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Ma C, Li S, Zeng Y, Lyu Y. DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications. BIOSENSORS 2024; 14:236. [PMID: 38785710 PMCID: PMC11117991 DOI: 10.3390/bios14050236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed.
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Affiliation(s)
- Chunran Ma
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Shiquan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yuqi Zeng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
- Furong Laboratory, Changsha 410082, China
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2
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Tanner CPN, Utterback JK, Portner J, Coropceanu I, Das A, Tassone CJ, Teitelbaum SW, Limmer DT, Talapin DV, Ginsberg NS. In Situ X-ray Scattering Reveals Coarsening Rates of Superlattices Self-Assembled from Electrostatically Stabilized Metal Nanocrystals Depend Nonmonotonically on Driving Force. ACS NANO 2024. [PMID: 38318795 PMCID: PMC10883038 DOI: 10.1021/acsnano.3c12186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Self-assembly of colloidal nanocrystals (NCs) into superlattices (SLs) is an appealing strategy to design hierarchically organized materials with promising functionalities. Mechanistic studies are still needed to uncover the design principles for SL self-assembly, but such studies have been difficult to perform due to the fast time and short length scales of NC systems. To address this challenge, we developed an apparatus to directly measure the evolving phases in situ and in real time of an electrostatically stabilized Au NC solution before, during, and after it is quenched to form SLs using small-angle X-ray scattering. By developing a quantitative model, we fit the time-dependent scattering patterns to obtain the phase diagram of the system and the kinetics of the colloidal and SL phases as a function of varying quench conditions. The extracted phase diagram is consistent with particles whose interactions are short in range relative to their diameter. We find the degree of SL order is primarily determined by fast (subsecond) initial nucleation and growth kinetics, while coarsening at later times depends nonmonotonically on the driving force for self-assembly. We validate these results by direct comparison with simulations and use them to suggest dynamic design principles to optimize the crystallinity within a finite time window. The combination of this measurement methodology, quantitative analysis, and simulation should be generalizable to elucidate and better control the microscopic self-assembly pathways of a wide range of bottom-up assembled systems and architectures.
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Affiliation(s)
- Christian P N Tanner
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - James K Utterback
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Joshua Portner
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Igor Coropceanu
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Avishek Das
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Christopher J Tassone
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Samuel W Teitelbaum
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy NanoSciences Institute, University of California, Berkeley, California 94720, United States
| | - Dmitri V Talapin
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60517, United States
| | - Naomi S Ginsberg
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Kavli Energy NanoSciences Institute, University of California, Berkeley, California 94720, United States
- Department of Physics, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Materials Sciences and Chemical Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- STROBE, NSF Science & Technology Center, Berkeley, California 94720, United States
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3
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Mathew SS, Ahamed AAS, Abraham I, Prabhu DD, John F, George J. Self‐Assemblies of DNA ‐ Amphiphiles Nanostructures for New Design Strategies of Varied Morphologies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - A A Subuhan Ahamed
- School of Chemistry University of Hyderabad Hyderabad 500046 Telangana India
| | - Ignatious Abraham
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Deepak D Prabhu
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Franklin John
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Jinu George
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
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4
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Wang F, Zhu F, Ren E, Zhu G, Lu GP, Lin Y. Recent Advances in Carbon-Based Iron Catalysts for Organic Synthesis. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12193462. [PMID: 36234590 PMCID: PMC9565280 DOI: 10.3390/nano12193462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 05/13/2023]
Abstract
Carbon-based iron catalysts combining the advantages of iron and carbon material are efficient and sustainable catalysts for green organic synthesis. The present review summarizes the recent examples of carbon-based iron catalysts for organic reactions, including reduction, oxidation, tandem and other reactions. In addition, the introduction strategies of iron into carbon materials and the structure and activity relationship (SAR) between these catalysts and organic reactions are also highlighted. Moreover, the challenges and opportunities of organic synthesis over carbon-based iron catalysts have also been addressed. This review will stimulate more systematic and in-depth investigations on carbon-based iron catalysts for exploring sustainable organic chemistry.
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Affiliation(s)
- Fei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Fuying Zhu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Enxiang Ren
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Guofu Zhu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Guo-Ping Lu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei Street, Nanjing 210094, China
- Correspondence: (G.-P.L.); (Y.L.)
| | - Yamei Lin
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (G.-P.L.); (Y.L.)
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5
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Kankanamalage DVDW, Tran JHT, Beltrami N, Meng K, Zhou X, Pathak P, Isaacs L, Burin AL, Ali MF, Jayawickramarajah J. DNA Strand Displacement Driven by Host-Guest Interactions. J Am Chem Soc 2022; 144:16502-16511. [PMID: 36063395 PMCID: PMC9479067 DOI: 10.1021/jacs.2c05726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Base-pair-driven toehold-mediated strand displacement (BP-TMSD) is a fundamental concept employed for constructing DNA machines and networks with a gamut of applications─from theranostics to computational devices. To broaden the toolbox of dynamic DNA chemistry, herein, we introduce a synthetic surrogate termed host-guest-driven toehold-mediated strand displacement (HG-TMSD) that utilizes bioorthogonal, cucurbit[7]uril (CB[7]) interactions with guest-linked input sequences. Since control of the strand-displacement process is salient, we demonstrate how HG-TMSD can be finely modulated via changes to the structure of the input sequence (including synthetic guest head-group and/or linker length). Further, for a given input sequence, competing small-molecule guests can serve as effective regulators (with fine and coarse control) of HG-TMSD. To show integration into functional devices, we have incorporated HG-TMSD into machines that control enzyme activity and layered reactions that detect specific microRNA.
