1
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Kou B, Wang Z, Mousavi S, Wang P, Ke Y. Dynamic Gold Nanostructures Based on DNA Self Assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308862. [PMID: 38143287 DOI: 10.1002/smll.202308862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/10/2023] [Indexed: 12/26/2023]
Abstract
The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10 nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.
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Affiliation(s)
- Bo Kou
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Zhichao Wang
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Shikufa Mousavi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
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2
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Aqib RM, Umer A, Li J, Liu J, Ding B. Light Responsive DNA Nanomaterials and Their Biomedical Applications. Chem Asian J 2024; 19:e202400226. [PMID: 38514391 DOI: 10.1002/asia.202400226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 03/23/2024]
Abstract
DNA nanomaterials have been widely employed for various biomedical applications. With rapid development of chemical modification of nucleic acid, serials of stimuli-responsive elements are included in the multifunctional DNA nanomaterials. In this review, we summarize the recent advances in light responsive DNA nanomaterials based on photocleavage/photodecage, photoisomerization, and photocrosslinking for efficient bioimaging (including imaging of small molecule, microRNA, and protein) and drug delivery (including delivery of small molecule, nucleic acid, and gene editing system). We also discuss the remaining challenges and future perspectives of the light responsive DNA nanomaterials in biomedical applications.
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Affiliation(s)
- Raja Muhammad Aqib
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Arsalan Umer
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jialin Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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3
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Guo S, Hu LY, Meng QY, Zhang YY, Zhang CC, Xing LJ, Yu H, Sun HL. Photocontrolled chiroptical switch based on the self-assembly of azobenzene-bridged bis-tryptophan enantiomers. J Colloid Interface Sci 2024; 657:913-920. [PMID: 38091914 DOI: 10.1016/j.jcis.2023.12.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 01/02/2024]
Abstract
Chirality dynamic tuning plays fundamental roles in chemistry, material science and biological system. Herein, a pair of azobenzene-bridged bis-tryptophan enantiomers (Azo-di-d/l-Trp) were designed and synthesized via simple reactions. With the fuel of glucono-δ-lactone (GdL), releasing protons during its hydrolysis, the alkaline solution of Azo-di-d/l-Trp gradually self-assembled into contrast chiral helical structures and displayed magnitude and mirror image of circular dichroism (CD) signals. While the chiral helices converted to CD silent nanoparticles when the azobenzene moiety isomerized from trans- to cis-form under UV irradiation. More importantly, this chiroptical switch, displaying reversible interconversion between chiral amplification and silent, can be smartly controlled via photoirradiation at various wavelengths.
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Affiliation(s)
- Shuo Guo
- College of Chemistry and Materials Science, Hebei Key Laboratory of Organic Functional Molecules, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Lin-Yi Hu
- College of Chemistry and Materials Science, Hebei Key Laboratory of Organic Functional Molecules, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Qing-Yu Meng
- College of Chemistry and Materials Science, Hebei Key Laboratory of Organic Functional Molecules, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Yu-Ying Zhang
- College of Chemistry and Materials Science, Hebei Key Laboratory of Organic Functional Molecules, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Cai-Cai Zhang
- College of Chemistry and Materials Science, Hebei Key Laboratory of Organic Functional Molecules, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Li-Juan Xing
- College of Chemistry and Materials Science, Hebei Key Laboratory of Organic Functional Molecules, Hebei Normal University, Shijiazhuang 050024, PR China.
| | - Haitao Yu
- College of Chemistry and Materials Science, Hebei Key Laboratory of Organic Functional Molecules, Hebei Normal University, Shijiazhuang 050024, PR China.
| | - He-Lue Sun
- College of Chemistry and Materials Science, Hebei Key Laboratory of Organic Functional Molecules, Hebei Normal University, Shijiazhuang 050024, PR China.
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4
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Chen J, Sun R, Zheng J, Zhang W, Huang Y, Shao J, Chi Y. Photochromic Perovskite Nanocrystals for Ultraviolet Dosimetry. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2311993. [PMID: 38363065 DOI: 10.1002/smll.202311993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/04/2024] [Indexed: 02/17/2024]
Abstract
Excessive ultraviolet (UV) radiation has serious damage to human's health, therefore the development of visible, portable, and wearable sensor for monitoring UV radiation, especially the cumulative UV dosage, is highly desired but full of challenges. Herein, a wearable and flexible UV dosimeter based on photochromic perovskite nanocrystals (PNCs) is designed. The obtained CsPbCl3 PNCs dispersed in dibromomethane (PNCs-DBM) undergo continuous, vivid, and multiple (from very weak purple to blue, cyan, and finally strong green) color change in response to UV radiation. It is demonstrated that the UV-induced degradation of DBM and subsequent anion-exchange reaction between CsPbCl3 and Br- , play a crucial role in the color change of PNCs-DBM. The properties of continuous fluorescence color change and enhanced fluorescence intensity enable the construction of sensitive and visible UV dosimeter. Furthermore, by integrated photochromic PNCs with flexible bracelet or PDMS substrate, a wearable UV sensor or a multi-indicator array for the detection of solar UV dosage is developed. This work may advance the fundamental understanding about photochromic perovskite, and show promising application of perovskite nanomaterials in easily fabricated, low-cost, visualized, and wearable solar UV dosimeter.
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Affiliation(s)
- Jie Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Ruifen Sun
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Jingcheng Zheng
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Weiwei Zhang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yun Huang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Jiwei Shao
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Yuwu Chi
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
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5
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Chen Z, Xie C, Chen K, Hu Y, Xu F, Pan L. Multimode adaptive logic gates based on temperature-responsive DNA strand displacement. NANOSCALE 2024; 16:3107-3112. [PMID: 38250822 DOI: 10.1039/d3nr05980d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Living organisms switch their intrinsic biological states to survive environmental turbulence, in which temperature changes are prevalent in nature. Most artificial temperature-responsive DNA nanosystems work as switch modules that transit between "ON-OFF" states, making it difficult to construct nanosystems with diverse functions. In this study, we present a general strategy to build multimode nanosystems based on a temperature-responsive DNA strand displacement reaction. The temperature-responsive DNA strand displacement was controlled by tuning the sequence of the substrate hairpin strands and the invading strands. The nanosystems were demonstrated as logic gates that performed a set of Boolean logical functions at specific temperatures. In addition, an adaptive logic gate was fabricated that could exhibit different logic functions when placed in different temperatures. Specifically, upon the same input strands, the logic gate worked as an XOR gate at 10 °C, an OR gate at 35 °C, an AND gate at 46 °C, and was reset at 55 °C. The design and fabrication of the multifunctional nanosystems would help construct advanced temperature-responsive systems that may be used for temperature-controlled multi-stage drug delivery and thermally-controlled multi-step assembly of nanostructures.
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Affiliation(s)
- Zhekun Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Chun Xie
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Kuiting Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang 050043, China
| | - Fei Xu
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
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6
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Kim T, Lee C, Lee JY, Kim DN. Controlling Chiroptical Responses via Chemo-Mechanical Deformation of DNA Origami Structures. ACS NANO 2024; 18:3414-3423. [PMID: 38236130 DOI: 10.1021/acsnano.3c10386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
DNA origami-based templates have been widely used to fabricate chiral plasmonic metamaterials due to their precise control of the placement of nanoparticles (NPs) in a desired configuration. However, achieving various chiroptical responses inevitably requires a change in the structure of DNA origami-based templates or binding sites on them, leading to the use of significantly different sets of DNA strands. Here, we propose an approach to controlling various chiroptical responses with a single DNA origami design using its chemo-mechanical deformation induced by DNA intercalators. The chiroptical response could be finely tuned by altering the concentration of intercalators only. The silver (Ag) enhancement was used to amplify the chiroptical signal by enlarging NPs and to maintain it by stiffening the template DNA structure. Furthermore, the sensitivity in the chiroptical signal change to the concentration of intercalators could be modulated by the type of intercalator, the mixture of two intercalators, and the stiffness of DNA origami structures. This approach would be useful in a variety of optical applications that require programmed spatial modification of chiroptical responses.
