origami mechanism called a waterbomb base (WBB) consisting of six panels connected by six joints is constructed. This nanoscale WBB can follow four distinct motion paths to transform between five distinct configurations including a flat square, two triangles, a rectangle, and a fully compacted trapezoidal shape. To achieve this, the sequence specificity of DNA base-pairing is leveraged for the selective actuation of joints and the ion-sensitivity of base-stacking interactions is employed for the flattening of joints. In addition, higher-order assembly of DNA WBBs into reconfigurable arrays is achieved. This work establishes a foundation for origami-inspired design for next generation synthetic molecular robots and reconfigurable nanomaterials enabling more complex and controllable motion.
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Affiliation(s)
- Lifeng Zhou
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Alexander E Marras
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Hai-Jun Su
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
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227
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Liu L, Chen K, Xiang N, Ni Z. Dielectrophoretic manipulation of nanomaterials: A review. Electrophoresis 2018; 40:873-889. [DOI: 10.1002/elps.201800342] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/26/2018] [Accepted: 09/30/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Linbo Liu
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments; Southeast University; Nanjing P. R. China
| | - Ke Chen
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments; Southeast University; Nanjing P. R. China
| | - Nan Xiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments; Southeast University; Nanjing P. R. China
| | - Zhonghua Ni
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments; Southeast University; Nanjing P. R. China
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228
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Zou M, Wang J, Yu Y, Sun L, Wang H, Xu H, Zhao Y. Composite Multifunctional Micromotors from Droplet Microfluidics. ACS APPLIED MATERIALS & INTERFACES 2018; 10:34618-34624. [PMID: 30212179 DOI: 10.1021/acsami.8b11976] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Inspired by natural biological machines, lots of effort has been invested in developing artificially functional micromotors which can convert energy into movement for carrying out tasks in diverse areas. Here, we present a capillary microfluidic system with dual inner injections for one-step generation of composite structured polymer micromotors with two distinct cores of platinum (Pt) nanoparticle-integrated and iron oxide (Fe3O4) nanoparticle-dispersed hydrogels. Because the flow rates of the prepolymerized fluids can be precisely tuned in the microfluidics, the diameters of the micromotors as well as the sizes and numbers of the inner cores can be well tailored to optimize the parameters of the resultant micromotors. When exposed to a hydrogen peroxide (H2O2) medium, the Pt-integrated cores of the micromotors could provide propulsion by expelling bubbles produced from the catalytic decomposition of H2O2, while the Fe3O4-dispersed cores could impart magnetic guidance for the micromotors. Benefiting from the close cooperation of these two types of cores, the micromotors were imparted with a strong propulsion and prominent recyclability for the delivery of both microscale and macroscale objects. These results manifest that this kind of composite micromotor has great diversity in various applications.
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Affiliation(s)
- Minhan Zou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Jie Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Yunru Yu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Lingyu Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Huan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Hua Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Yuanjin Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , China
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229
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Switchable DNA-origami nanostructures that respond to their environment and their applications. Biophys Rev 2018; 10:1283-1293. [PMID: 30280371 DOI: 10.1007/s12551-018-0462-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/18/2018] [Indexed: 12/22/2022] Open
Abstract
Structural DNA nanotechnology, in which Watson-Crick base pairing drives the formation of self-assembling nanostructures, has rapidly expanded in complexity and functionality since its inception in 1981. DNA nanostructures can now be made in arbitrary three-dimensional shapes and used to scaffold many other functional molecules such as proteins, metallic nanoparticles, polymers, fluorescent dyes and small molecules. In parallel, the field of dynamic DNA nanotechnology has built DNA circuits, motors and switches. More recently, these two areas have begun to merge-to produce switchable DNA nanostructures, which change state in response to their environment. In this review, we summarise switchable DNA nanostructures into two major classes based on response type: molecular actuation triggered by local chemical changes such as pH or concentration and external actuation driven by light, electric or magnetic fields. While molecular actuation has been well explored, external actuation of DNA nanostructures is a relatively new area that allows for the remote control of nanoscale devices. We discuss recent applications for DNA nanostructures where switching is used to perform specific functions-such as opening a capsule to deliver a molecular payload to a target cell. We then discuss challenges and future directions towards achieving synthetic nanomachines with complexity on the level of the protein machinery in living cells.