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Affiliation(s)
| | - Jennifer H T Tran
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Noah Beltrami
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Kun Meng
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Xiao Zhou
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Pravin Pathak
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Mehnaaz F Ali
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
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6
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Amadi EV, Venkataraman A, Papadopoulos C. Nanoscale self-assembly: concepts, applications and challenges. NANOTECHNOLOGY 2022; 33. [PMID: 34874297 DOI: 10.1088/1361-6528/ac3f54] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/02/2021] [Indexed: 05/09/2023]
Abstract
Self-assembly offers unique possibilities for fabricating nanostructures, with different morphologies and properties, typically from vapour or liquid phase precursors. Molecular units, nanoparticles, biological molecules and other discrete elements can spontaneously organise or form via interactions at the nanoscale. Currently, nanoscale self-assembly finds applications in a wide variety of areas including carbon nanomaterials and semiconductor nanowires, semiconductor heterojunctions and superlattices, the deposition of quantum dots, drug delivery, such as mRNA-based vaccines, and modern integrated circuits and nanoelectronics, to name a few. Recent advancements in drug delivery, silicon nanoelectronics, lasers and nanotechnology in general, owing to nanoscale self-assembly, coupled with its versatility, simplicity and scalability, have highlighted its importance and potential for fabricating more complex nanostructures with advanced functionalities in the future. This review aims to provide readers with concise information about the basic concepts of nanoscale self-assembly, its applications to date, and future outlook. First, an overview of various self-assembly techniques such as vapour deposition, colloidal growth, molecular self-assembly and directed self-assembly/hybrid approaches are discussed. Applications in diverse fields involving specific examples of nanoscale self-assembly then highlight the state of the art and finally, the future outlook for nanoscale self-assembly and potential for more complex nanomaterial assemblies in the future as technological functionality increases.
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Affiliation(s)
- Eberechukwu Victoria Amadi
- University of Victoria, Department of Electrical and Computer Engineering, PO BOX 1700 STN CSC, Victoria, BC, V8W 2Y2, Canada
| | - Anusha Venkataraman
- University of Victoria, Department of Electrical and Computer Engineering, PO BOX 1700 STN CSC, Victoria, BC, V8W 2Y2, Canada
| | - Chris Papadopoulos
- University of Victoria, Department of Electrical and Computer Engineering, PO BOX 1700 STN CSC, Victoria, BC, V8W 2Y2, Canada
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7
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Recent advance in dual-functional luminescent probes for reactive species and common biological ions. Anal Bioanal Chem 2022; 414:5087-5103. [DOI: 10.1007/s00216-021-03792-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Indexed: 01/17/2023]
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8
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Guan C, Zhu X, Feng C. DNA Nanodevice-Based Drug Delivery Systems. Biomolecules 2021; 11:1855. [PMID: 34944499 PMCID: PMC8699395 DOI: 10.3390/biom11121855] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 12/20/2022] Open
Abstract
DNA, a natural biological material, has become an ideal choice for biomedical applications, mainly owing to its good biocompatibility, ease of synthesis, modifiability, and especially programmability. In recent years, with the deepening of the understanding of the physical and chemical properties of DNA and the continuous advancement of DNA synthesis and modification technology, the biomedical applications based on DNA materials have been upgraded to version 2.0: through elaborate design and fabrication of smart-responsive DNA nanodevices, they can respond to external or internal physical or chemical stimuli so as to smartly perform certain specific functions. For tumor treatment, this advancement provides a new way to solve the problems of precise targeting, controllable release, and controllable elimination of drugs to a certain extent. Here, we review the progress of related fields over the past decade, and provide prospects for possible future development directions.
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Affiliation(s)
- Chaoyang Guan
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
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9
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Zhao H, Zhang Z, Zuo D, Li L, Li F, Yang D. A Synergistic DNA-polydopamine-MnO 2 Nanocomplex for Near-Infrared-Light-Powered DNAzyme-Mediated Gene Therapy. NANO LETTERS 2021; 21:5377-5385. [PMID: 34100622 DOI: 10.1021/acs.nanolett.1c01727] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNAzyme is emerging for gene therapy. The administration of the in vivo catalytic activity of DNAzyme has proven important but challenging for clinical applications. Herein, we report a synergistic DNA-polydopamine-MnO2 nanocomplex, which enables near-infrared (NIR)-light-powered catalytic activity of DNAzyme in vivo. The nanocomplex has a hierarchical structure: a DNA nanoframework as the scaffold and polydopamine-MnO2 (PM) as the coating layer. The DNA nanoframework contains repeated DNAzyme sequences. PM assembles on the surface of the DNA nanoframework. When the nanocomplex accumulates at tumor sites, upon NIR-light radiation, polydopamine induces a temperature elevation at tumor sites via photothermal conversion; meanwhile, glutathione triggers decomposition of PM to release Mn2+ to activate DNAzyme in the cytoplasm for gene regulation. In vitro and in vivo experiments show that the PM-induced temperature elevation enhances the Egr-1 mRNA cleavage activity of DNAzyme, promoting downregulation of the Egr-1 protein in tumor cells. In addition, the temperature elevation induces heat stress, achieving a synergistic tumor ablation effect.