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Affiliation(s)
- Taehwi Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Do-Nyun Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
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7
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Vogt M, List J, Langecker M, Santiago I, Simmel FC, Kopperger E. Electrokinetic Torque Generation by DNA Nanorobotic Arms Studied via Single-Molecule Fluctuation Analysis. J Phys Chem B 2023; 127:10710-10722. [PMID: 38060372 DOI: 10.1021/acs.jpcb.3c05959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
DNA nanotechnology has enabled the creation of supramolecular machines, whose shape and function are inspired from traditional mechanical engineering as well as from biological examples. As DNA inherently is a highly charged biopolymer, the external application of electric fields provides a versatile, computer-programmable way to control the movement of DNA-based machines. However, the details of the electrohydrodynamic interactions underlying the electrical manipulation of these machines are complex, as the influence of their intrinsic charge, the surrounding cloud of counterions, and the effect of electrokinetic fluid flow have to be taken into account. In this work, we identify the relevant effects involved in this actuation mechanism by determining the electric response of an established DNA-based nanorobotic arm to varying design and operation parameters. Borrowing an approach from single-molecule biophysics, we determined the electrical torque exerted on the nanorobotic arms by analyzing their thermal fluctuations when oriented in an electric field. We analyze the influence of various experimental and design parameters on the "actuatability" of the nanostructures and optimize the generated torque according to these parameters. Our findings give insight into the physical processes involved in the actuation mechanism and provide general guidelines that aid in designing and efficiently operating electrically driven nanorobotic devices made from DNA.
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Affiliation(s)
- Matthias Vogt
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Jonathan List
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Martin Langecker
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Ibon Santiago
- CIC nanoGUNE BRTA, Donostia-San Sebastián 20018, Spain
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Enzo Kopperger
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
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8
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Li HD, Ma PQ, Wang JY, Yin BC, Ye BC. A DNA Nanodevice-Based Platform with Diverse Capabilities. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302301. [PMID: 37140089 DOI: 10.1002/smll.202302301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/21/2023] [Indexed: 05/05/2023]
Abstract
Social biotic colonies often perform intricate tasks by interindividual communication and cooperation. Inspired by these biotic behaviors, a DNA nanodevice community is proposed as a universal and scalable platform. The modular nanodevice as the infrastructure of platform contains a DNA origami triangular prism framework and a hairpin-swing arm machinery core. By coding and decoding a signal domain on the shuttled output strand in different nanodevices, an orthogonal inter-nanodevice communication network is established to connect multi-nanodevices into a functional platform. The nanodevice platform enables implementation of diverse tasks, including signal cascading and feedback, molecular input recording, distributed logic computing, and modeling of simulation for virus transmission. The nanodevice platform with powerful compatibility and programmability presents an elegant example of the combination of the distributed operation of multiple devices and the complicated interdevice communication network, and may become a new generation of intelligent DNA nanosystems.
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Affiliation(s)
- Hua-Dong Li
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Pei-Qiang Ma
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jin-Yu Wang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, P. R. China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, P. R. China
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, Xinjiang, 832000, China
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9
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Cai YY, Choi YC, Kagan CR. Chemical and Physical Properties of Photonic Noble-Metal Nanomaterials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2108104. [PMID: 34897837 DOI: 10.1002/adma.202108104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Colloidal noble metal nanoparticles (NPs) are composed of metal cores and organic or inorganic ligand shells. These NPs support size- and shape-dependent plasmonic resonances. They can be assembled from dispersions into artificial metamolecules which have collective plasmonic resonances originating from coupled bright and dark optical electric and magnetic modes that form depending on the size and shape of the constituent NPs and their number, arrangement, and interparticle distance. NPs can also be assembled into extended 2D and 3D metamaterials that are glassy thin films or ordered thin films or crystals, also known as superlattices and supercrystals. The metamaterials have tunable optical properties that depend on the size, shape, and composition of the NPs, and on the number of NP layers and their interparticle distance. Interestingly, strong light-matter interactions in superlattices form plasmon polaritons. Tunable interparticle distances allow designer materials with dielectric functions tailorable from that characteristic of an insulator to that of a metal, and serve as strong optical absorbers or scatterers, respectively. In combination with lithography techniques, these extended assemblies can be patterned to create subwavelength NP superstructures and form large-area 2D and 3D metamaterials that manipulate the amplitude, phase, and polarization of transmitted or reflected light.
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Affiliation(s)
- Yi-Yu Cai
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yun Chang Choi
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Cherie R Kagan
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
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10
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Chen Y, Zhu F, Leng J, Ying T, Jiang JW, Zhou Q, Chang T, Guo W, Gao H. Fluctuotaxis: Nanoscale directional motion away from regions of fluctuation. Proc Natl Acad Sci U S A 2023; 120:e2220500120. [PMID: 37487105 PMCID: PMC10401016 DOI: 10.1073/pnas.2220500120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/27/2023] [Indexed: 07/26/2023] Open
Abstract
Regulating the motion of nanoscale objects on a solid surface is vital for a broad range of technologies such as nanotechnology, biotechnology, and mechanotechnology. In spite of impressive advances achieved in the field, there is still a lack of a robust mechanism which can operate under a wide range of situations and in a controllable manner. Here, we report a mechanism capable of controllably driving directed motion of any nanoobjects (e.g., nanoparticles, biomolecules, etc.) in both solid and liquid forms. We show via molecular dynamics simulations that a nanoobject would move preferentially away from the fluctuating region of an underlying substrate, a phenomenon termed fluctuotaxis-for which the driving force originates from the difference in atomic fluctuations of the substrate behind and ahead of the object. In particular, we find that the driving force can depend quadratically on both the amplitude and frequency of the substrate and can thus be tuned flexibly. The proposed driving mechanism provides a robust and controllable way for nanoscale mass delivery and has potential in various applications including nanomotors, molecular machines, etc.
