51
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Semchenko IV, Mikhalka IS, Khakhomov SA, Samofalov AL, Balmakou AP. DNA-like Helices as Nanosized Polarizers of Electromagnetic Waves. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.794213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The possibility of using a conducting double DNA-like helix as the basis of an electromagnetic wave polarizer, which converts an incident linearly polarized wave into a reflected wave with circular polarization, has been shown. A high-frequency resonance is studied, at which the wavelength of the incident radiation is approximately equal to the length of a helical turn. The simulation of a double DNA-like helix has been carried out. The electric currents arising in the helical strands under waves with circular polarization at high-frequency resonance have been analyzed. Fundamentally different behavior of the double DNA-like helix concerning waves with right-hand or left-hand circular polarization has been established, which can be called the effect of polarization selectivity. This effect is manifested in the fact that a double DNA-like helix at high-frequency resonance can create a reflected wave having only one sign of circular polarization. The electric vector of the reflected wave produces a turn in space with the opposite winding direction compared to the double helix. These studies also highlight the electromagnetic forces of interaction between helical strands. The equilibrium of the double DNA-like helix has been studied, including as an element of metamaterials and as an object with a high potential for use in nanotechnology.
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52
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Masukawa M, Sato Y, Yu F, Tsumoto K, Yoshikawa K, Takinoue M. Water-in-water droplets selectively uptake self-assembled DNA nano/microstructures: a versatile method for purification in DNA nanotechnology. Chembiochem 2022; 23:e202200240. [PMID: 35686962 PMCID: PMC9544409 DOI: 10.1002/cbic.202200240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/08/2022] [Indexed: 11/10/2022]
Abstract
DNA is an excellent material for constructing self-assembled nano/microstructures. Owing to the widespread use of DNA as a building block in laboratories and industry, it is desirable to increase the efficiency of all steps involved in producing self-assembled DNA structures. One of the bottlenecks is the purification required to separate the excess components from the target structures. This paper describes a purification method based on the fractionation by water-in-water (W/W) droplets composed of phase-separated dextran-rich droplets in a polyethylene glycol (PEG)-rich continuous phase. The dextran-rich droplets facilitate the selective uptake of self-assembled DNA nano/microstructures and allow the separation of the target structure. This study investigates the ability to purify DNA origami, DNA hydrogels, and DNA microtubes. The W/W-droplet fractionation allows the purification of structures of a broad size spectrum without changes to the protocol. By quantifying the activity of deoxyribozyme-modified DNA origami after W/W-droplet purification, this study demonstrates that this method sufficiently preserves the accessibility to the surface of a functional DNA nanostructure. It is considered that the W/W-droplet fractionation could become one of the standard methods for the purification of self-assembled DNA nano/microstructures for biomedical and nanotechnology applications owing to its low cost and simplicity.
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Affiliation(s)
- Marcos Masukawa
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku, Computer Science, JAPAN
| | - Yusuke Sato
- Kyushu Institute of Technology - Iizuka Campus: Kyushu Kogyo Daigaku - Iizuka Campus, Intelligent and Control Systems, JAPAN
| | - Fujio Yu
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku, Computer Science, JAPAN
| | - Kanta Tsumoto
- Mie University: Mie Daigaku, Chemistry for Materials, JAPAN
| | - Kenichi Yoshikawa
- Kyoto University: Kyoto Daigaku, Center for Integrative Medicine and Physics, Institute for Advanced Study, JAPAN
| | - Masahiro Takinoue
- Tokyo Institute of Technology, Department of Computer Science, 4259-J2-36 Nagatsuta-cho, Midori-ku, 226-8502, Yokohama, JAPAN
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53
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Zhou X, Lin S, Yan H. Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine. J Nanobiotechnology 2022; 20:257. [PMID: 35658974 PMCID: PMC9164479 DOI: 10.1186/s12951-022-01449-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.
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Affiliation(s)
- Xu Zhou
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Su Lin
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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54
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Cao S, Wang F, Wang L, Fan C, Li J. DNA nanotechnology-empowered finite state machines. NANOSCALE HORIZONS 2022; 7:578-588. [PMID: 35502877 DOI: 10.1039/d2nh00060a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A finite state machine (FSM, or automaton) is an abstract machine that can switch among a finite number of states in response to temporally ordered inputs, which allows storage and processing of information in an order-sensitive manner. In recent decades, DNA molecules have been actively exploited to develop information storage and nanoengineering materials, which hold great promise for smart nanodevices and nanorobotics under the framework of FSM. In this review, we summarize recent progress in utilizing DNA self-assembly and DNA nanostructures to implement FSMs. We describe basic principles for representative DNA FSM prototypes and highlight their advantages and potential in diverse applications. The challenges in this field and future directions have also been discussed.
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Affiliation(s)
- Shuting Cao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wang
- 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.
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200127, 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.
| | - Jiang 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.
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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55
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Yu L, Cheng J, Wang D, Pan V, Chang S, Song J, Ke Y. Stress in DNA Gridiron Facilitates the Formation of Two-Dimensional Crystalline Structures. J Am Chem Soc 2022; 144:9747-9752. [PMID: 35578912 DOI: 10.1021/jacs.2c02009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Programmable DNA nanotechnology has generated some of the most intricate self-assembled nanostructures and has been employed in a growing number of applications, including functional nanomaterials, nanofabrication, biophysics, photonics, molecular machines, and drug delivery. An important design rule for DNA nanostructures is to minimize the mechanical stress to reduce the potential energy in these nanostructures whenever it is possible. This work revisits the DNA gridiron design consisting of Holliday junctions and compares the self-assembly of the canonical DNA gridiron with a new design of DNA gridiron, which has a higher degree of mechanical stress because of the interweaving of DNA helices. While the interweaving DNA gridiron indeed exhibits lower yield, compared to its canonical counterpart of a similar size, we discover that the mechanical stress within the interweaving gridiron can promote the formation of the two-dimensional crystalline lattice instead of nanotubes. Furthermore, tuning the design of interweaving gridiron leads to the change of overall crystal size and regularity of geometry. Interweaving DNA double helices represents a new design strategy in the self-assembly of DNA nanostructures. Furthermore, the discovery of the new role of mechanical stress in the self-assembly of DNA nanostructures provides useful knowledge to DNA nanotechnology practitioners: a more balanced view regarding mechanical stress can be considered when designing future DNA nanostructures.
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Affiliation(s)
- Lei Yu
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongfang Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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56
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Hu P, Dong Y, Yao C, Yang D. Construction of branched DNA-based nanostructures for diagnosis, therapeutics and protein engineering. Chem Asian J 2022; 17:e202200310. [PMID: 35468254 DOI: 10.1002/asia.202200310] [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: 03/26/2022] [Revised: 04/23/2022] [Indexed: 11/08/2022]
Abstract
Branched DNA with multibranch-like anisotropic topology serves as a promising and powerful building block in constructing multifunctional-integrated nanomaterials in a programmable and controllable manner. Recently, a series of branched DNA-based functional nanomaterials were developed by elaborate molecular design. In this review, we focused on the construction of branched DNA-based nanostructures for biological and biomedical applications. First, the molecular design and synthesis method of branched DNA monomer were briefly described. Then, the construction strategies of branched DNA-based nanostructures were categorially discussed, including target-triggered polymerization, enzymatic extension and hybrid assembly. Finally, the biological and biomedical applications including diagnosis, therapeutics and protein engineering were summarized. We envision that the review will contribute to the further development of branched DNA-based nanomaterials with great application potential in the field of biomedicine, thus building a new bridge between material chemistry and biomedicine.