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Affiliation(s)
- Huaixin Zhao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Zhili Zhang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Duo Zuo
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, People's Republic of China
| | - Linghui Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
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10
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Chakraborty A, Ravi SP, Shamiya Y, Cui C, Paul A. Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications. Chem Soc Rev 2021; 50:7779-7819. [PMID: 34036968 DOI: 10.1039/d0cs01387k] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.
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Affiliation(s)
- Aishik Chakraborty
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada.
| | - Shruthi Polla Ravi
- School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Yasmeen Shamiya
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Caroline Cui
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada. and School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada and Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
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11
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Atchimnaidu S, Thelu HVP, Perumal D, Harikrishnan KS, Varghese R. Efficient Capturing of Polycyclic Aromatic Micropollutants From Water Using Physically Crosslinked DNA Nanoparticles. Front Chem 2020; 8:2. [PMID: 32064246 PMCID: PMC6999083 DOI: 10.3389/fchem.2020.00002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/06/2020] [Indexed: 11/20/2022] Open
Abstract
Design and synthesis of physically (non-covalently) cross-linked nanoparticles through host-guest interaction between β-CD and adamantane is reported. Specific molecular recognition between β-CD functionalized branched DNA nanostructures (host) and a star-shaped adamantyl-terminated 8-arm poly(ethylene glycol) polymer (guest) is explored for the design of the nanoparticles. The most remarkable structural features of DNA nanoparticles include their excellent biocompatibility and the possibility of various non-covalent interactions with both hydrophobic and hydrophilic organic molecules. Potential of DNA nanoparticles for the rapid and efficient capture of various micropollutants typically present in water including carcinogens (hydrophobic micropollutants), organic dyes (hydrophilic), and pharmaceutical molecules (hydrophilic) is also demonstrated. The capture of micropollutants by DNA nanoparticles is attributed to the various non-covalent interactions between DNA nanoparticles and the micropollutants. Our results clearly suggest that DNA based nanomaterials would be an ideal candidate for the capturing and removal of both hydrophilic and hydrophobic micropollutants typically present in water.
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Affiliation(s)
- Siriki Atchimnaidu
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Thiruvananthapuram, India
| | - Hari Veera Prasad Thelu
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Thiruvananthapuram, India
| | - Devanathan Perumal
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Thiruvananthapuram, India
| | - Kaloor S Harikrishnan
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Thiruvananthapuram, India
| | - Reji Varghese
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Thiruvananthapuram, India
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12
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Tang W, Zhong W, Tan Y, Wang GA, Li F, Liu Y. DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants. Top Curr Chem (Cham) 2020; 378:10. [PMID: 31894426 DOI: 10.1007/s41061-019-0274-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023]
Abstract
Single-nucleotide variants (SNVs) that are strongly associated with many genetic diseases and tumors are important both biologically and clinically. Detection of SNVs holds great potential for disease diagnosis and prognosis. Recent advances in DNA nanotechnology have offered numerous principles and strategies amenable to the detection and quantification of SNVs with high sensitivity, specificity, and programmability. In this review, we will focus our discussion on emerging techniques making use of DNA strand displacement, a basic building block in dynamic DNA nanotechnology. Based on their operation principles, we classify current SNV detection methods into three main categories, including strategies using toehold-mediated strand displacement reactions, toehold-exchange reactions, and enzyme-mediated strand displacement reactions. These detection methods discriminate SNVs from their wild-type counterparts through subtle differences in thermodynamics, kinetics, or response to enzymatic manipulation. The remarkable programmability of dynamic DNA nanotechnology also allows the predictable design and flexible operation of diverse strand displacement probes and/or primers. Here, we offer a systematic survey of current strategies, with an emphasis on the molecular mechanisms and their applicability to in vitro diagnostics.
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Affiliation(s)
- Weiyang Tang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yun Tan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Guan A Wang
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada
| | - Feng Li
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada. .,College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China. .,Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Wuhan University, Wuhan, China.
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13
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Ha SYY, Ng DKP. Constructing a four-input molecular keypad lock with a multi-stimuli-responsive phthalocyanine. Chem Commun (Camb) 2020; 56:14601-14604. [DOI: 10.1039/d0cc06251k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A novel phthalocyanine has been designed and synthesised whose response towards different stimuli can be manipulated to enable it to function as a four-input molecular keypad lock.