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Affiliation(s)
- Yang Chen
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Fangyan Zhu
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Jiantao Leng
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Tianquan Ying
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Jin-Wu Jiang
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
- Joint-Research Center for Computational Materials, Zhejiang Laboratory, Hangzhou311100, China
| | - Quan Zhou
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Tienchong Chang
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
- Joint-Research Center for Computational Materials, Zhejiang Laboratory, Hangzhou311100, China
- Shanghai Institute of Aircraft Mechanics and Control, Tongji University, Shanghai200092, China
| | - Wanlin Guo
- Key Laboratory for Intelligent Nano Materials and Devices of the Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, Institute of Nanoscience of Nanjing University of Aeronautics and Astronautics, Nanjing210016, China
| | - Huajian Gao
- School of Mechanical and Aerospace Engineering, College of Engineering, Nanyang Technological University, Singapore639798, Singapore
- Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore138632, Singapore
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11
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Yang J, Jahnke K, Xin L, Jing X, Zhan P, Peil A, Griffo A, Škugor M, Yang D, Fan S, Göpfrich K, Yan H, Wang P, Liu N. Modulating Lipid Membrane Morphology by Dynamic DNA Origami Networks. NANO LETTERS 2023. [PMID: 37440701 DOI: 10.1021/acs.nanolett.3c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Membrane morphology and its dynamic adaptation regulate many cellular functions, which are often mediated by membrane proteins. Advances in DNA nanotechnology have enabled the realization of various protein-inspired structures and functions with precise control at the nanometer level, suggesting a viable tool to artificially engineer membrane morphology. In this work, we demonstrate a DNA origami cross (DOC) structure that can be anchored onto giant unilamellar vesicles (GUVs) and subsequently polymerized into micrometer-scale reconfigurable one-dimensional (1D) chains or two-dimensional (2D) lattices. Such DNA origami-based networks can be switched between left-handed (LH) and right-handed (RH) conformations by DNA fuels and exhibit potent efficacy in remodeling the membrane curvatures of GUVs. This work sheds light on designing hierarchically assembled dynamic DNA systems for the programmable modulation of synthetic cells for useful applications.
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Affiliation(s)
- Juanjuan Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127, People's Republic of China
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Kevin Jahnke
- Biophysical Engineering Group, Max Planck Institute for Medical Research Heidelberg, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Ling Xin
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Xinxin Jing
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Pengfei Zhan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Andreas Peil
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Alessandra Griffo
- Biophysical Engineering Group, Max Planck Institute for Medical Research Heidelberg, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Marko Škugor
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127, People's Republic of China
| | - Sisi Fan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research Heidelberg, Jahnstr. 29, 69120 Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheime Feld 329, 69120 Heidelberg, Germany
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics at Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127, People's Republic of China
| | - Na Liu
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
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12
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Kim M, Lee C, Jeon K, Lee JY, Kim YJ, Lee JG, Kim H, Cho M, Kim DN. Harnessing a paper-folding mechanism for reconfigurable DNA origami. Nature 2023; 619:78-86. [PMID: 37407684 DOI: 10.1038/s41586-023-06181-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/09/2023] [Indexed: 07/07/2023]
Abstract
The paper-folding mechanism has been widely adopted in building of reconfigurable macroscale systems because of its unique capabilities and advantages in programming variable shapes and stiffness into a structure1-5. However, it has barely been exploited in the construction of molecular-level systems owing to the lack of a suitable design principle, even though various dynamic structures based on DNA self-assembly6-9 have been developed10-23. Here we propose a method to harness the paper-folding mechanism to create reconfigurable DNA origami structures. The main idea is to build a reference, planar wireframe structure24 whose edges follow a crease pattern in paper folding so that it can be folded into various target shapes. We realized several paper-like folding and unfolding patterns using DNA strand displacement25 with high yield. Orthogonal folding, repeatable folding and unfolding, folding-based microRNA detection and fluorescence signal control were demonstrated. Stimuli-responsive folding and unfolding triggered by pH or light-source change were also possible. Moreover, by employing hierarchical assembly26 we could expand the design space and complexity of the paper-folding mechanism in a highly programmable manner. Because of its high programmability and scalability, we expect that the proposed paper-folding-based reconfiguration method will advance the development of complex molecular systems.
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Affiliation(s)
- Myoungseok Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea
| | - Kyounghwa Jeon
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea
| | - Young-Joo Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Jae Gyung Lee
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Hyunsu Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Maenghyo Cho
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Do-Nyun Kim
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea.
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea.
- Institute of Engineering Research, Seoul National University, Seoul, Korea.
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13
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Abstract
DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these "robotic" features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations ("open" and "closed" states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with "pH-latches" that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.
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Affiliation(s)
- Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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14
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Farag N, Đorđević M, Del Grosso E, Ricci F. Dynamic and Reversible Decoration of DNA-Based Scaffolds. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211274. [PMID: 36739507 DOI: 10.1002/adma.202211274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/24/2023] [Indexed: 05/05/2023]
Abstract
An approach to achieving dynamic and reversible decoration of DNA-based scaffolds is demonstrated here. To do this, rationally engineered DNA tiles containing enzyme-responsive strands covalently conjugated to different molecular labels are employed. These strands are designed to be recognized and degraded by specific enzymes (i.e., Ribonuclease H, RNase H, or Uracil DNA Glycosylase, UDG) inducing their spontaneous de-hybridization from the assembled tile and replacement by a new strand conjugated to a different label. Multiple enzyme-responsive strands that specifically respond to different enzymes allow for dynamic, orthogonal, and reversible decoration of the DNA structures. As a proof-of-principle of the strategy, the possibility to orthogonally control the distribution of different labels (i.e., fluorophores and small molecules) on the same scaffold without crosstalk is demonstrated. By doing so, DNA scaffolds that display different antibody recognition patterns are obtained. The approach offers the possibility to control the decoration of higher-order supramolecular assemblies (including origami) with several functional moieties to achieve functional biomaterials with improved adaptability, precision, and sensing capabilities.
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Affiliation(s)
- Nada Farag
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - Milan Đorđević
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
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15
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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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16
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Shao X, Zhu C, Kumar P, Wang Y, Lu J, Cha M, Yao L, Cao Y, Mao X, Heinz H, Kotov NA. Voltage-Modulated Untwist Deformations and Multispectral Optical Effects from Ion Intercalation into Chiral Ceramic Nanoparticles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206956. [PMID: 36808775 DOI: 10.1002/adma.202206956] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Reconfiguration of chiral ceramic nanostructures after ion intercalation should favor specific nanoscale twists leading to strong chiroptical effects. In this work, V2 O3 nanoparticles are shown to have "built-in" chiral distortions caused by binding of tartaric acid enantiomers to the nanoparticle surface. As evidenced by spectroscopy/microscopy techniques and calculations of nanoscale chirality measures, the intercalation of Zn2+ ions into the V2 O3 lattice results in particle expansion, untwist deformations, and chirality reduction. Coherent deformations in the particle ensemble manifest as changes in sign and positions of circular polarization bands at ultraviolet, visible, mid-infrared (IR), near-IR (NIR), and IR wavelengths. The g-factors observed for IR and NIR spectral diapasons are ≈100-400 times higher than those for previously reported dielectric, semiconductor, and plasmonic nanoparticles. Nanocomposite films layer-by-layer assembled (LBL) from V2 O3 nanoparticles reveal cyclic-voltage-driven modulation of optical activity. Device prototypes for IR and NIR range problematic for liquid crystals and other organic materials are demonstrated. High optical activity, synthetic simplicity, sustainable processability, and environmental robustness of the chiral LBL nanocomposites provide a versatile platform for photonic devices. Similar reconfigurations of particle shapes are expected for multiple chiral ceramic nanostructures, leading to unique optical, electrical, and magnetic properties.