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Affiliation(s)
- Pin Hu
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Yuhang Dong
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Chi Yao
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Dayong Yang
- Tianjin University, Chemistry Department, Room 328, Building 54, 300350, Tianjin, CHINA
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57
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Li J, Huang J. Fuel‐powered DNA nanomachines for biosensing and cancer therapy. Chempluschem 2022; 87:e202200098. [DOI: 10.1002/cplu.202200098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/12/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jing Li
- Yangzhou University School of Chemistry and Chemical Engineering CHINA
| | - Jin Huang
- Hunan University Chemistry lushan road 410082 Changsha CHINA
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58
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Taher M, Maity B, Nakane T, Abe S, Ueno T, Mazumdar S. Controlled Uptake of an Iridium Complex inside Engineered apo‐Ferritin Nanocages: Study of Structure and Catalysis**. Angew Chem Int Ed Engl 2022; 61:e202116623. [DOI: 10.1002/anie.202116623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Indexed: 12/17/2022]
Affiliation(s)
- Mohd Taher
- Department of Chemical Sciences Tata Institute of Fundamental Research Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Basudev Maity
- School of Life science and Technology Tokyo Institute of Technology Nagatsuta-cho 4259, Midori-ku Yokohama 226-8501 Japan
| | - Taiki Nakane
- School of Life science and Technology Tokyo Institute of Technology Nagatsuta-cho 4259, Midori-ku Yokohama 226-8501 Japan
| | - Satoshi Abe
- School of Life science and Technology Tokyo Institute of Technology Nagatsuta-cho 4259, Midori-ku Yokohama 226-8501 Japan
| | - Takafumi Ueno
- School of Life science and Technology Tokyo Institute of Technology Nagatsuta-cho 4259, Midori-ku Yokohama 226-8501 Japan
- World Research Hub Initiative (WRHI) Tokyo Institute of Technology Nagatsuta-cho 4259, Midori-ku Yokohama 226-8501 Japan
| | - Shyamalava Mazumdar
- Department of Chemical Sciences Tata Institute of Fundamental Research Homi Bhabha Road, Colaba Mumbai 400005 India
- World Research Hub Initiative (WRHI) Tokyo Institute of Technology Nagatsuta-cho 4259, Midori-ku Yokohama 226-8501 Japan
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59
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Riolo J, Steckl AJ. Comparative analysis of genome code complexity and manufacturability with engineering benchmarks. Sci Rep 2022; 12:2808. [PMID: 35181687 PMCID: PMC8857313 DOI: 10.1038/s41598-022-06723-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
When knowledge has advanced to a state that includes a predictive understanding of the relationship between genome sequence and organism phenotype it will be possible for future engineers to design and produce synthetic organisms. However, the possibility of synthetic biology does not necessarily guarantee its feasibility, in much the same way that the possibility of a brute force attack fails to ensure the timely breaking of robust encryption. The size and range of natural genomes, from a few million base pairs for bacteria to over 100 billion base pairs for some plants, suggests it is necessary to evaluate the practical limits of designing genomes of similar complexity. This analysis characterizes the complexity of natural genomes, compares them to existing engineering benchmarks, and shows that existing large software programs are on similar scale with the genome of complex natural organisms.
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Affiliation(s)
- Joseph Riolo
- Nanoelectronics Laboratory, Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221-0030, USA
| | - Andrew J Steckl
- Nanoelectronics Laboratory, Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221-0030, USA.
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60
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Malik S, Kumar V, Liu CH, Shih KC, Krueger S, Nieh MP, Bahal R. Head on Comparison of Self- and Nano-assemblies of Gamma Peptide Nucleic Acid Amphiphiles. ADVANCED FUNCTIONAL MATERIALS 2022; 32:2109552. [PMID: 35210986 PMCID: PMC8863176 DOI: 10.1002/adfm.202109552] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Indexed: 05/14/2023]
Abstract
Peptide nucleic acids (PNAs) are nucleic acid analogs with superior hybridization properties and enzymatic stability than deoxyribonucleic acid (DNA). In addition to gene targeting applications, PNAs have garnered significant attention as bio-polymer due to the Watson-Crick -based molecular recognition and flexibility of synthesis. Here, we engineered PNA amphiphiles using chemically modified gamma PNA (8 mer in length) containing hydrophilic diethylene glycol units at the gamma position and covalently conjugated lauric acid (C12) as a hydrophobic moiety. Gamma PNA (γPNA) amphiphiles self-assemble into spherical vesicles. Further, we formulate nano-assemblies using the amphiphilic γPNA as a polymer via ethanol injection-based protocols. We perform comprehensive head-on comparison of the physicochemical and cellular uptake properties of PNA derived self- and nano-assemblies. Small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS) analysis reveal ellipsoidal morphology of γPNA nano-assemblies that results in superior cellular delivery compate to the spherical self-assembly. Next, we compare the functional activities of γPNA self-and nano-assemblies in lymphoma cells via multiple endpoints, including gene expression, cell viability, and apoptosis-based assays. Overall, we establish that γPNA amphiphile is a functionally active bio-polymer to formulate nano-assemblies for a wide range of biomedical applications.
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Affiliation(s)
- Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Vikas Kumar
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Chung-Hao Liu
- Polymer Program, Institute of Material Sciences, University of Connecticut, 191 Auditorium Road, Storrs, CT, 06269, USA
| | - Kuo-Chih Shih
- Polymer Program, Institute of Material Sciences, University of Connecticut, 191 Auditorium Road, Storrs, CT, 06269, USA
| | - Susan Krueger
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6102, USA
| | - Mu-Ping Nieh
- Polymer Program, Institute of Material Sciences, University of Connecticut, 191 Auditorium Road, Storrs, CT, 06269, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
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61
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Abstract
Stimuli-responsive DNA-based hydrogels are attracting growing interest because of their smart responsiveness, excellent biocompatibility, regulated biodegradability, and programmable design properties. Integration of reconfigurable DNA architectures and switchable supramolecular moieties (as cross-linkers) in hydrogels by responding to external stimuli provides an ideal approach for the reversible tuning structural and mechanical properties of the hydrogels, which can be exploited in the development of intelligent DNA-based materials. This review highlights recent advances in the design of responsive pure DNA hydrogels, DNA-polymer hybrid hydrogels, and autonomous DNA-based hydrogels with transient behaviors. A variety of chemically and physically triggered DNA-based stimuli-responsive hydrogels and their versatile applications in biosensing, biocatalysis, cell culture and separation, drug delivery, shape memory, self-healing, and robotic actuators are summarized. Finally, we address the key challenges that the field will face in the coming years, and future prospects are identified.