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Affiliation(s)
- Summer Y. Y. Ha
- Department of Chemistry
- The Chinese University of Hong Kong
- Shatin
- China
| | - Dennis K. P. Ng
- Department of Chemistry
- The Chinese University of Hong Kong
- Shatin
- China
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14
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15
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Jiang Q, Zhao S, Liu J, Song L, Wang ZG, Ding B. Rationally designed DNA-based nanocarriers. Adv Drug Deliv Rev 2019; 147:2-21. [PMID: 30769047 DOI: 10.1016/j.addr.2019.02.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 01/08/2019] [Accepted: 02/08/2019] [Indexed: 01/01/2023]
Abstract
Nanomaterials employed for enhanced drug delivery and therapeutic effects have been extensively investigated in the past decade. The outcome of current anticancer treatments based on conventional nanoparticles is suboptimal, due to the lack of biocompatibility, the deficient tumor targeting, the limited drug accumulation in the diseased region, etc. Alternatively, DNA-based nanocarriers have emerged as a novel and versatile platform to integrate the advantages of nanotechnologies and biological sciences, which shows great promise in addressing the key issues for biomedical studies. Rather than a genetic information carrier, DNA molecules can work as building blocks to fabricate programmable and bio-functional nanostructures based on Watson Crick base-pairing rules. The DNA-based materials have demonstrated unique properties, such as uniform sizes and shapes, pre-designable and programmable nanostructures, site-specific surface functionality and excellent biocompatibility. These intrigue features allow DNA nanostructures to carry functional moieties to realize precise tumor recognition, customized therapeutic functions and stimuli-responsive drug release, making them highly attractive in many aspects of cancer treatment. In this review, we focus on the recent progress in DNA-based self-assembled materials for the biomedical applications, such as molecular imaging, drug delivery for in vitro or in vivo cancer treatments. We introduce the general strategies and essential requirements for fabricating DNA-based nanocarriers. We summarize the advances of DNA-based nanocarriers according to their functionalities and structural properties for cancer diagnosis and therapy. Finally, we discuss the challenges and future perspectives regarding the detailed in vivo parameters of DNA materials and the design of intelligent DNA nanomedicine for individualized cancer therapy.
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16
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Li F, Xiao M, Pei H. DNA‐Based Chemical Reaction Networks. Chembiochem 2019; 20:1105-1114. [DOI: 10.1002/cbic.201800721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Fan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road 200241 Shanghai P.R. China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound ImagingLaboratory of Evolutionary TheranosticsSchool of Biomedical EngineeringHealth Science CenterShenzhen University Nanhai Avenue 3688 518060 Shenzhen Guangzhou P.R. China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road 200241 Shanghai P.R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical ProcessesSchool of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road 200241 Shanghai P.R. China
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17
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Xu X, Zhang P, Zhang R, Zhang N, Jiang W. A DNA walker powered by endogenous enzymes for imaging uracil-DNA glycosylase activity in living cells. Chem Commun (Camb) 2019; 55:6026-6029. [DOI: 10.1039/c9cc01912j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A DNA walker powered by endogenous enzymes detects uracil-DNA glycosylase activity in living cells.
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Affiliation(s)
- Xiaowen Xu
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Pingping Zhang
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Ruiyuan Zhang
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
| | - Nan Zhang
- Department of Oncology
- Jinan Central Hospital Affiliated to Shandong University
- 250012 Jinan
- P. R. China
| | - Wei Jiang
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P. R. China
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18
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Buddolla AL, Kim S. Recent insights into the development of nucleic acid-based nanoparticles for tumor-targeted drug delivery. Colloids Surf B Biointerfaces 2018; 172:315-322. [DOI: 10.1016/j.colsurfb.2018.08.057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/14/2018] [Accepted: 08/27/2018] [Indexed: 12/12/2022]
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19
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Target-triggered three-way junction in conjugation with catalytic concatemers-functionalized nanocomposites provides a highly sensitive colorimetric method for miR-21 detection. Biosens Bioelectron 2018; 117:567-574. [PMID: 30005375 DOI: 10.1016/j.bios.2018.06.051] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 12/20/2022]
Abstract
With the great advances in DNA nanotechnology, scientists have shown interest in developing dynamic nanostructures for theranostic applications, analyte sensing and cargo delivery. Here, we present a specific enzyme-free ultrasensitive platform based on a multilayer coupled signal amplification strategy to quantify miR-21 molecule. The biosensor was integrated based on three signal amplification gadgets, namely a translator-mediated catalytic hairpin assembly (CHA), a multilayer DNA concatemer on the surface of gold decorated magnetic nanoparticle (GMNP), and a DNAzyme-mediated catalytic signal amplification. MiR-21 mediates the release of a DNA translator from an immobilized duplex to engage in a CHA reaction using three hairpins, including a GMNP-conjugated hairpin 1 (H1), biotin-labeled hairpin 2 (H2) and a GMNP-conjugated hairpin 3 (H3) to form a three-way junction (3WJ). Meanwhile, a plenty of initiator strand 0 (S0) on GMNPs - each of which has been bifunctionalized with S0/H1 or S0/H3 - drive several multilayer peroxidase-mimicking DNAzyme concatemers in the presence of two accessory oligonucleotides; strand 1 (S1) and strand 2 (S2). Since a G-rich sequence was attached at the 5'-end of S1 strand, in the presence of hemin cofactor, an active G-quadruplex DNAzyme with peroxidase activity was formed. The concatemers on the surface of GMNPs can convert a colorless substrate to a green product. The biosensor can detect as low as 1 aM of miR-21 and provide an excellent capability to discriminate single-base mismatches. The required time for the formulation of the assay reagents is about three days and the reaction time for the detection of miR-21 takes place in less than four hours.