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Affiliation(s)
- Xiao Shao
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Tianjin Key Laboratory of Applied Catalysis Science and Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300354, China
| | - Cheng Zhu
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Prashant Kumar
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yanan Wang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jun Lu
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Minjeong Cha
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lin Yao
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yuan Cao
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiaoming Mao
- Department of Physics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, 80309, USA
- Materials Science and Engineering Program, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Nicholas A Kotov
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
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17
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Jedrych A, Pawlak M, Gorecka E, Lewandowski W, Wojcik MM. Light-Responsive Supramolecular Nanotubes-Based Chiral Plasmonic Assemblies. ACS NANO 2023; 17:5548-5560. [PMID: 36897199 PMCID: PMC10062029 DOI: 10.1021/acsnano.2c10955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
We describe the fabrication of dual-responsive (thermo/light) chiral plasmonic films. The idea is based on using photoswitchable achiral liquid crystal (LCs) forming chiral nanotubes for templating helical assemblies of Au NPs. Circular dichroism spectroscopy (CD) confirms chiroptical properties coming from the arrangement of organic and inorganic components, with up to 0.2 dissymmetry factor (g-factor). Upon exposure to UV light, organic molecules isomerize, resulting in controlled melting of organic nanotubes and/or inorganic nanohelices. The process can be reversed using visible light and further modified by varying the temperature, offering a control of chiroptical response of the composite material. These properties can play a key role in the future development of chiral plasmonics, metamaterials, and optoelectronic devices.
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18
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Mills A, Aissaoui N, Finkel J, Elezgaray J, Bellot G. Mechanical DNA Origami to Investigate Biological Systems. Adv Biol (Weinh) 2023; 7:e2200224. [PMID: 36509679 DOI: 10.1002/adbi.202200224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to self-assemble DNA nanodevices with programmed structural dynamics that can sense and respond to the local environment can enable transformative applications in fields including mechanobiology and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. In this review, the current state-of-the-art in constructing complex DNA geometries with dynamic and mechanical properties to enable a molecular scale force measurement is first summarized. Next, an overview of engineering modular DNA devices that interact with cell surfaces is highlighted detailing examples of mechanosensitive proteins and the force-induced dynamic molecular interaction on the downstream biochemical signaling. Finally, the challenges and an outlook on this promising class of DNA devices acting as nanomachines to operate at a low piconewton range suitable for a majority of biological effects or as hybrid materials to achieve higher tension exertion required for other biological investigations, are discussed.
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Affiliation(s)
- Allan Mills
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Nesrine Aissaoui
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, Paris, 75006, France
| | - Julie Finkel
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Juan Elezgaray
- CRPP, CNRS, UMR 5031, Université de Bordeaux, Pessac, 33600, France
| | - Gaëtan Bellot
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
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19
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Natarajan AK, Ryssy J, Kuzyk A. A DNA origami-based device for investigating DNA bending proteins by transmission electron microscopy. NANOSCALE 2023; 15:3212-3218. [PMID: 36722916 DOI: 10.1039/d2nr05366g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The DNA origami technique offers precise positioning of nanoscale objects with high accuracy. This has facilitated the development of DNA origami-based functional nanomechanical devices that enable the investigation of DNA-protein interactions at the single particle level. Herein, we used the DNA origami technique to fabricate a nanoscale device for studying DNA bending proteins. For a proof of concept, we used TATA-box binding protein (TBP) to evaluate our approach. Upon binding to the TATA box, TBP causes a bend to DNA of ∼90°. Our device translates this bending into an angular change that is readily observable with a conventional transmission electron microscope (TEM). Furthermore, we investigated the roles of transcription factor II A (TF(II)A) and transcription factor II B (TF(II)B). Our results indicate that TF(II)A introduces additional bending, whereas TF(II)B does not significantly alter the TBP-DNA structure. Our approach can be readily adopted to a wide range of DNA-bending proteins and will aid the development of DNA-origami-based devices tailored for the investigation of DNA-protein interactions.
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Affiliation(s)
- Ashwin Karthick Natarajan
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
| | - Joonas Ryssy
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
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20
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Périllat VJ, Del Grosso E, Berton C, Ricci F, Pezzato C. Controlling DNA nanodevices with light-switchable buffers. Chem Commun (Camb) 2023; 59:2146-2149. [PMID: 36727426 PMCID: PMC9933455 DOI: 10.1039/d2cc06525h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Control over synthetic DNA-based nanodevices can be achieved with a variety of physical and chemical stimuli. Actuation with light, however, is as advantageous as difficult to implement without modifying DNA strands with photo-switchable groups. Herein, we show that DNA nanodevices can be controlled using visible light in photo-switchable aqueous buffer solutions in a reversible and highly programmable fashion. The strategy presented here is non-invasive and allows the remote control with visible light of complex operations of DNA-based nanodevices such as the reversible release/loading of cargo molecules.
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Affiliation(s)
- Valentin Jean Périllat
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata Via della Ricerca Scientifica, 00133 Rome, Italy.
| | - Cesare Berton
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata Via della Ricerca Scientifica, 00133 Rome, Italy.
| | - Cristian Pezzato
- Institut des Sciences et Ingénierie Chimiques École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,Department of Chemical Sciences, University of Padua Via Marzolo 1, 35131 Padua, Italy.
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21
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Yang D, Xu F, Wang P. Reconfigurable Two-Dimensional DNA Molecular Arrays. Methods Mol Biol 2023; 2639:69-81. [PMID: 37166711 DOI: 10.1007/978-1-0716-3028-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In biology, molecular cascade signaling is an essential tool to mediate various pathways and downstream behaviors. Mimicking these molecular cascades plays an important role in synthetic biology. The use of DNA self-assembly represents an elegant way to build sophisticated molecular cascades. For instance, a DNA molecular array connected by a number of dynamic anti-junction units was able to realize prescribed, multistep, long-range cascaded transformation. The dynamic DNA molecular array is able to execute transformations with programmable initiation, propagation, and regulation. The transformation of the array can be initiated at selected units and then propagated, without addition of extra triggers, to neighboring units and eventually the entire array.
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Affiliation(s)
- Donglei Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao, Tong University, Shanghai, China
| | - Fan Xu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao, Tong University, Shanghai, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao, Tong University, Shanghai, China.
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22
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Bogawat Y, Krishnan S, Simmel FC, Santiago I. Tunable 2D diffusion of DNA nanostructures on lipid membranes. Biophys J 2022; 121:4810-4818. [PMID: 36243925 PMCID: PMC9811667 DOI: 10.1016/j.bpj.2022.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/02/2022] [Accepted: 10/11/2022] [Indexed: 01/07/2023] Open
Abstract
DNA nanotechnology facilitates the synthesis of biomimetic models for studying biological systems. This work uses lipid bilayers as platforms for two-dimensional single-particle tracking of the dynamics of DNA nanostructures. Three different DNA origami structures adhere to the membrane through hybridization with cholesterol-modified strands. Their two-dimensional diffusion coefficient is modulated by changing the concentration of monovalent and divalent salts and the number of anchors. In addition, the diffusion coefficient is tuned by targeting cholesterol-modified anchor strands with strand-displacement reactions. We demonstrate a responsive system with changing diffusivity by selectively displacing membrane-bound anchor strands. We also show the programmed release of origami structures from the lipid membranes.
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Affiliation(s)
- Yash Bogawat
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Swati Krishnan
- Physics Department E14, Technical University of Munich, Garching, Germany; Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Friedrich C Simmel
- Physics Department E14, Technical University of Munich, Garching, Germany.
| | - Ibon Santiago
- Physics Department E14, Technical University of Munich, Garching, Germany; CIC nanoGUNE BRTA, Donostia-San Sebastián, Spain.