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Affiliation(s)
- Chen Wang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Junji Zhang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science & Technology, No. 130 Meilong Road, Shanghai 200237, China
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62
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Fabrini G, Minard A, Brady RA, Di Antonio M, Di Michele L. Cation-Responsive and Photocleavable Hydrogels from Noncanonical Amphiphilic DNA Nanostructures. NANO LETTERS 2022; 22:602-611. [PMID: 35026112 PMCID: PMC8796241 DOI: 10.1021/acs.nanolett.1c03314] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/01/2021] [Indexed: 05/26/2023]
Abstract
Thanks to its biocompatibility, versatility, and programmable interactions, DNA has been proposed as a building block for functional, stimuli-responsive frameworks with applications in biosensing, tissue engineering, and drug delivery. Of particular importance for in vivo applications is the possibility of making such nanomaterials responsive to physiological stimuli. Here, we demonstrate how combining noncanonical DNA G-quadruplex (G4) structures with amphiphilic DNA constructs yields nanostructures, which we termed "Quad-Stars", capable of assembling into responsive hydrogel particles via a straightforward, enzyme-free, one-pot reaction. The embedded G4 structures allow one to trigger and control the assembly/disassembly in a reversible fashion by adding or removing K+ ions. Furthermore, the hydrogel aggregates can be photo-disassembled upon near-UV irradiation in the presence of a porphyrin photosensitizer. The combined reversibility of assembly, responsiveness, and cargo-loading capabilities of the hydrophobic moieties make Quad-Stars a promising candidate for biosensors and responsive drug delivery carriers.
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Affiliation(s)
- Giacomo Fabrini
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Aisling Minard
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Ryan A. Brady
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Marco Di Antonio
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Lorenzo Di Michele
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
- Department
of Physics—Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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63
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Taher M, Maity B, Nakane T, Abe S, Ueno T, Mazumdar S. Controlled Uptake of an Iridium Complex inside Engineered apo‐Ferritin Nanocages: Study of Structure and Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mohd Taher
- Tata Institute of Fundamental Research Department of Chemical Sciences Homi Bhabha RoadNavy NagarColaba 400005 Mumbai INDIA
| | - Basudev Maity
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku School of Life Science and Technology Nagatsuta-Cho4259-B55 226-8501 Midori-ku JAPAN
| | - Taiki Nakane
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku School of Life Science and technology Nagatsuta-Cho4259-B55 226-8501 Midori-ku JAPAN
| | - Satoshi Abe
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku School of Life Science and Technology Nagatsuta-Cho4259-B55 226-8501 Midori-ku JAPAN
| | - Takafumi Ueno
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku School of Life Science and Technology Nagatsuta-cho4259-B55 226-8501 Midori-ku JAPAN
| | - Shyamalava Mazumdar
- Tata Institute of Fundamental Research Department of Chemical Sciences Homi Bhabha RoadColaba 400005 Mumbai INDIA
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64
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Poppleton E, Mallya A, Dey S, Joseph J, Šulc P. Nanobase.org: a repository for DNA and RNA nanostructures. Nucleic Acids Res 2022; 50:D246-D252. [PMID: 34747480 PMCID: PMC8728195 DOI: 10.1093/nar/gkab1000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
We introduce a new online database of nucleic acid nanostructures for the field of DNA and RNA nanotechnology. The database implements an upload interface, searching and database browsing. Each deposited nanostructures includes an image of the nanostructure, design file, an optional 3D view, and additional metadata such as experimental data, protocol or literature reference. The database accepts nanostructures in any preferred format used by the uploader for the nanostructure design. We further provide a set of conversion tools that encourage design file conversion into common formats (oxDNA and PDB) that can be used for setting up simulations, interactive editing or 3D visualization. The aim of the repository is to provide to the DNA/RNA nanotechnology community a resource for sharing their designs for further reuse in other systems and also to function as an archive of the designs that have been achieved in the field so far. Nanobase.org is available at https://nanobase.org/.
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Affiliation(s)
- Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Aatmik Mallya
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Swarup Dey
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- Wyss Institute, Harvard University, Boston, MA 02115, USA
| | - Joel Joseph
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
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65
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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: 32] [Impact Index Per Article: 16.0] [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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66
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Xia LY, Tang YN, Zhang J, Dong TY, Zhou RX. Advances in the DNA Nanotechnology for the Cancer Biomarkers Analysis: Attributes and Applications. Semin Cancer Biol 2022; 86:1105-1119. [PMID: 34979273 DOI: 10.1016/j.semcancer.2021.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023]
Abstract
The most commonly used clinical methods are enzyme-linked immunosorbent assay (ELISA) and quantitative PCR (qPCR) in which ELISA was applied for the detection of protein biomarkers and qPCR was especially applied for nucleic acid biomarker analysis. Although these constructed methods have been applied in wide range, they also showed some inherent shortcomings such as low sensitivity, large sample volume and complex operations. At present, many methods have been successfully constructed on the basis of DNA nanotechnology with the merits of high accuracy, rapid and simple operation for cancer biomarkers assay. In this review, we summarized the bioassay strategies based on DNA nanotechnology from the perspective of the analytical attributes for the first time and discussed and the feasibility of the reported strategies for clinical application in the future.
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Affiliation(s)
- Ling-Ying Xia
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China; Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Ya-Nan Tang
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Jie Zhang
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Tian-Yu Dong
- College of Chemistry, Sichuan University Chengdu, Sichuan 610064, PR China
| | - Rong-Xing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China.
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67
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Tang D, Fan W, Xiong M, Li M, Xiong B, Zhang XB. Topological DNA Tetrahedron Encapsulated Gold Nanoparticle Enables Precise Ligand Engineering for Targeted Cell Imaging. Anal Chem 2021; 93:17036-17042. [PMID: 34910458 DOI: 10.1021/acs.analchem.1c03682] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ligand-functionalized plasmonic nanoparticles have been widely used for targeted imaging in living systems. However, ligand presentation and encoding on the nanoparticle's surface in a stoichiometrically controllable manner remains a great challenge. Herein, we propose a method to construct ligand-engineered plasmonic nanoprobes by using nanoparticle encapsulation with topological DNA tetrahedrons, which enables the programmed ligand loading for precise regulation of targeting efficiency of nanoprobes in biorelated applications. With this method, we demonstrated the preparation of functionalized plasmonic nanoprobes by programmed loading of RGD peptides and aptamers onto the DNA tetrahedron encapsulated gold nanoparticles with controllable stoichiometric ratios. The cell imaging and particle counting assays suggested that the targeting efficiency of the nanoprobes could be readily modulated by tailoring the number and stoichiometric ratios of the loaded ligands, respectively. It can be anticipated that this robust strategy could provide new opportunities for the construction of efficacious nanoprobes and delivery systems for versatile bioapplications.
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Affiliation(s)
- Decui Tang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Wenjun Fan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Mili Li
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Bin Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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68
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Sidharthan DS, Abhinandan R, Balagangadharan K, Selvamurugan N. Advancements in nucleic acids-based techniques for bone regeneration. Biotechnol J 2021; 17:e2100570. [PMID: 34882984 DOI: 10.1002/biot.202100570] [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: 10/19/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 12/21/2022]
Abstract
The dynamic biology of bone involving an enormous magnitude of cellular interactions and signaling transduction provides ample biomolecular targets, which can be enhanced or repressed to mediate a rapid regeneration of the impaired bone tissue. The delivery of nucleic acids such as DNA and RNA can enhance the expression of osteogenic proteins. Members of the RNA interference pathway such as miRNA and siRNA can repress negative osteoblast differentiation regulators. Advances in nanomaterials have provided researchers with a plethora of delivery modules that can ensure proper transfection. Combining the nucleic acid carrying vectors with bone scaffolds has met with tremendous success in accomplishing bone formation. Recent years have witnessed the advent of CRISPR and DNA nanostructures in regenerative medicine. This review focuses on the delivery of nucleic acids and touches upon the prospect of CRISPR and DNA nanostructures for bone tissue engineering, emphasizing their potential in treating bone defects.