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20
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Shang Y, Shi J, Liu H, Liu X, Wang ZG, Ding B. A bumpy gold nanostructure exhibiting DNA-engineered stimuli-responsive SERS signals. NANOSCALE 2018; 10:9455-9459. [PMID: 29749418 DOI: 10.1039/c8nr00986d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present a SERS-active gold nanostructure with built-in electromagnetic hotspots formed by densely packed gold nanoparticles on a gold nanorod. Cy3 labeled stimuli-responsive DNA motifs were introduced to the SERS-active nanostructure. The SERS signals can be switched ON and OFF reversibly in response to external stimuli (pH, metal ions or organic molecules).
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Affiliation(s)
- Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R.China.
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21
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Angell C, Kai M, Xie S, Dong X, Chen Y. Bioderived DNA Nanomachines for Potential Uses in Biosensing, Diagnostics, and Therapeutic Applications. Adv Healthc Mater 2018; 7:e1701189. [PMID: 29350489 DOI: 10.1002/adhm.201701189] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/23/2017] [Indexed: 12/28/2022]
Abstract
Beside its genomic properties, DNA is also recognized as a novel material in the field of nanoengineering. The specific bonding of base pairs can be used to direct the assembly of highly structured materials with specific nanoscale features such as periodic 2D arrays, 3D nanostructures, assembly of nanomaterials, and DNA nanomachines. In recent years, a variety of DNA nanomachines are developed because of their many potential applications in biosensing, diagnostics, and therapeutic applications. In this review, the fuel-powered motors and secondary structure motors, whose working mechanisms are inspired or derived from natural phenomena and nanomachines, are discussed. The combination of DNA motors with other platforms is then discussed. In each section of these motors, their mechanisms and their usage in the biomedical field are described. Finally, it is believed that these DNA-based nanomachines and hybrid motifs will become an integral point-of-care diagnostics and smart, site-specific therapeutic delivery.
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Affiliation(s)
- Chava Angell
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Mingxuan Kai
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Sibai Xie
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Xiangyi Dong
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Yi Chen
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
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22
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Chen J, Zuehlke A, Deng B, Peng H, Hou X, Zhang H. A Target-Triggered DNAzyme Motor Enabling Homogeneous, Amplified Detection of Proteins. Anal Chem 2017; 89:12888-12895. [PMID: 29099172 DOI: 10.1021/acs.analchem.7b03529] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We report here the concept of a self-powered, target-triggered DNA motor constructed by engineering a DNAzyme to adapt into binding-induced DNA assembly. An affinity ligand was attached to the DNAzyme motor via a DNA spacer, and a second affinity ligand was conjugated to the gold nanoparticle (AuNP) that was also decorated with hundreds of substrate strands serving as a high-density, three-dimensional track for the DNAzyme motor. Binding of a target molecule to the two ligands induced hybridization between the DNAzyme and its substrate on the AuNP, which are otherwise unable to spontaneously hybridize. The hybridization of DNAzyme with the substrate initiates the cleavage of the substrate and the autonomous movement of the DNAzyme along the AuNP. Each moving step restores the fluorescence of a dye molecule, enabling monitoring of the operation of the DNAzyme motor in real time. A simple addition or depletion of the cofactor Mg2+ allows for fine control of the DNAzyme motor. The motor can translate a single binding event into cleavage of hundreds of substrates, enabling amplified detection of proteins at room temperature without the need for separation.
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Affiliation(s)
- Junbo Chen
- Analytical and Testing Center, Sichuan University , 29 Wangjiang Road, Chengdu, Sichuan 610064, China.,Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta T6G 2G3, Canada
| | - Albert Zuehlke
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta T6G 2G3, Canada
| | - Bin Deng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta T6G 2G3, Canada
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta T6G 2G3, Canada
| | - Xiandeng Hou
- Analytical and Testing Center, Sichuan University , 29 Wangjiang Road, Chengdu, Sichuan 610064, China.,College of Chemistry, Sichuan University , 29 Wangjiang Road, Chengdu, Sichuan 610064, China
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta T6G 2G3, Canada
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23
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Zhang C, Wu R, Li Y, Zhang Q, Yang J. Programmable Regulation of DNA Conjugation to Gold Nanoparticles via Strand Displacement. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:12285-12290. [PMID: 28976767 DOI: 10.1021/acs.langmuir.7b02620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Methods for conjugating DNA to gold nanoparticles (AuNPs) have recently attracted considerable attention. The ability to control such conjugation in a programmable way is of great interest. Here, we have developed a logic-based method for manipulating the conjugation of thiolated DNA species to AuNPs via cascading DNA strand displacement. Using this method, several logic-based operation systems are established and up to three kinds of DNA signals are introduced at the same time. In addition, a more sensitive catalytic logic-based operation is also achieved based on an entropy-driven process. In the experiment, all of the DNA/AuNPs conjugation results are verified by agrose gel. This strategy promises great potential for automatically conjugating DNA stands onto label-free gold nanoparticles and can be extended to constructing DNA/nanoparticle devices for applications in diagnostics, biosensing, and molecular robotics.