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23
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Stasi M, Monferrer A, Babl L, Wunnava S, Dirscherl CF, Braun D, Schwille P, Dietz H, Boekhoven J. Regulating DNA-Hybridization Using a Chemically Fueled Reaction Cycle. J Am Chem Soc 2022; 144:21939-21947. [PMID: 36442850 PMCID: PMC9732876 DOI: 10.1021/jacs.2c08463] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular machines, such as ATPases or motor proteins, couple the catalysis of a chemical reaction, most commonly hydrolysis of nucleotide triphosphates, to their conformational change. In essence, they continuously convert a chemical fuel to drive their motion. An outstanding goal of nanotechnology remains to synthesize a nanomachine with similar functions, precision, and speed. The field of DNA nanotechnology has given rise to the engineering precision required for such a device. Simultaneously, the field of systems chemistry developed fast chemical reaction cycles that convert fuel to change the function of molecules. In this work, we thus combined a chemical reaction cycle with the precision of DNA nanotechnology to yield kinetic control over the conformational state of a DNA hairpin. Future work on such systems will result in out-of-equilibrium DNA nanodevices with precise functions.
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Affiliation(s)
- Michele Stasi
- School
of Natural Sciences, Department of Chemistry, Technical University of Munich, Garching85748, Germany
| | - Alba Monferrer
- School
of Natural Sciences, Department of Physics, Technical University of Munich, Am Coulombwall 4, Garching85748, Germany,Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, Garching85748, Germany
| | - Leon Babl
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried82152,Germany
| | - Sreekar Wunnava
- Center
for NanoScience (CeNS) and Systems Biophysics, Ludwig-Maximilian University Munich, Munich80799, Germany
| | | | - Dieter Braun
- Center
for NanoScience (CeNS) and Systems Biophysics, Ludwig-Maximilian University Munich, Munich80799, Germany
| | - Petra Schwille
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried82152,Germany
| | - Hendrik Dietz
- School
of Natural Sciences, Department of Physics, Technical University of Munich, Am Coulombwall 4, Garching85748, Germany,Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, Garching85748, Germany
| | - Job Boekhoven
- School
of Natural Sciences, Department of Chemistry, Technical University of Munich, Garching85748, Germany,
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24
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Mao X, Liu M, Li Q, Fan C, Zuo X. DNA-Based Molecular Machines. JACS AU 2022; 2:2381-2399. [PMID: 36465542 PMCID: PMC9709946 DOI: 10.1021/jacsau.2c00292] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/02/2022] [Accepted: 07/08/2022] [Indexed: 05/17/2023]
Abstract
Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.
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Affiliation(s)
- Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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25
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Torres-Huerta AL, Antonio-Pérez A, García-Huante Y, Alcázar-Ramírez NJ, Rueda-Silva JC. Biomolecule-Based Optical Metamaterials: Design and Applications. BIOSENSORS 2022; 12:962. [PMID: 36354471 PMCID: PMC9688573 DOI: 10.3390/bios12110962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.
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Affiliation(s)
- Ana Laura Torres-Huerta
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Aurora Antonio-Pérez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Yolanda García-Huante
- Departamento de Ciencias Básicas, Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional (UPIITA-IPN), Mexico City 07340, Mexico
| | - Nayelhi Julieta Alcázar-Ramírez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Juan Carlos Rueda-Silva
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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26
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Liu L, Xiong Q, Xie C, Pincet F, Lin C. Actuating tension-loaded DNA clamps drives membrane tubulation. SCIENCE ADVANCES 2022; 8:eadd1830. [PMID: 36223466 PMCID: PMC9555772 DOI: 10.1126/sciadv.add1830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Membrane dynamics in living organisms can arise from proteins adhering to, assembling on, and exerting force on cell membranes. Programmable synthetic materials, such as self-assembled DNA nanostructures, offer the capability to drive membrane-remodeling events that resemble protein-mediated dynamics but with user-defined outcomes. An illustrative example is the tubular deformation of liposomes by DNA nanostructures with purposely designed shapes, surface modifications, and self-assembling properties. However, stimulus-responsive membrane tubulation mediated by DNA reconfiguration remains challenging. Here, we present the triggered formation of membrane tubes in response to specific DNA signals that actuate membrane-bound DNA clamps from an open state to various predefined closed states, releasing prestored energy to activate membrane deformation. We show that the timing and efficiency of vesicle tubulation, as well as the membrane tube widths, are modulated by the conformational change of DNA clamps, marking a solid step toward spatiotemporal control of membrane dynamics in an artificial system.
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Affiliation(s)
- Longfei Liu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Qiancheng Xiong
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Chun Xie
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Frederic Pincet
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Laboratoire de Physique de l’Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
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27
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Wang P, Krasavin AV, Liu L, Jiang Y, Li Z, Guo X, Tong L, Zayats AV. Molecular Plasmonics with Metamaterials. Chem Rev 2022; 122:15031-15081. [PMID: 36194441 PMCID: PMC9562285 DOI: 10.1021/acs.chemrev.2c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular plasmonics, the area which deals with the interactions between surface plasmons and molecules, has received enormous interest in fundamental research and found numerous technological applications. Plasmonic metamaterials, which offer rich opportunities to control the light intensity, field polarization, and local density of electromagnetic states on subwavelength scales, provide a versatile platform to enhance and tune light-molecule interactions. A variety of applications, including spontaneous emission enhancement, optical modulation, optical sensing, and photoactuated nanochemistry, have been reported by exploiting molecular interactions with plasmonic metamaterials. In this paper, we provide a comprehensive overview of the developments of molecular plasmonics with metamaterials. After a brief introduction to the optical properties of plasmonic metamaterials and relevant fabrication approaches, we discuss light-molecule interactions in plasmonic metamaterials in both weak and strong coupling regimes. We then highlight the exploitation of molecules in metamaterials for applications ranging from emission control and optical modulation to optical sensing. The role of hot carriers generated in metamaterials for nanochemistry is also discussed. Perspectives on the future development of molecular plasmonics with metamaterials conclude the review. The use of molecules in combination with designer metamaterials provides a rich playground both to actively control metamaterials using molecular interactions and, in turn, to use metamaterials to control molecular processes.
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Affiliation(s)
- Pan Wang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou310027, China.,Department of Physics and London Centre for Nanotechnology, King's College London, Strand, LondonWC2R 2LS, U.K.,Jiaxing Key Laboratory of Photonic Sensing & Intelligent Imaging, Jiaxing314000, China.,Intelligent Optics & Photonics Research Center, Jiaxing Research Institute, Zhejiang University, Jiaxing314000, China
| | - Alexey V Krasavin
- Department of Physics and London Centre for Nanotechnology, King's College London, Strand, LondonWC2R 2LS, U.K
| | - Lufang Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou310027, China
| | - Yunlu Jiang
- Department of Physics and London Centre for Nanotechnology, King's College London, Strand, LondonWC2R 2LS, U.K
| | - Zhiyong Li
- Jiaxing Key Laboratory of Photonic Sensing & Intelligent Imaging, Jiaxing314000, China.,Intelligent Optics & Photonics Research Center, Jiaxing Research Institute, Zhejiang University, Jiaxing314000, China
| | - Xin Guo
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou310027, China.,Jiaxing Key Laboratory of Photonic Sensing & Intelligent Imaging, Jiaxing314000, China.,Intelligent Optics & Photonics Research Center, Jiaxing Research Institute, Zhejiang University, Jiaxing314000, China
| | - Limin Tong
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou310027, China
| | - Anatoly V Zayats
- Department of Physics and London Centre for Nanotechnology, King's College London, Strand, LondonWC2R 2LS, U.K
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28
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Zhang J, Song C, Wang L. DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications. Phys Chem Chem Phys 2022; 24:23959-23979. [PMID: 36168789 DOI: 10.1039/d2cp02100e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.