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Affiliation(s)
- Dharmaraj Saleth Sidharthan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Ranganathan Abhinandan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Kalimuthu Balagangadharan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Nagarajan Selvamurugan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
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69
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Arshad R, Fatima I, Sargazi S, Rahdar A, Karamzadeh-Jahromi M, Pandey S, Díez-Pascual AM, Bilal M. Novel Perspectives towards RNA-Based Nano-Theranostic Approaches for Cancer Management. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:3330. [PMID: 34947679 PMCID: PMC8708502 DOI: 10.3390/nano11123330] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/24/2021] [Accepted: 12/05/2021] [Indexed: 12/19/2022]
Abstract
In the fight against cancer, early diagnosis is critical for effective treatment. Traditional cancer diagnostic technologies, on the other hand, have limitations that make early detection difficult. Therefore, multi-functionalized nanoparticles (NPs) and nano-biosensors have revolutionized the era of cancer diagnosis and treatment for targeted action via attaching specified and biocompatible ligands to target the tissues, which are highly over-expressed in certain types of cancers. Advancements in multi-functionalized NPs can be achieved via modifying molecular genetics to develop personalized and targeted treatments based on RNA interference. Modification in RNA therapies utilized small RNA subunits in the form of small interfering RNAs (siRNA) for overexpressing the specific genes of, most commonly, breast, colon, gastric, cervical, and hepatocellular cancer. RNA-conjugated nanomaterials appear to be the gold standard for preventing various malignant tumors through focused diagnosis and delivering to a specific tissue, resulting in cancer cells going into programmed death. The latest advances in RNA nanotechnology applications for cancer diagnosis and treatment are summarized in this review.
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Affiliation(s)
- Rabia Arshad
- Faculty of Pharmacy, University of Lahore, Lahore 45320, Pakistan;
| | - Iqra Fatima
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan 98167-43463, Iran;
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol 98613-35856, Iran
| | | | - Sadanand Pandey
- Department of Chemistry, College of Natural Science, Yeungnam University, 280 Daehak-Ro, Gyeongsan 38541, Korea;
| | - Ana M. Díez-Pascual
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona, Km. 33.6, 28805 Alcalá de Henares, Madrid, Spain
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China;
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70
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Lee C, Kim YJ, Kim KS, Lee JY, Kim DN. Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules. Nucleic Acids Res 2021; 49:12591-12599. [PMID: 34850119 PMCID: PMC8643692 DOI: 10.1093/nar/gkab1119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/06/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
Recent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.
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Affiliation(s)
- Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Young-Joo Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Kyung Soo Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea.,Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea.,Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
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71
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Matsuda H, Ito H, Nukaga Y, Uehara S, Sato K, Hara RI, Wada T. Solid-phase synthesis of oligouridine boranophosphates using the H-boranophosphonate method with 2′-O-(2-cyanoethoxymethyl) protection. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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72
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Matsuda H, Yoshida E, Shinoda T, Sato K, Hara RI, Wada T. Solution-phase synthesis of oligodeoxyribonucleotides using the H-phosphonate method with N-unprotected 5'-phosphite monomers. RSC Adv 2021; 11:38094-38107. [PMID: 35498072 PMCID: PMC9044012 DOI: 10.1039/d1ra06619f] [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: 09/03/2021] [Accepted: 11/17/2021] [Indexed: 11/21/2022] Open
Abstract
Recent advances in nucleic acid therapeutics increase the requirements for developing efficient methods for the chemical synthesis of oligodeoxyribonucleotides (ODNs). In this study, we report a new approach for the solution-phase synthesis of ODNs using the H-phosphonate method with N-unprotected 5'-phosphite monomers. The 5'-phosphite monomers are synthesized in a single step from unprotected 2'-deoxyribonucleosides using 5'-O-selective phosphitylation and can be applied to the synthetic cycle of the H-phosphonate method. We synthesized four kinds of 5'-phosphite monomers and then optimized the conditions for the condensation between the 3'-hydroxy groups of the 5'-phosphite monomers and the H-phosphonate monoesters. As a result of various investigations, solution-phase synthesis of trithymidine diphosphate (TTT) and tetramers containing four kinds of nucleobases was achieved according to the procedure consisting of repeated condensation, deprotection, and purification using simple extraction or precipitation.
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Affiliation(s)
- Hiromasa Matsuda
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
- CMC Production Technology Laboratories, MTPC Production Technology & Supply Chain Management Division, Mitsubishi Tanabe Pharma Corporation 3-16-89 Kashima, Yodogawa-ku Osaka 532-8505 Japan
| | - Erina Yoshida
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
| | - Takaaki Shinoda
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
| | - Rintaro Iwata Hara
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University 1-5-45 Yushima, Bunkyo-ku Tokyo 113-8519 Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science 2641 Yamazaki Noda Chiba 278-8510 Japan
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73
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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: 172] [Impact Index Per Article: 57.3] [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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74
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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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75
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Thapa K, Liu W, Wang R. Nucleic acid-based electrochemical biosensor: Recent advances in probe immobilization and signal amplification strategies. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 14:e1765. [PMID: 34734485 DOI: 10.1002/wnan.1765] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/06/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022]
Abstract
With the increasing importance of accurate and early disease diagnosis and the development of personalized medicine, DNA-based electrochemical biosensor has attracted broad scientific and clinical interests in the past decades due to its unique hybridization specificity, fast response time, and potential for miniaturization. In order to achieve high detection sensitivity, the design of DNA electrochemical biosensors depends critically on the improvement of the accessibility of target molecules and the enhancement of signal readout. Here, we summarize the recent advances in DNA probe immobilization and signal amplification strategies with a special focus on DNA nanostructure-supported DNA probe immobilization method, which provides the opportunity to rationally control the distance between probes and keep them in upright confirmation, as well as the contribution of functional nanomaterials in enhancing the signal amplification. The next challenge of biosensors will be the fabrication of point-of-care devices for clinical testing. The advancement of multidisciplinary areas, including nanofabrication, material science, and biochemistry, has exhibited profound promise in achieving such portable sensing devices. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
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Affiliation(s)
- Krishna Thapa
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri, USA
| | - Wenyan Liu
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri, USA.,Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri, USA
| | - Risheng Wang
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri, USA
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76
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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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77
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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: 39] [Impact Index Per Article: 13.0] [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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78
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Mo L, Liang D, He W, Yang C, Lin W. Ratiometric and amplified fluorescence nanosensor based on a DNA tetrahedron for miRNA imaging in living cells. J Mater Chem B 2021; 9:8341-8347. [PMID: 34528052 DOI: 10.1039/d1tb01537k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme-free signal amplification approaches have attracted considerable attention in the field of intracellular miRNA analysis. However, the application of nucleic acid amplification has been limited by intracellular delivery of multiple oligonucleotide components with precise stoichiometry. In this work, we propose a new DNA tetrahedron (DTN)-based sensing platform addressing the delivery and stoichiometric control of nucleic components for enzyme-free amplification. The nanosensor is composed of two DTN probes; DTN-F served as the target recognition and signal output unit, and DTN-H served as the signal amplification unit. DTNs could facilitate the cell internalization of the nucleic acid probes and protect them from nuclease degradation. In the absence of target miRNA, the fluorescent strands (F) hybridize with the hanging sequences of DTN, and FAM and TAMRA labeled on F will be separated, blocking fluorescence resonance energy transfer (FRET). In the presence of the target miRNA, F will be displaced by the target and the hairpin structure will be restored, bringing the FRET pair into close proximity and inducing a FRET signal. Moreover, the helper strands (H) on DTN-H could liberate target miRNA through strand displacement, which will initiate a new round of reaction, generating an amplified FRET signal. The DTN nanosensor realized sensitive and selective detection of let-7a in buffer solution and 10% FBS solution. In addition, imaging of miRNA in the different cell lines and monitoring of intracellular miRNA fluctuations were carried out The developed method offers a new tool for bioanalytical and biomedical research.