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Affiliation(s)
- Cheng Zhang
- Institute of Software, School of Electronics Engineering and Computer Science, Peking University, Key laboratory of High Confidence Software Technologies, Ministry of Education, Beijing 100871, China
| | - Ranfeng Wu
- School of Control and Computer Engineering, North China Electric Power University , Beijing 102206, China
| | - Yifan Li
- School of Control and Computer Engineering, North China Electric Power University , Beijing 102206, China
| | - Qiang Zhang
- College of Computer Science and Technology, Dalian University of Technology , Dalian, 116624, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University , Beijing 102206, China
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24
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Albert SK, Golla M, Thelu HVP, Krishnan N, Varghese R. A pH-Responsive DNAsome from the Self-Assembly of DNA-Phenyleneethynylene Hybrid Amphiphile. Chemistry 2017; 23:8348-8352. [PMID: 28489295 DOI: 10.1002/chem.201701446] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Indexed: 12/18/2022]
Abstract
A pH-responsive DNAsome derived from the amphiphilicity-driven self-assembly of DNA amphiphile containing C-rich DNA sequence is reported. The acidification of DNAsome induces a structural change of C-rich DNA from random coil to an i-motif structure that triggers the disassembly of DNAsome and its subsequent morphological transformation into an open entangled network. The encapsulation of a hydrophobic guest into the membrane of DNAsome and its pH-triggered release upon acidification of DNAsome is also demonstrated.
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Affiliation(s)
- Shine K Albert
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram (IISER-TVM), CET campus, Trivandrum-, 695016, India
| | - Murali Golla
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram (IISER-TVM), CET campus, Trivandrum-, 695016, India
| | - Hari Veera Prasad Thelu
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram (IISER-TVM), CET campus, Trivandrum-, 695016, India
| | - Nithiyanandan Krishnan
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram (IISER-TVM), CET campus, Trivandrum-, 695016, India
| | - Reji Varghese
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram (IISER-TVM), CET campus, Trivandrum-, 695016, India
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25
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26
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Xu L, Hong S, Shen X, Zhou L, Wang J, Zhang J, Pei R. DNA Triplexes-Guided Assembly of G-Quadruplexes for Constructing Label-free Fluorescent Logic Gates. Chem Asian J 2016; 11:1892-5. [DOI: 10.1002/asia.201600626] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Xiaoqiang Shen
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
- School of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Lu Zhou
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
| | - Jine Wang
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
| | - Jianye Zhang
- School of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
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27
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De Stefano M, Vesterager Gothelf K. Dynamic Chemistry of Disulfide Terminated Oligonucleotides in Duplexes and Double-Crossover Tiles. Chembiochem 2016; 17:1122-6. [PMID: 26994867 DOI: 10.1002/cbic.201600076] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Indexed: 02/03/2023]
Abstract
Designed nanostructures formed by self-assembly of multiple DNA strands suffer from low stability at elevated temperature and under other denaturing conditions. Here, we propose a method for covalent coupling of DNA strands in such structures by the formation of disulfide bonds; this allows disassembly of the structure under reducing conditions. The dynamic chemistry of disulfides and thiols was applied to crosslink DNA strands with terminal disulfide modifications. The formation of disulfide-linked DNA duplexes consisting of three strands is demonstrated, as well as a more-complex DNA double-crossover tile. All the strands in the fully disulfide-linked structures are covalently and geometrically interlocked, and it is demonstrated that the structures are stable under heating and in the presence of denaturants. Such a reversible system can be exploited in applications where higher DNA stability is needed only temporarily, such as delivery of cargoes to cells by DNA nanostructures.
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Affiliation(s)
- Mattia De Stefano
- Danish National Research Foundation, Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Kurt Vesterager Gothelf
- Danish National Research Foundation, Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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28
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Santamaría-Díaz N, Méndez-Arriaga JM, Salas JM, Galindo MA. Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600924] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Noelia Santamaría-Díaz
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - José M. Méndez-Arriaga
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Juan M. Salas
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Miguel A. Galindo
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
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29
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Santamaría-Díaz N, Méndez-Arriaga JM, Salas JM, Galindo MA. Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs. Angew Chem Int Ed Engl 2016; 55:6170-4. [DOI: 10.1002/anie.201600924] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Noelia Santamaría-Díaz
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - José M. Méndez-Arriaga
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Juan M. Salas
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Miguel A. Galindo
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
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30
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Krissanaprasit A, Madsen M, Knudsen JB, Gudnason D, Surareungchai W, Birkedal V, Gothelf KV. Programmed Switching of Single Polymer Conformation on DNA Origami. ACS NANO 2016; 10:2243-2250. [PMID: 26766635 DOI: 10.1021/acsnano.5b06894] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA nanotechnology offers precise geometrical control of the positioning of materials, and it is increasingly also being used in the development of nanomechanical devices. Here we describe the development of a nanomechanical device that allows switching of the position of a single-molecule conjugated polymer. The polymer is functionalized with short single-stranded (ss) DNA strands that extend from the backbone of the polymer and serve as handles. The DNA polymer conjugate can be aligned on DNA origami in three well-defined geometries (straight line, left-turned, and right-turned pattern) by DNA hybridization directed by single-stranded guiding strands and ssDNA tracks extending from the origami surface and polymer handle. We demonstrate switching of a conjugated organic polymer conformation between left- and right-turned conformations of the polymer on DNA origami based on toehold-mediated strand displacement. The switching is observed by atomic force microscopy and by Förster resonance energy transfer between the polymer and two different organic dyes positioned in close proximity to the respective patterns. Using this method, the polymer conformation can be switched six times successively. This controlled nanomechanical switching of conjugated organic polymer conformation demonstrates unique control of the shape of a single polymer molecule, and it may constitute a new component for the development of reconfigurable nanophotonic and nanoelectronic devices.