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Affiliation(s)
- Jingjing Zhang
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| | - Chunyuan Song
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| | - Lianhui Wang
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
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29
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Wang X, Zhang C, Chen F, Xiang J, Wang S, Liu Z, Ding T. Optically Triggered Nanoscale Plasmonic Dynamite. ACS NANO 2022; 16:13667-13673. [PMID: 35920563 DOI: 10.1021/acsnano.2c02402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Photons as energy carriers are clean and abundant, which can be conveniently applied for nanoactuation but the response is usually slow with very low energy efficiency/density. Here, we underpin the concept of robust nanoscale plasmonic dynamite by incorporating fullerene (C60). The Au@C60 core-shell nanoparticles can be triggered to explode in nanoscale with synergy of plasmon-enhanced photochemical and photothermal effects. It is suggested that a sensible amount of CO2 was generated and pressurized in nanometric volume in an extremely short time scale (∼ns), which triggers the nanoexplosion, rendering the ejection of Au NPs at the speed over 300 m/s. The ejection generates extremely large local forces (∼1 μN) with thermomechanical energy efficiency up to ∼30%, which is demonstrated as a powerful nanoengine for controlled mobilization of micro-objects on solid surfaces. Such nanoscale plasmonic dynamite is highly exploitable for different types of nanomachines, which provides a powerful energy source for nanoactuation and nanomigration.
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Affiliation(s)
- Xujie Wang
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Chi Zhang
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Fangqi Chen
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Junxiang Xiang
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei 430072, China
| | - Shuangshuang Wang
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Ze Liu
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei 430072, China
- State Key Laboratory of Water Resources & Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
| | - Tao Ding
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
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30
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Liang L, Jia S, Barman I. DNA-POINT: DNA Patterning of Optical Imprint for Nanomaterials Topography. ACS APPLIED MATERIALS & INTERFACES 2022; 14:38388-38397. [PMID: 35969693 DOI: 10.1021/acsami.2c10908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Engineering well-defined scale-spanning structures through transfer of diverse biomolecules and materials to a surface is of tremendous interest in life sciences research yet remains profoundly challenging. Here, we report a novel method, termed as DNA patterning of optical imprint for nanomaterials topography (DNA-POINT), for rapid photopatterning of large area, geometrically complex surfaces via light-responsive DNA. Our method employs top-down multiphoton-driven patterning of azobenzene-modified DNA strands, offering precise position control of molecules and nanoparticles along the axial plane and a template for bottom-up self-assembly of multiple layers of different chemical composition along the vertical plane. We demonstrate the surface patterning of plasmonic gold nanoparticles, fluorophore-labeled oligonucleotides, and multiple layers consisting of molecule-nanoparticle hybrid patterns into preconceived shapes without compromising on the functionality of the biomolecules. Furthermore, we exhibit scanning mode operation of DNA-POINT, thereby paving the way for maskless and cleanroom-free fast fabrication of biochips for high-throughput diagnostics and biosensing applications.
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Affiliation(s)
- Le Liang
- Department of Ophthalmology, Zhongnan Hospital of Wuhan University, The Institute for Advanced Studies, Wuhan University, Wuhan 430071, China
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sisi Jia
- Zhangjiang Laboratory, Shanghai 201210, China
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- Department of Radiology & Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
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31
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Farag N, Ercolani G, Del Grosso E, Ricci F. DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes. Angew Chem Int Ed Engl 2022; 61:e202208367. [DOI: 10.1002/anie.202208367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 12/18/2022]
Affiliation(s)
- Nada Farag
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Gianfranco Ercolani
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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32
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Nakamura M, Yoshioka H, Takada T. Conformational Switching of Pyrenes Associated on Hairpin Loop Region by DNA B‐Z Transition. ChemistrySelect 2022. [DOI: 10.1002/slct.202200696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Hibiki Yoshioka
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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33
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A modular spring-loaded actuator for mechanical activation of membrane proteins. Nat Commun 2022; 13:3182. [PMID: 35902570 PMCID: PMC9334261 DOI: 10.1038/s41467-022-30745-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
How cells respond to mechanical forces by converting them into biological signals underlie crucial cellular processes. Our understanding of mechanotransduction has been hindered by technical barriers, including limitations in our ability to effectively apply low range piconewton forces to specific mechanoreceptors on cell membranes without laborious and repetitive trials. To overcome these challenges we introduce the Nano-winch, a robust, easily assembled, programmable DNA origami-based molecular actuator. The Nano-winch is designed to manipulate multiple mechanoreceptors in parallel by exerting fine-tuned, low- piconewton forces in autonomous and remotely activated modes via adjustable single- and double-stranded DNA linkages, respectively. Nano-winches in autonomous mode can land and operate on the cell surface. Targeting the device to integrin stimulated detectable downstream phosphorylation of focal adhesion kinase, an indication that Nano-winches can be applied to study cellular mechanical processes. Remote activation mode allowed finer extension control and greater force exertion. We united remotely activated Nano-winches with single-channel bilayer experiments to directly observe the opening of a channel by mechanical force in the force responsive gated channel protein, BtuB. This customizable origami provides an instrument-free approach that can be applied to control and explore a diversity of mechanotransduction circuits on living cells. Studies on mechanotransduction are limited by our ability to apply low range forces to specific mechanoreceptors on cell membranes. Here the authors report the Nano-winch, a programmable DNA origami-based molecular actuator, to manipulate multiple mechanoreceptors in parallel by exerting piconewton forces.
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34
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Xie C, Hu Y, Chen Z, Chen K, Pan L. Tuning curved DNA origami structures through mechanical design and chemical adducts. NANOTECHNOLOGY 2022; 33:405603. [PMID: 35772292 DOI: 10.1088/1361-6528/ac7d62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
The bending and twisting of DNA origami structures are important features for controlling the physical properties of DNA nanodevices. It has not been fully explored yet how to finely tune the bending and twisting of curved DNA structures. Traditional tuning of the curved DNA structures was limited to controlling the in-plane-bending angle through varying the numbers of base pairs of deletions and insertions. Here, we developed two tuning strategies of curved DNA origami structures fromin silicoandin vitroaspects.In silico, the out-of-plane bending and twisting angles of curved structures were introduced, and were tuned through varying the patterns of base pair deletions and insertions.In vitro, a chemical adduct (ethidium bromide) was applied to dynamically tune a curved spiral. The 3D structural conformations, like chirality, of the curved DNA structures were finely tuned through these two strategies. The simulation and TEM results demonstrated that the patterns of base pair insertions and deletions and chemical adducts could effectively tune the bending and twisting of curved DNA origami structures. These strategies expand the programmable accuracy of curved DNA origami structures and have potential in building efficient dynamic functional nanodevices.