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Affiliation(s)
- Liuting Mo
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China.
| | - Danlian Liang
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China.
| | - Wanqi He
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China.
| | - Chan Yang
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China.
| | - Weiying Lin
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China.
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79
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The biological applications of DNA nanomaterials: current challenges and future directions. Signal Transduct Target Ther 2021; 6:351. [PMID: 34620843 PMCID: PMC8497566 DOI: 10.1038/s41392-021-00727-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 02/08/2023] Open
Abstract
DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.
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80
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81
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Gür FN, Kempter S, Schueder F, Sikeler C, Urban MJ, Jungmann R, Nickels PC, Liedl T. Double- to Single-Strand Transition Induces Forces and Motion in DNA Origami Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2101986. [PMID: 34337805 PMCID: PMC7611957 DOI: 10.1002/adma.202101986] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/07/2021] [Indexed: 05/30/2023]
Abstract
The design of dynamic, reconfigurable devices is crucial for the bottom-up construction of artificial biological systems. DNA can be used as an engineering material for the de-novo design of such dynamic devices. A self-assembled DNA origami switch is presented that uses the transition from double- to single-stranded DNA and vice versa to create and annihilate an entropic force that drives a reversible conformational change inside the switch. It is distinctively demonstrated that a DNA single-strand that is extended with 0.34 nm per nucleotide - the extension this very strand has in the double-stranded configuration - exerts a contractive force on its ends leading to large-scale motion. The operation of this type of switch is demonstrated via transmission electron microscopy, DNA-PAINT super-resolution microscopy and darkfield microscopy. The work illustrates the intricate and sometimes counter-intuitive forces that act in nanoscale physical systems that operate in fluids.
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Affiliation(s)
- Fatih N Gür
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Susanne Kempter
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Florian Schueder
- Research Group Molecular Imaging and Bionanotechnology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, 06510, United States
| | - Christoph Sikeler
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Maximilian J Urban
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Research Group Molecular Imaging and Bionanotechnology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Philipp C Nickels
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
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82
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A dissipative pathway for the structural evolution of DNA fibres. Nat Chem 2021; 13:843-849. [PMID: 34373598 DOI: 10.1038/s41557-021-00751-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 06/14/2021] [Indexed: 11/08/2022]
Abstract
Biochemical networks interconnect, grow and evolve to express new properties as different chemical pathways are selected during a continuous cycle of energy consumption and transformation. In contrast, synthetic systems that push away from equilibrium usually return to the same self-assembled state, often generating waste that limits system recyclability and prevents the formation of adaptable networks. Here we show that annealing by slow proton dissipation selects for otherwise inaccessible morphologies of fibres built from DNA and cyanuric acid. Using single-molecule fluorescence microscopy, we observe that proton dissipation influences the growth mechanism of supramolecular polymerization, healing gaps within fibres and converting highly branched, interwoven networks into nanocable superstructures. Just as the growth kinetics of natural fibres determine their structural attributes to modulate function, our system of photoacid-enabled depolymerization and repolymerization selects for healed materials to yield organized, robust fibres. Our method provides a chemical route for error-checking, distinct from thermal annealing, that improves the morphologies and properties of supramolecular materials using out-of-equilibrium systems.
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83
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Correction to: DNA Nanotechnology for Multimodal Synergistic Theranostics. JOURNAL OF ANALYSIS AND TESTING 2021. [DOI: 10.1007/s41664-021-00190-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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84
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Ye J, Aftenieva O, Bayrak T, Jain A, König TAF, Erbe A, Seidel R. Complex Metal Nanostructures with Programmable Shapes from Simple DNA Building Blocks. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2100381. [PMID: 34085729 DOI: 10.1002/adma.202100381] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Advances in DNA nanotechnology allow the design and fabrication of highly complex DNA structures, uisng specific programmable interactions between smaller nucleic acid building blocks. To convey this concept to the fabrication of metallic nanoparticles, an assembly platform is developed based on a few basic DNA structures that can serve as molds. Programming specific interactions between these elements allows the assembly of mold superstructures with a range of different geometries. Subsequent seeded growth of gold within the mold cavities enables the synthesis of complex metal structures including tightly DNA-caged particles, rolling-pin- and dumbbell-shaped particles, as well as T-shaped and loop particles with high continuity. The method further supports the formation of higher-order assemblies of the obtained metal geometries. Based on electrical and optical characterizations, it is expected that the developed platform is a valuable tool for a self-assembly-based fabrication of nanoelectronic and nanooptic devices.