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Affiliation(s)
- Abhichart Krissanaprasit
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi , Bangkhuntien Campus, Bangkok 10150, Thailand
| | | | | | | | - Werasak Surareungchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi , Bangkhuntien Campus, Bangkok 10150, Thailand
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31
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Singleton DG, Hussain R, Siligardi G, Kumar P, Hrdlicka PJ, Berova N, Stulz E. Increased duplex stabilization in porphyrin-LNA zipper arrays with structure dependent exciton coupling. Org Biomol Chem 2016; 14:149-57. [PMID: 26416024 PMCID: PMC4766578 DOI: 10.1039/c5ob01681a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/18/2015] [Indexed: 12/23/2022]
Abstract
Porphyrins were attached to LNA uridine building blocks via rigid 5-acetylene or more flexible propargyl-amide linkers and incorporated into DNA strands. The systems show a greatly increased thermodynamic stability when using as little as three porphyrins in a zipper arrangement. Thermodynamic analysis reveals clustering of the strands into more ordered duplexes with both greater negative ΔΔS and ΔΔH values, and less ordered duplexes with small positive ΔΔS differences, depending on the combination of linkers used. The exciton coupling between the porphyrins is dependent on the flanking DNA sequence in the single stranded form, and on the nature of the linker between the nucleobase and the porphyrin in the double stranded form; it is, however, also strongly influenced by intermolecular interactions. This system is suitable for the formation of stable helical chromophore arrays with sequence and structure dependent exciton coupling.
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Affiliation(s)
- Daniel G. Singleton
- School of Chemistry and Institute for Life Sciences , University of Southampton , Highfield , Southampton , SO17 1BJ , UK . ; http://www.southampton.ac.uk/chemistry/about/staff/est.page?
| | - Rohanah Hussain
- Diamond Light Source , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0DE , UK
| | - Giuliano Siligardi
- Diamond Light Source , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0DE , UK
| | - Pawan Kumar
- Department of Chemistry , University of Idaho , Moscow , ID 83844 , USA
| | | | - Nina Berova
- Department of Chemistry , Columbia University , 3000 Broadway , New York , NY 10027 , USA
| | - Eugen Stulz
- School of Chemistry and Institute for Life Sciences , University of Southampton , Highfield , Southampton , SO17 1BJ , UK . ; http://www.southampton.ac.uk/chemistry/about/staff/est.page?
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32
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Xu J, Wu ZS, Shen W, Xu H, Li H, Jia L. Cascade DNA nanomachine and exponential amplification biosensing. Biosens Bioelectron 2015; 73:19-25. [DOI: 10.1016/j.bios.2015.05.045] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/15/2015] [Accepted: 05/21/2015] [Indexed: 01/13/2023]
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33
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Zhang H, Lai M, Zuehlke A, Peng H, Li XF, Le XC. Binding-Induced DNA Nanomachines Triggered by Proteins and Nucleic Acids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506312] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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34
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Zhang H, Lai M, Zuehlke A, Peng H, Li X, Le XC. Binding‐Induced DNA Nanomachines Triggered by Proteins and Nucleic Acids. Angew Chem Int Ed Engl 2015; 54:14326-30. [DOI: 10.1002/anie.201506312] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/17/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3 (Canada)
| | - Maode Lai
- Department of Pathology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058 (China)
| | - Albert Zuehlke
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3 (Canada)
| | - Hanyong Peng
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3 (Canada)
| | - Xing‐Fang Li
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3 (Canada)
| | - X. Chris Le
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, T6G 2G3 (Canada)
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35
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Kim K, Guo J, Xu X, Fan DL. Recent Progress on Man-Made Inorganic Nanomachines. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:4037-4057. [PMID: 26114572 DOI: 10.1002/smll.201500407] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/17/2015] [Indexed: 06/04/2023]
Abstract
The successful development of nanoscale machinery, which can operate with high controllability, high precision, long lifetimes, and tunable driving powers, is pivotal for the realization of future intelligent nanorobots, nanofactories, and advanced biomedical devices. However, the development of nanomachines remains one of the most difficult research areas, largely due to the grand challenges in fabrication of devices with complex components and actuation with desired efficiency, precision, lifetime, and/or environmental friendliness. In this work, the cutting-edge efforts toward fabricating and actuating various types of nanomachines and their applications are reviewed, with a special focus on nanomotors made from inorganic nanoscale building blocks, which are introduced according to the employed actuation mechanism. The unique characteristics and obstacles for each type of nanomachine are discussed, and perspectives and challenges of this exciting field are presented.