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Affiliation(s)
- Chun Xie
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, People's Republic of China
| | - Zhekun Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Kuiting Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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35
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Farag N, Ercolani G, Del Grosso E, Ricci F. DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nada Farag
- Universita degli Studi di Roma Tor Vergata Chemistry ITALY
| | | | | | - Francesco Ricci
- University of Rome, Tor Vergata Department of Chemistry Via della Ricerca Scientifica 00133 Rome ITALY
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36
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Jahnke K, Huth V, Mersdorf U, Liu N, Göpfrich K. Bottom-Up Assembly of Synthetic Cells with a DNA Cytoskeleton. ACS NANO 2022; 16:7233-7241. [PMID: 35377150 PMCID: PMC9134502 DOI: 10.1021/acsnano.1c10703] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Cytoskeletal elements, like actin and myosin, have been reconstituted inside lipid vesicles toward the vision to reconstruct cells from the bottom up. Here, we realize the de novo assembly of entirely artificial DNA-based cytoskeletons with programmed multifunctionality inside synthetic cells. Giant unilamellar lipid vesicles (GUVs) serve as cell-like compartments, in which the DNA cytoskeletons are repeatedly and reversibly assembled and disassembled with light using the cis-trans isomerization of an azobenzene moiety positioned in the DNA tiles. Importantly, we induced ordered bundling of hundreds of DNA filaments into more rigid structures with molecular crowders. We quantify and tune the persistence length of the bundled filaments to achieve the formation of ring-like cortical structures inside GUVs, resembling actin rings that form during cell division. Additionally, we show that DNA filaments can be programmably linked to the compartment periphery using cholesterol-tagged DNA as a linker. The linker concentration determines the degree of the cortex-like network formation, and we demonstrate that the DNA cortex-like network can deform GUVs from within. All in all, this showcases the potential of DNA nanotechnology to mimic the diverse functions of a cytoskeleton in synthetic cells.
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Affiliation(s)
- Kevin Jahnke
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
| | - Vanessa Huth
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
| | - Ulrike Mersdorf
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Na Liu
- 2nd
Physics Institute, University of Stuttgart, Im Pfaffenwaldring 57, D-70569 Stuttgart, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
| | - Kerstin Göpfrich
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
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37
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Hua Y, Ma J, Li D, Wang R. DNA-Based Biosensors for the Biochemical Analysis: A Review. BIOSENSORS 2022; 12:bios12030183. [PMID: 35323453 PMCID: PMC8945906 DOI: 10.3390/bios12030183] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.
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38
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Wen X, Wang S, Liu R, Duan R, Hu S, Jiao T, Zhang L, Liu M. Selenocystine and Photo-Irradiation Directed Growth of Helically Grooved Gold Nanoarrows. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104301. [PMID: 34825484 DOI: 10.1002/smll.202104301] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/28/2021] [Indexed: 06/13/2023]
Abstract
The fabrication of discrete nanostructures with both plasmonic circular dichroism (PCD) and chiral features is still a challenge. Here, gold nanoarrows (GNAs) with both chiroptical responses and chiral morphologies are achieved by using L-selenocystine (L-SeCys2 ) as a chiral inducer. While L-SeCys2 generates GNAs with a weak PCD signal, the irradiated L-SeCys2 (irr-L-SeCys2 ) leads to GNAs with featured helical grooves (HeliGNAs) accompanying with a strong PCD signal. It is revealed that when L-SeCys2 is photo-irradiated, the emergence of selenyl radicals plays an important role in the formation of HeliGNAs and enhancement of the chiroptical signal. In comparison with L-SeCys2 and the other kinds of sulfur-containing amino acids, the formation mechanism of helical grooves on the surface of GNAs is proposed. Both HeliGNAs and GNAs are used to discriminate amino acids by utilizing surface enhanced Raman scattering (SERS) effect. In the presence of either GNAs or HeliGNAs as the substrate, Fmoc-L-Phe shows more significant SERS than Fmoc-D-Phe. This study may advance the design of discrete plasmonic nanomaterials with both chiral morphology and potential applications in discrimination of chiral molecules.
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Affiliation(s)
- Xin Wen
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, 066004, P. R. China
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Song Wang
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Rulin Liu
- Shenzhen Institute of Artificial Intelligence and Robotics for Society (AIRS), Shenzhen, 518172, P. R. China
| | - Ran Duan
- Key Laboratory of Photochemistry Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Song Hu
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Tifeng Jiao
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, 066004, P. R. China
| | - Li Zhang
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Minghua Liu
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
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Abstract
Controlled assembly of inorganic nanoparticles with different compositions, sizes and shapes into higher-order structures of collective functionalities is a central pursued objective in chemistry, physics, materials science and nanotechnology. The emerging chiral superstructures, which break spatial symmetries at the nanoscale, have attracted particular attention, owing to their unique chiroptical properties and potential applications in optics, catalysis, biology and so on. Various bottom-up strategies have been developed to build inorganic chiral superstructures based on the intrinsic configurational preference of the building blocks, external fields or chiral templates. Self-assembled inorganic chiral superstructures have demonstrated significant superior optical activity from the strong electric/magnetic coupling between the building blocks, as compared with the organic counterparts. In this Review, we discuss recent progress in preparing self-assembled inorganic chiral superstructures, with an emphasis on the driving forces that enable symmetry breaking during the assembly process. The chiroptical properties and applications are highlighted and a forward-looking trajectory of where research efforts should be focused is discussed.
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40
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Narayanan RP, Abraham L. Structural DNA nanotechnology: Immobile Holliday junctions to artificial robots. Curr Top Med Chem 2022; 22:668-685. [PMID: 35023457 DOI: 10.2174/1568026622666220112143401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 12/01/2021] [Accepted: 12/05/2021] [Indexed: 11/22/2022]
Abstract
DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds off from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the 'tile' based approach covering 1D, 2D, and 3D building blocks, after which, the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through the various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.
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Affiliation(s)
- Raghu Pradeep Narayanan
- Centre for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe-85281, USA
| | - Leeza Abraham
- Centre for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe-85281, USA
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41
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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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42
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Tanjeem N, Minnis MB, Hayward RC, Shields CW. Shape-Changing Particles: From Materials Design and Mechanisms to Implementation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2105758. [PMID: 34741359 PMCID: PMC9579005 DOI: 10.1002/adma.202105758] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/06/2021] [Indexed: 05/05/2023]
Abstract
Demands for next-generation soft and responsive materials have sparked recent interest in the development of shape-changing particles and particle assemblies. Over the last two decades, a variety of mechanisms that drive shape change have been explored and integrated into particulate systems. Through a combination of top-down fabrication and bottom-up synthesis techniques, shape-morphing capabilities extend from the microscale to the nanoscale. Consequently, shape-morphing particles are rapidly emerging in a variety of contexts, including photonics, microfluidics, microrobotics, and biomedicine. Herein, the key mechanisms and materials that facilitate shape changes of microscale and nanoscale particles are discussed. Recent progress in the applications made possible by these particles is summarized, and perspectives on their promise and key open challenges in the field are discussed.
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Affiliation(s)
- Nabila Tanjeem
- Department of Chemical & Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA
| | - Montana B Minnis
- Department of Chemical & Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA
| | - Ryan C Hayward
- Department of Chemical & Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA
| | - Charles Wyatt Shields
- Department of Chemical & Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303, USA
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43
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Gao S, Wu R, Zhang Q. A novel strategy for programmable DNA tile self-assembly with a DNAzyme-mediated DNA cross circuit. NEW J CHEM 2022. [DOI: 10.1039/d1nj06012k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The proposed strategy promotes the controllability and modularization of trigger elements, realizes programmable molecular self-assembly, and has broad applications for the construction of DNA nanodevices.