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Affiliation(s)
- Jingjing Ye
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01069, Dresden, Germany
| | - Olha Aftenieva
- Leibniz-Institut für Polymerforschung Dresden e. V., Hohe Straße 6, 01069, Dresden, Germany
| | - Türkan Bayrak
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01069, Dresden, Germany
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328, Dresden, Germany
| | - Archa Jain
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328, Dresden, Germany
- Faculty of Electrical Engineering and Information Technology, Chair of Nanoelectronics Technologies, Technische Universität Chemnitz, 09107, Chemnitz, Germany
| | - Tobias A F König
- Leibniz-Institut für Polymerforschung Dresden e. V., Hohe Straße 6, 01069, Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01069, Dresden, Germany
| | - Artur Erbe
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01069, Dresden, Germany
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328, Dresden, Germany
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01069, Dresden, Germany
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85
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Yang J, Zhao N, Liang Y, Lu Z, Zhang C. Structure-flexible DNA origami translocation through a solid-state nanopore. RSC Adv 2021; 11:23471-23476. [PMID: 35479792 PMCID: PMC9036576 DOI: 10.1039/d1ra04267j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/27/2021] [Indexed: 12/30/2022] Open
Abstract
Nanopore detection is a label-free detection method designed to analyze single molecules by comparing specific translocation events with high signal-to-noise ratios. However, it is still challenging to understand the influences of structural flexibility of 100 nm DNA origami on nanopore translocations. Here, we used solid-state nanopores to characterize the translocation of “nunchaku” origami structures, the flexibility of which can be regulated by introducing specific DNA strands and streptavidin protein. The structural changes can result in significant variations in the translocation signals and distributions. It is anticipated that such a method of the flexible DNA origami translocation through a solid-state nanopore will find further applications in molecular detection as well as biosensing. Using a solid-state nanopore to characterize the translocation of “nunchaku” origami with tunable-structures.![]()
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Affiliation(s)
- Jing Yang
- School of Control and Computer Engineering, North China Electric Power University Beijing 102206 China .,School of Electronics Engineering and Computer Science, Peking University Beijing 100871 China
| | - Nan Zhao
- School of Control and Computer Engineering, North China Electric Power University Beijing 102206 China
| | - Yuan Liang
- School of Control and Computer Engineering, North China Electric Power University Beijing 102206 China
| | - Zuhong Lu
- The State Key Laboratory of Bioelectronics, Southeast University Nanjing 211189 China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University Beijing 100871 China
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86
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Cheng X, Bao Y, Liang S, Li B, Liu Y, Wu H, Ma X, Chu Y, Shao Y, Meng Q, Zhou G, Song Q, Zou B. Flap Endonuclease 1-Assisted DNA Walkers for Sensitively and Specifically Sensing ctDNAs. Anal Chem 2021; 93:9593-9601. [PMID: 34191475 DOI: 10.1021/acs.analchem.1c01765] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA walkers have shown superior performance in biosensing due to their programmability to design molecular walking behaviors with specific responses to different biological targets. However, it is still challenging to make DNA walkers capable of distinguishing DNA targets with single-base differences, so that DNA walkers that can be used for circulating tumor DNA sensing are rarely reported. Herein, a flap endonuclease 1 (FEN 1)-assisted DNA walker has been proposed to achieve mutant biosensing. The target DNA is captured on a gold nanoparticle (AuNP) as a walking strand to walk by hybridizing to the track strands on the surface of the AuNP. FEN 1 is employed to report the walking events by cleaving the track strands that must form a three-base overlapping structure recognized by FEN 1 after hybridizing with the captured target DNA. Owing to the high specificity of FEN 1 for structure recognition, the one-base mutant DNA target can be discriminated from wild-type DNA. By constructing a sensitivity-enhanced DNA walker system, as low as 1 fM DNA targets and 0.1% mutation abundance can be sensed, and the theoretical detection limits for detecting the DNA target and mutation abundance achieve 0.22 fM and 0.01%, respectively. The results of epidermal growth factor receptor (EGFR) L858R mutation detection on cell-free DNA samples from 15 patients with nonsmall cell lung cancer were completely consistent with that of next-generation sequencing, indicating that our DNA walker has potential for liquid biopsy.
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Affiliation(s)
- Xianyi Cheng
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yaofei Bao
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Shuo Liang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Bo Li
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yunlong Liu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haiping Wu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmacy, Southern Medical University, Guangzhou 510515, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Yang Shao
- Nanjing Shihe Gene Biotechnology Co., Ltd., Nanjing 210032, China
| | - Qi Meng
- Nanjing Shihe Gene Biotechnology Co., Ltd., Nanjing 210032, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmacy, Southern Medical University, Guangzhou 510515, China
| | - Qinxin Song
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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87
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Feng C, Zhang C, Guo J, Li G, Ye B, Zou L. Novel preparation method of bipedal DNA walker based on hybridization chain reaction for ultrasensitive DNA biosensing. Anal Chim Acta 2021; 1176:338781. [PMID: 34399897 DOI: 10.1016/j.aca.2021.338781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/05/2021] [Accepted: 06/15/2021] [Indexed: 11/27/2022]
Abstract
In this work, a novel strategy for preparation of bipedal DNA walker (BDW) based on hybridization chain reaction (HCR) with the assistance of Exonuclease III (Exo III) was proposed. Based on this strategy, an electrochemical biosensor was constructed to achieve sensitive detection of CYFRA 21-1 DNA. Firstly, target recognition and circulation were achieved through a one-step catalytic hairpin assembly (CHA) reaction. For further amplification, hybridization chain reaction (HCR) was employed to form duplex-stranded DNA (dsDNA) nanostructure in homogeneous solution. In particular, the elongated single strand of the hairpin DNA for HCR was designed as the Mg2+ DNAzyme sequence. With the assistance of Exo III, dsDNA nanostructure can be digested and transformed into large amounts of BDW. These BDW can cleave the signal probe driven by Mg2+, which was modified on the electrode surface and thus achieved "signal-off" detection of target. This BDW preparation method based on HCR with the digestion of Exo III converted one target input into large amount of BDW. Coupled with the walking cleavage of BDW, a series of cascade amplification endowed high sensitivity with this biosensor and realized ultrasensitive detection of target DNA with the detection limit as low as 3.01 aM.
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Affiliation(s)
- Changrui Feng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Chi Zhang
- Department of Orthopedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, PR China
| | - Jiaxin Guo
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Gaiping Li
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Baoxian Ye
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lina Zou
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China.
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88
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Hong T, Zheng R, Qiu L, Zhou S, Chao H, Li Y, Rui W, Cui P, Ni X, Tan S, Jiang P, Wang J. Fluorescence coupled capillary electrophoresis as a strategy for tetrahedron DNA analysis. Talanta 2021; 228:122225. [PMID: 33773730 DOI: 10.1016/j.talanta.2021.122225] [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: 10/18/2020] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 10/22/2022]
Abstract
A strategy based on fluorescence coupled capillary electrophoresis (CE-FL) was developed for analyzing tetrahedron DNA (TD) and TD-doxorubicin (DOX) conjugate. Capillary gel electrophoresis exhibited desirable performance for separating TD and DNA strands. Under the optimized conditions, satisfactory repeatability concerning run-to-run and interday repeatability was obtained, and relative standard deviation value of resolution (n = 6) was 0.64%. Furthermore, the combination of CE and fluorescence detection provided a sensitive platform for quantifying TD concentration and calculating the damage degree of TD. The electrophoretograms indicated that CE-FL was a suitable TD assay method with high specificity and sensitivity. In addition, the application of CE-FL for TD fluorescence resonance energy transfer (FRET) research was also explored. Two types of DNA strands were utilized to interfere the formation of TD. The impact of partially complementary chain and completely complementary chain on FRET signal was explored, and the influence mechanism was discussed. After applying CE-FL for characterizing TD, we also combine CE and FRET to analyze TD-DOX conjugate. CE presented a favourable technique to monitor DOX loading and releasing processes. These noteworthy results offered a stepping stone for DNA nanomaterials assay by using CE-FL.
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Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Ronghui Zheng
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Lin Qiu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Shuwen Zhou
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Hufei Chao
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Ying Li
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Wen Rui
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Pengfei Cui
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China
| | - Xinye Ni
- The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, Jiangsu, PR China.
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China; Jiangsu Dawning Pharmaceutical Co., Ltd., Changzhou, Jiangsu, 213100, China.
| | - Pengju Jiang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China.
| | - Jianhao Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu, 213164, China; Changzhou Le Sun Pharmaceuticals Co., Ltd., Changzhou, Jiangsu, 213125, China; Jiangsu Yue Zhi Biopharmaceutical Co., Ltd., Changzhou, Jiangsu, 213125, China.