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230
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Marras AE, Shi Z, Lindell MG, Patton RA, Huang CM, Zhou L, Su HJ, Arya G, Castro CE. Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices. ACS NANO 2018; 12:9484-9494. [PMID: 30169013 DOI: 10.1021/acsnano.8b04817] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability to design and control DNA nanodevices with programmed conformational changes has established a foundation for molecular-scale robotics with applications in nanomanufacturing, drug delivery, and controlling enzymatic reactions. The most commonly used approach for actuating these devices, DNA binding and strand displacement, allows devices to respond to molecules in solution, but this approach is limited to response times of minutes or greater. Recent advances have enabled electrical and magnetic control of DNA structures with sub-second response times, but these methods utilize external components with additional fabrication requirements. Here, we present a simple and broadly applicable actuation method based on the avidity of many weak base-pairing interactions that respond to changes in local ionic conditions to drive large-scale conformational transitions in devices on sub-second time scales. To demonstrate such ion-mediated actuation, we modified a DNA origami hinge with short, weakly complementary single-stranded DNA overhangs, whose hybridization is sensitive to cation concentrations in solution. We triggered conformational changes with several different types of ions including mono-, di-, and trivalent ions and also illustrated the ability to engineer the actuation response with design parameters such as number and length of DNA overhangs and hinge torsional stiffness. We developed a statistical mechanical model that agrees with experimental data, enabling effective interpretation and future design of ion-induced actuation. Single-molecule Förster resonance energy-transfer measurements revealed that closing and opening transitions occur on the millisecond time scale, and these transitions can be repeated with time resolution on the scale of one second. Our results advance capabilities for rapid control of DNA nanodevices, expand the range of triggering mechanisms, and demonstrate DNA nanomachines with tunable analog responses to the local environment.
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Affiliation(s)
| | - Ze Shi
- Department of NanoEngineering , University of California San Diego , La Jolla , California 92093 , United States
| | | | | | | | | | | | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science , Duke University , Durham , North Carolina 27708 , United States
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231
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Choi Y, Choi H, Lee AC, Kwon S. Design and Synthesis of a Reconfigurable DNA Accordion Rack. J Vis Exp 2018. [PMID: 30176014 DOI: 10.3791/58364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
DNA nanostructure-based mechanical systems or DNA nanomachines, which produce complex nanoscale motion in 2D and 3D in the nanometer to ångström resolution, show great potential in various fields of nanotechnology such as the molecular reactors, drug delivery, and nanoplasmonic systems. The reconfigurable DNA accordion rack, which can collectively manipulate a 2D or 3D nanoscale network of elements, in multiple stages in response to the DNA inputs, is described. The platform has potential to increase the number of elements that DNA nanomachines can control from a few elements to a network scale with multiple stages of reconfiguration. In this protocol, we describe the entire experimental process of the reconfigurable DNA accordion rack of 6 by 6 meshes. The protocol includes a design rule and simulation procedure of the structures and a wet-lab experiment for synthesis and reconfiguration. In addition, analysis of the structure using TEM (transmission electron microscopy) and FRET (fluorescence resonance energy transfer) is included in the protocol. The novel design and simulation methods covered in this protocol will assist researchers to use the DNA accordion rack for further applications.