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Affiliation(s)
- Siqi Gao
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
| | - Ranfeng Wu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
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44
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Mutations in artificial self-replicating tiles: A step toward Darwinian evolution. Proc Natl Acad Sci U S A 2021; 118:2111193118. [PMID: 34873040 PMCID: PMC8685680 DOI: 10.1073/pnas.2111193118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 11/24/2022] Open
Abstract
In nature, mutation is the first step of evolution, where it provides the genetic variation for the natural selection to act. Here we take a system of artificial self-replicating tiles, DNA origami, that exhibit templated reproduction. We can generate a small fraction of mutations by introducing a mismatch in hybridization between parent and daughter. We can modify the origami functionality to affect the growth rate of the mutated species, giving it less or more evolutionary advantage, and to become dominant in several generations. The introduction of mutations into an artificial self-replicating system provides new directions for research into self-assembly processes. Artificial self-replication and exponential growth holds the promise of gaining a better understanding of fundamental processes in nature but also of evolving new materials and devices with useful properties. A system of DNA origami dimers has been shown to exhibit exponential growth and selection. Here we introduce mutation and growth advantages to study the possibility of Darwinian-like evolution. We seed and grow one dimer species, AB, from A and B monomers that doubles in each cycle. A similar species from C and D monomers can replicate at a controlled growth rate of two or four per cycle but is unseeded. Introducing a small mutation rate so that AB parents infrequently template CD offspring we show experimentally that the CD species can take over the system in approximately six generations in an advantageous environment. This demonstration opens the door to the use of evolution in materials design.
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45
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De Fazio AF, Misatziou D, Baker YR, Muskens OL, Brown T, Kanaras AG. Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly. Chem Soc Rev 2021; 50:13410-13440. [PMID: 34792047 PMCID: PMC8628606 DOI: 10.1039/d1cs00632k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 12/26/2022]
Abstract
The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.
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Affiliation(s)
- Angela F De Fazio
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Doxi Misatziou
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Ysobel R Baker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Otto L Muskens
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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46
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Zheng J, Cheng X, Zhang H, Bai X, Ai R, Shao L, Wang J. Gold Nanorods: The Most Versatile Plasmonic Nanoparticles. Chem Rev 2021; 121:13342-13453. [PMID: 34569789 DOI: 10.1021/acs.chemrev.1c00422] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gold nanorods (NRs), pseudo-one-dimensional rod-shaped nanoparticles (NPs), have become one of the burgeoning materials in the recent years due to their anisotropic shape and adjustable plasmonic properties. With the continuous improvement in synthetic methods, a variety of materials have been attached around Au NRs to achieve unexpected or improved plasmonic properties and explore state-of-the-art technologies. In this review, we comprehensively summarize the latest progress on Au NRs, the most versatile anisotropic plasmonic NPs. We present a representative overview of the advances in the synthetic strategies and outline an extensive catalogue of Au-NR-based heterostructures with tailored architectures and special functionalities. The bottom-up assembly of Au NRs into preprogrammed metastructures is then discussed, as well as the design principles. We also provide a systematic elucidation of the different plasmonic properties associated with the Au-NR-based structures, followed by a discussion of the promising applications of Au NRs in various fields. We finally discuss the future research directions and challenges of Au NRs.
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Affiliation(s)
- Jiapeng Zheng
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Xizhe Cheng
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Han Zhang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Xiaopeng Bai
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Ruoqi Ai
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Lei Shao
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Jianfang Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
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47
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Affiliation(s)
- Jun Lu
- Department of Chemical Engineering University of Michigan Ann Arbor MI 48109 USA
- Biointerfaces Institute University of Michigan Ann Arbor MI 48109 USA
| | - Yao Xue
- State Key Laboratory of Supramolecular Structure and Materials College of Chemistry Jilin University Changchun China
| | - Nicholas A. Kotov
- Department of Chemical Engineering University of Michigan Ann Arbor MI 48109 USA
- Biointerfaces Institute University of Michigan Ann Arbor MI 48109 USA
- Department of Materials Science University of Michigan Ann Arbor Michigan 48109 United States
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48
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Wang Y, Wang Z, Wu X, Liu S, Liu F, Jiang Q, Ding B. DNA Nanodevices: from Mechanical Motions to Biomedical Applications. Curr Top Med Chem 2021; 22:640-651. [PMID: 34749612 DOI: 10.2174/1568026621666211105100240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022]
Abstract
Inspired by molecular machines in nature, artificial nanodevices have been designed to realize various biomedical functions. Self-assembled deoxyribonucleic acid (DNA) nanostructures that feature designed geometries, excellent spatial accuracy, nanoscale addressability and marked biocompatibility provide an attractive candidate for constructing dynamic nanodevices with biomarker-targeting and stimuli-responsiveness for biomedical applications. Here, a summary of typical construction strategies of DNA nanodevices and their operating mechanisms are presented. We also introduced recent advances in employing DNA nanodevices as platforms for biosensing and intelligent drug delivery. Finally, the broad prospects and main challenges of the DNA nanodevices in biomedical applications are discussed.
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Affiliation(s)
- Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Zhaoran Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Xiaohui Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Shaoli Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Fengsong Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing. China
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49
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Pitikultham P, Wang Z, Wang Y, Shang Y, Jiang Q, Ding B. Stimuli-Responsive DNA Origami Nanodevices and Their Biological Applications. ChemMedChem 2021; 17:e202100635. [PMID: 34729948 DOI: 10.1002/cmdc.202100635] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/29/2021] [Indexed: 02/05/2023]
Abstract
DNA origami nanotechnology has provided predictable static nanoarchitectures and dynamic nanodevices with rationally designed geometries, precise spatial addressability, and marked biocompatibility. Multiple functional elements, such as peptides, aptamers, nanoparticles, fluorescence probes, and proteins, etc. can be easily integrated into DNA origami templates with nanoscale precision, leading to a variety of promising applications. Triggered by chemical/physical stimuli, dynamic DNA origami nanodevices can switch between defined conformations or translocate autonomously, providing powerful tools for intelligent biosensing and drug delivery. In this minireview, we summarize the recent progress of dynamic DNA origami nanodevices with desired reconfigurability and feasibility to perform multiple biological tasks. We introduce varieties of DNA nanodevices that can be controlled by different molecular triggers and external stimuli. Subsequently, we highlight the recent advances in employing DNA nanodevices as biosensors and drug delivery vehicles. At last, future possibilities and perspectives are also discussed.
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Affiliation(s)
- Piyawat Pitikultham
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China.,School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoran Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China
| | - Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China.,School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China.,School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao ZhongGuanCun, Beijing, 100190, China.,School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
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50
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Kim JM, Lee C, Lee Y, Lee J, Park SJ, Park S, Nam JM. Synthesis, Assembly, Optical Properties, and Sensing Applications of Plasmonic Gap Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2006966. [PMID: 34013617 DOI: 10.1002/adma.202006966] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Plasmonic gap nanostructures (PGNs) have been extensively investigated mainly because of their strongly enhanced optical responses, which stem from the high intensity of the localized field in the nanogap. The recently developed methods for the preparation of versatile nanogap structures open new avenues for the exploration of unprecedented optical properties and development of sensing applications relying on the amplification of various optical signals. However, the reproducible and controlled preparation of highly uniform plasmonic nanogaps and the prediction, understanding, and control of their optical properties, especially for nanogaps in the nanometer or sub-nanometer range, remain challenging. This is because subtle changes in the nanogap significantly affect the plasmonic response and are of paramount importance to the desired optical performance and further applications. Here, recent advances in the synthesis, assembly, and fabrication strategies, prediction and control of optical properties, and sensing applications of PGNs are discussed, and perspectives toward addressing these challenging issues and the future research directions are presented.
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Affiliation(s)
- Jae-Myoung Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Chungyeon Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Yeonhee Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Jinhaeng Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, 16419, South Korea
| | - So-Jung Park
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, South Korea
| | - Sungho Park
- Department of Chemistry, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
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