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89
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Barcenas G, Biaggne A, Mass OA, Wilson CK, Obukhova OM, Kolosova OS, Tatarets AL, Terpetschnig E, Pensack RD, Lee J, Knowlton WB, Yurke B, Li L. First-principles studies of substituent effects on squaraine dyes. RSC Adv 2021; 11:19029-19040. [PMID: 35478639 PMCID: PMC9033489 DOI: 10.1039/d1ra01377g] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 05/17/2021] [Indexed: 01/21/2023] Open
Abstract
Dye molecules that absorb light in the visible region are key components in many applications, including organic photovoltaics, biological fluorescent labeling, super-resolution microscopy, and energy transport. One family of dyes, known as squaraines, has received considerable attention recently due to their favorable electronic and photophysical properties. In addition, these dyes have a strong propensity for aggregation, which results in emergent materials properties, such as exciton delocalization. This will be of benefit in charge separation and energy transport along with fundamental studies in quantum information. Given the high structural tunability of squaraine dyes, it is possible that exciton delocalization could be tailored by modifying the substituents attached to the π-conjugated network. To date, limited theoretical studies have explored the role of substituent effects on the electronic and photophysical properties of squaraines in the context of DNA-templated dye aggregates and resultant excitonic behavior. We used ab initio theoretical methods to determine the effects of substituents on the electronic and photophysical properties for a series of nine different squaraine dyes. Solvation free energy was also investigated as an insight into changes in hydrophobic behavior from substituents. The role of molecular symmetry on these properties was also explored via conformation and substitution. We found that substituent effects are correlated with the empirical Hammett constant, which demonstrates their electron donating or electron withdrawing strength. Electron withdrawing groups were found to impact solvation free energy, transition dipole moment, static dipole difference, and absorbance more than electron donating groups. All substituents showed a redshift in absorption for the squaraine dye. In addition, solvation free energy increases with Hammett constant. This work represents a first step toward establishing design rules for dyes with desired properties for excitonic applications. Squaraine dyes are candidates for DNA-templated excitonic interactions. This work presents substituent effects on the electronic and photophysicalproperties of squaraine dyes and a correlation between empirical Hammettconstant and those properties.![]()
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Affiliation(s)
- German Barcenas
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Olga A Mass
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Christopher K Wilson
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Olena M Obukhova
- SSI "Institute for Single Crystals" of National Academy of Sciences of Ukraine Kharkov 61072 Ukraine
| | - Olga S Kolosova
- SSI "Institute for Single Crystals" of National Academy of Sciences of Ukraine Kharkov 61072 Ukraine
| | - Anatoliy L Tatarets
- SSI "Institute for Single Crystals" of National Academy of Sciences of Ukraine Kharkov 61072 Ukraine.,SETA BioMedicals Urbana IL 61802 USA
| | | | - Ryan D Pensack
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Department of Chemistry and Biochemistry, Boise State University Boise ID 83725 USA
| | - William B Knowlton
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Department of Electrical and Computer Engineering, Boise State University Boise ID 83725 USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Department of Electrical and Computer Engineering, Boise State University Boise ID 83725 USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Center for Advanced Energy Studies Idaho Falls ID 83401 USA
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90
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Gao L, Liu L, Tian Y, Yang Q, Wu P, Fan C, Zhao Q, Li F. Probing the Formation Kinetics and Thermodynamics with Rationally Designed Analytical Tools Enables One-Pot Synthesis and Purification of a Tetrahedral DNA Nanostructure. Anal Chem 2021; 93:7045-7053. [PMID: 33886303 DOI: 10.1021/acs.analchem.1c00363] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of robust analytical tools capable of probing the formation kinetics and thermodynamics of DNA nanostructures is a crucial step toward better understanding and manufacturing of diverse DNA-based materials. Herein, we introduce a real-time fluorescence anisotropy assay and rationally designed DNA reaction termination probes (DRTPs) as a set of new tools for exploring the formation mechanisms of DNA nanostructures. We deployed these tools for probing the formation of a classic tetrahedral DNA nanostructure (TDN) as a model system. Our tools revealed that the formation of TDN was dominated by simultaneous hybridization, whereas its undesired side products were caused mainly through step-wise hybridization. An optimal reaction temperature exists that favors the formation of TDN over side products. With insight into the TDN formation mechanism, we further engineered magnetic DRTPs to achieve single-step purification of TDN, enabling 10-fold improvement in the ratio between the targeted TDN and undesired side products without tedious procedures or bulky instruments. Combining the optimal reaction and purification conditions, we finally demonstrated the one-pot synthesis and purification of TDN. The analytical techniques offered in this work may hold potential to find wide applications and inspire new analytical methods for structural DNA nanotechnology.
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Affiliation(s)
- Lu Gao
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Liying Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunfei Tian
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Qianfan Yang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Peng Wu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 201240, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, P. R. China.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
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92
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93
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Kumaravel S, Karthick K, Sankar SS, Karmakar A, Madhu R, Kundu S. Prospects in interfaces of biomolecule DNA and nanomaterials as an effective way for improvising surface enhanced Raman scattering: A review. Adv Colloid Interface Sci 2021; 291:102399. [PMID: 33774595 DOI: 10.1016/j.cis.2021.102399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 01/20/2023]
Abstract
Surface Enhanced Raman Scattering (SERS) is a field of research that has shown promising application in the analysis of various substrate molecules by means of rough metallic surfaces. In directing the enhancement of substrate molecules in micro and nano-molar concentrations, plasmonic coupling of metal nanoparticles (NPs), morphology of metal NPs and the closely arrangement of rough metal surfaces that produces 'hot spots' can effectively increase the so-called enhancement factor (EF) that will be applicable in various fields. As the mechanistic aspects are still not clear, research has been triggered all over the world for the past two decades to have a clear understanding in chemical and electromagnetic effects. As the reproducibility of intensity of signals at low concentrations of probe molecules is of a big concern, metal NPs with various scaffolds were prepared and recently bio-molecule, DNA has been studied and showed promising advantages. This review first time highlights metal NPs with DNA interface as an effective rough metallic surface for SERS with high intensity and also with better reproducibility. Based on this review, similar kinds of scaffolds like DNA can be used to further analyze SERS activities of various metal NPs with different morphologies to have high intense signals at low concentrations of probe molecules.
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Affiliation(s)
- Sangeetha Kumaravel
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kannimuthu Karthick
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Selvasundarasekar Sam Sankar
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Arun Karmakar
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ragunath Madhu
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Subrata Kundu
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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94
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Fan Z, Yao B, Ding Y, Zhao J, Xie M, Zhang K. Entropy-driven amplified electrochemiluminescence biosensor for RdRp gene of SARS-CoV-2 detection with self-assembled DNA tetrahedron scaffolds. Biosens Bioelectron 2021; 178:113015. [PMID: 33493896 PMCID: PMC7817442 DOI: 10.1016/j.bios.2021.113015] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/14/2021] [Accepted: 01/17/2021] [Indexed: 12/24/2022]
Abstract
Dependable, specific and rapid diagnostic methods for severe acute respiratory syndrome β-coronavirus (SARS-CoV-2) detection are needed to promote public health interventions for coronavirus disease 2019 (COVID-19). Herein, we have established an entropy-driven amplified electrochemiluminescence (ECL) strategy to detect the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 known as RdRp-COVID which as the target for SARS-CoV-2 plays an essential role in the diagnosis of COVID-19. For the construction of the sensors, DNA tetrahedron (DT) is modified on the surface of the electrode to furnish robust and programmable scaffolds materials, upon which target DNA-participated entropy-driven amplified reaction is efficiently conducted to link the Ru (bpy)32+ modified S3 to the linear ssDNA at the vertex of the tetrahedron and eventually present an "ECL on" state. The rigid tetrahedral structure of the DT probe enhances the ECL intensity and avoids the cross-reactivity between single-stranded DNA, thus increasing the sensitivity of the assays. The enzyme-free entropy-driven reaction prevents the use of expensive enzyme reagents and facilitates the realization of large-scale screening of SARS-CoV-2 patients. Our DT-based ECL sensor has demonstrated significant specificity and high sensitivity for SARS-CoV-2 with a limit of detection (LOD) down to 2.67 fM. Additionally, our operational method has achieved the detection of RdRp-COVID in human serum samples, which supplies a reliable and feasible sensing platform for the clinical bioanalysis.