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Affiliation(s)
- Yeongjae Choi
- Department of Electrical and Computer Engineering, Seoul National University
| | - Hansol Choi
- Department of Electrical and Computer Engineering, Seoul National University
| | - Amos C Lee
- Interdisciplinary Program for Bioengineering, Seoul National University
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University; Interdisciplinary Program for Bioengineering, Seoul National University; Institute of Entrepreneurial Bio Convergence, Seoul National University; Seoul National University Hospital Biomedical Research Institute, Seoul National University Hospital;
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232
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Keya JJ, Kabir AMR, Inoue D, Sada K, Hess H, Kuzuya A, Kakugo A. Control of swarming of molecular robots. Sci Rep 2018; 8:11756. [PMID: 30082825 PMCID: PMC6079095 DOI: 10.1038/s41598-018-30187-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022] Open
Abstract
Recently we demonstrated swarming of a self-propelled biomolecular motor system microtubule (MT)-kinesin where interactions among thousands of motile MTs were regulated in a highly programmable fashion by using DNA as a processor. However, precise control of this potential system is yet to be achieved to optimize the swarm behavior. In this work, we systematically controlled swarming of MTs on kinesin adhered surface by different physicochemical parameters of MT-kinesin and DNA. Tuning the length of DNA sequences swarming was precisely controlled with thermodynamic and kinetic feasibility. In addition, swarming was regulated using different concentration of DNA crosslinkers. Reversibility of swarming was further controlled by changing the concentration of strand displacement DNA signal allowing dissociation of swarm. The control over the swarm was accompanied by variable stiffness of MTs successfully, providing translational and circular motion. Moreover, the morphology of swarm was also found to be changed not only depending on the stiffness but also body length of MTs. Such detail study of precise control of swarming would provide new insights in developing a promising molecular swarm robotic system with desired functions.
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Affiliation(s)
- Jakia Jannat Keya
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | | | - Daisuke Inoue
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Ave., New York, NY, 10027, USA
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University, Osaka, 564-8680, Japan.
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Ave., New York, NY, 10027, USA.
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233
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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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234
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Chen Y, Ke G, Ma Y, Zhu Z, Liu M, Liu Y, Yan H, Yang CJ. A Synthetic Light-Driven Substrate Channeling System for Precise Regulation of Enzyme Cascade Activity Based on DNA Origami. J Am Chem Soc 2018; 140:8990-8996. [DOI: 10.1021/jacs.8b05429] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yahong Chen
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Guoliang Ke
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yanli Ma
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute and School of Molecular Sciences at Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute and School of Molecular Sciences at Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design and Biomimetics, Biodesign Institute and School of Molecular Sciences at Arizona State University, Tempe, Arizona 85287, United States
| | - Chaoyong James Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200127, China
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235
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Abstract
Nucleic acids have been actively exploited to develop various exquisite nanostructures due to their unparalleled programmability. Especially, framework nucleic acids (FNAs) with tailorable functionality and precise addressability hold great promise for biomedical applications. In this review, we summarize recent progress of FNA-enabled biosensing in homogeneous solutions, on heterogeneous surfaces, and inside cells. We describe the strategies to translate the structural order and rigidity of FNAs to interfacial engineering with high controllability, and approaches to realize multiplexing for highly parallel in vitro detection. We also envision the marriage of the currently available FNA tool sets with other emerging technologies to develop a new generation of biosensors for precision diagnosis and bioimaging.
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Affiliation(s)
- Fan Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Chunhai Fan
- 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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236
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Singh HR, Kopperger E, Simmel FC. A DNA Nanorobot Uprises against Cancer. Trends Mol Med 2018; 24:591-593. [PMID: 29802035 DOI: 10.1016/j.molmed.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/03/2018] [Indexed: 12/31/2022]
Abstract
DNA-based nanorobots have been shown to sense and respond to molecular triggers, such as intracellular pH and cell surface receptors. A recent report describes DNA nanorobots as potential cancer therapeutic agents that can be programmed to trigger coagulation inside blood vessels at the tumor site, starving tumor cells to death.
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Affiliation(s)
- Hari R Singh
- Physics Department E14, Technical University Munich, 85748 Garching, Germany; These authors contributed equally.
| | - Enzo Kopperger
- Physics Department E14, Technical University Munich, 85748 Garching, Germany; These authors contributed equally
| | - Friedrich C Simmel
- Physics Department E14, Technical University Munich, 85748 Garching, Germany.
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237
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Abstract
A DNA nanodevice can be manipulated with an applied electric field
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Affiliation(s)
- Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
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