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Affiliation(s)
- Zhenqiang Fan
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Bo Yao
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China; Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, PR China
| | - Yuedi Ding
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China
| | - Jing Zhao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Minhao Xie
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China; Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Kai Zhang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, 214063, China.
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95
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Sun W, Wang Z, Liu J, Jiang C, Chen W, Yu B, Wang W, Lu L. On-demand degradable magnetic resonance imaging nanoprobes. Sci Bull (Beijing) 2021; 66:676-684. [PMID: 36654443 DOI: 10.1016/j.scib.2020.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 01/20/2023]
Abstract
Theranostic nanoprobes can potentially integrate imaging and therapeutic capabilities into a single platform, offering a new personalized cancer diagnostic tool. However, there is a growing concern that their clinical application is not safe, particularly due to metal-containing elements, such as the gadolinium used in magnetic resonance imaging (MRI). We demonstrate for the first time that the photothermal melting of the DNA duplex helix was a reliable and versatile strategy that enables the on-demand degradation of the gadolinium-containing MRI reporter gene from polydopamine (PDA)-based theranostic nanoprobes. The combination of chemotherapy (doxorubicin) and photothermal therapy, which leads to the enhanced anti-tumor effect. In vivo MRI tracking reveals that renal filtration was able to rapidly clear the free gadolinium-containing MRI reporter from the mice body. This results in a decrease in the long-term toxic effect of theranostic MRI nanoprobes. Our findings may pave the way to address toxicity issues of the theranostic nanoprobes.
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Affiliation(s)
- Wenbo Sun
- College of Materials Science and Engineering, College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao 266071, China; State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zonghua Wang
- College of Materials Science and Engineering, College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Jianhua Liu
- Department of Radiology, Second Hospital of Jilin University, Changchun 130041, China
| | - Chunhuan Jiang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Weihua Chen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Bin Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Wei Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Lehui Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China.
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96
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Procyk J, Poppleton E, Šulc P. Coarse-grained nucleic acid-protein model for hybrid nanotechnology. SOFT MATTER 2021; 17:3586-3593. [PMID: 33398312 DOI: 10.1039/d0sm01639j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The emerging field of hybrid DNA-protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with the versatility of protein interactions. However, the design and computational study of these hybrid structures is difficult due to the system sizes involved. To aid in the design and in silico analysis process, we introduce here a coarse-grained DNA/RNA-protein model that extends the oxDNA/oxRNA models of DNA/RNA with a coarse-grained model of proteins based on an anisotropic network model representation. Fully equipped with analysis scripts and visualization, our model aims to facilitate hybrid nanomaterial design towards eventual experimental realization, as well as enabling study of biological complexes. We further demonstrate its usage by simulating DNA-protein nanocage, DNA wrapped around histones, and a nascent RNA in polymerase.
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Affiliation(s)
- Jonah Procyk
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA.
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97
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Zhao S, Yu L, Yang S, Tang X, Chang K, Chen M. Boolean logic gate based on DNA strand displacement for biosensing: current and emerging strategies. NANOSCALE HORIZONS 2021; 6:298-310. [PMID: 33877218 DOI: 10.1039/d0nh00587h] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA computers are considered one of the most prominent next-generation molecular computers that perform Boolean logic using DNA elements. DNA-based Boolean logic gates, especially DNA strand displacement-based logic gates (SDLGs), have shown tremendous potential in biosensing since they can perform the logic analysis of multi-targets simultaneously. Moreover, SDLG biosensors generate a unique output in the form of YES/NO, which is contrary to the quantitative measurement used in common biosensors. In this review, the recent achievements of SDLG biosensing strategies are summarized. Initially, the development and mechanisms of Boolean logic gates, strand-displacement reaction, and SDLGs are introduced. Afterwards, the diversified input and output of SDLG biosensors are elaborated. Then, the state-of-the-art SDLG biosensors are reviewed in the classification of different signal-amplification methods, such as rolling circle amplification, catalytic hairpin assembly, strand-displacement amplification, DNA molecular machines, and DNAzymes. Most importantly, limitations and future trends are discussed. The technology reviewed here is a promising tool for multi-input analysis and lays a foundation for intelligent diagnostics.
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Affiliation(s)
- Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
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98
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Wang J, Yu S, Wu Q, Gong X, He S, Shang J, Liu X, Wang F. A Self‐Catabolic Multifunctional DNAzyme Nanosponge for Programmable Drug Delivery and Efficient Gene Silencing. Angew Chem Int Ed Engl 2021; 60:10766-10774. [DOI: 10.1002/anie.202101474] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Jing Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
- Oil Crops Research Institute Chinese Academy of Agricultural Sciences Hubei Key Laboratory of Lipid Chemistry and Nutrition, Key Laboratory of Oilseeds Processing Ministry of Agriculture 430062 Wuhan P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Qiong Wu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xue Gong
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Shizhen He
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
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99
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Wang J, Yu S, Wu Q, Gong X, He S, Shang J, Liu X, Wang F. A Self‐Catabolic Multifunctional DNAzyme Nanosponge for Programmable Drug Delivery and Efficient Gene Silencing. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101474] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jing Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
- Oil Crops Research Institute Chinese Academy of Agricultural Sciences Hubei Key Laboratory of Lipid Chemistry and Nutrition, Key Laboratory of Oilseeds Processing Ministry of Agriculture 430062 Wuhan P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Qiong Wu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xue Gong
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Shizhen He
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
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Abstract
The field of single nanoparticle plasmonics has grown enormously. There is no doubt that a wide diversity of the nanoplasmonic techniques and nanostructures represents a tremendous opportunity for fundamental biomedical studies as well as sensing and imaging applications. Single nanoparticle plasmonic biosensors are efficient in label-free single-molecule detection, as well as in monitoring real-time binding events of even several biomolecules. In the present review, we have discussed the prominent advantages and advances in single particle characterization and synthesis as well as new insight into and information on biomedical diagnosis uniquely obtained using single particle approaches. The approaches include the fundamental studies of nanoplasmonic behavior, two typical methods based on refractive index change and characteristic light intensity change, exciting innovations of synthetic strategies for new plasmonic nanostructures, and practical applications using single particle sensing, imaging, and tracking. The basic sphere and rod nanostructures are the focus of extensive investigations in biomedicine, while they can be programmed into algorithmic assemblies for novel plasmonic diagnosis. Design of single nanoparticles for the detection of single biomolecules will have far-reaching consequences in biomedical diagnosis.
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Affiliation(s)
- Xingyi Ma
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea.
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea.
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