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Affiliation(s)
- Kwanoh Kim
- Department of Mechanical Engineering, the University of Texas at Austin, Austin, TX, 78712, USA
| | - Jianhe Guo
- Materials Science and Engineering Program, the University of Texas at Austin, Austin, TX, 78712, USA
| | - Xiaobin Xu
- Materials Science and Engineering Program, the University of Texas at Austin, Austin, TX, 78712, USA
| | - D L Fan
- Department of Mechanical Engineering, the University of Texas at Austin, Austin, TX, 78712, USA
- Materials Science and Engineering Program, the University of Texas at Austin, Austin, TX, 78712, USA
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36
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Guo Y, Wu J, Ju H. Target-driven DNA association to initiate cyclic assembly of hairpins for biosensing and logic gate operation. Chem Sci 2015; 6:4318-4323. [PMID: 29218202 PMCID: PMC5707516 DOI: 10.1039/c5sc01215e] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 05/11/2015] [Indexed: 01/22/2023] Open
Abstract
Target-driven DNA association is designed for initiating the cyclic assembly of hairpins for target detection and logic gate operation.
A target-driven DNA association was designed to initiate cyclic assembly of hairpins, which led to an enzyme-free amplification strategy for detection of a nucleic acid or aptamer substrate and flexible construction of logic gates. The cyclic system contained two ssDNA (S1 and S2) and two hairpins (H1 and H2). These ssDNA could co-recognize the target to produce an S1–target–S2 structure, which brought their toehold and branch-migration domains into close proximity to initiate the cyclic assembly of hairpins. The assembly product further induced the dissociation of a double-stranded probe DNA (Q:F) via toehold-mediated strand displacement to switch the fluorescence signal. This method could detect DNA and ATP as model analytes down to 21.6 pM and 38 nM, respectively. By designing different DNA input strands, the “AND”, “INHIBIT” and “NAND” logic gates could be activated to achieve the output signal. The proposed biosensing and logic gate operation platform showed potential applications in disease diagnosis.
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Affiliation(s)
- Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , P. R. China . ; ; Tel: +86 25 83593593
| | - Jie Wu
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , P. R. China . ; ; Tel: +86 25 83593593
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , P. R. China . ; ; Tel: +86 25 83593593
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Ye B, Wang H, Ding H, Zhao Y, Pu Y, Gu Z. Colorimetric logic response based on aptamer functionalized colloidal crystal hydrogels. NANOSCALE 2015; 7:7565-7568. [PMID: 25874602 DOI: 10.1039/c5nr00586h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A novel colorimetric logic system based on the aptamer-cross-linked colloidal crystal hydrogel (CCH) was developed. With the input stimuli of Hg(2+) and Ag(+), the CCH displayed shrinking response and colour change corresponding to the logical "OR" and "AND" gate. The visualization of the logic output signals is realized.
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Affiliation(s)
- Baofen Ye
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, China.
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Zhang Z, Cao H, Jiang S, Liu Z, He X, Yu H, Li Y. Nanoassembly of probucol enables novel therapeutic efficacy in the suppression of lung metastasis of breast cancer. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:4735-4745. [PMID: 24930590 DOI: 10.1002/smll.201400799] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/10/2014] [Indexed: 06/03/2023]
Abstract
Metastasis is one of the major obstacles hindering the success of cancer therapy. The directed nanoassembly of probucol results in the "DNP" system, which greatly improves the oral delivery of probucol and subsequently leads to a novel therapeutic efficacy of probucol in the suppression of lung metastasis of breast cancer. DNP is formed by employing the intermolecular hydrophobic interactions between probucol and polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether (also known as Triton X-100). After oral administration, the probucol concentration in the intestines is surprisingly about 200 times higher if it is applied as DNP rather than free probucol; it can be absorbed into intestinal enterocytes via clathrin-mediated endocytosis and transported into the systemic circulation through the lymphatic pathway. Moreover, the oral bioavailability of probucol is significantly higher-13.55 times higher-when applied as DNP in place of free probucol. The drug concentration in major organs is also significantly increased. The in vitro measurements show that the migration and invasion abilities of 4T1 cells are obviously inhibited by DNP. In particular, in an orthotopic metastatic breast cancer model, the notable suppression of lung metastasis from DNP is observed, but no effect is seen from the free-probucol suspension. As a result, the directed drug nanoassembly may open a new route for enhancing oral drug delivery and enable new therapeutic abilities for probucol against cancer metastasis.
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Affiliation(s)
- Zhiwen Zhang
- Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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Torelli E, Marini M, Palmano S, Piantanida L, Polano C, Scarpellini A, Lazzarino M, Firrao G. A DNA origami nanorobot controlled by nucleic acid hybridization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:2918-2926. [PMID: 24648163 DOI: 10.1002/smll.201400245] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/26/2014] [Indexed: 06/03/2023]
Abstract
A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators.
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Affiliation(s)
- Emanuela Torelli
- Department of Agricultural and Environmental Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
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Wang ZG, Ding B. Engineering DNA self-assemblies as templates for functional nanostructures. Acc Chem Res 2014; 47:1654-62. [PMID: 24588320 DOI: 10.1021/ar400305g] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CONSPECTUS: DNA is a well-known natural molecule that carries genetic information. In recent decades, DNA has been used beyond its genetic role as a building block for the construction of engineering materials. Many strategies, such as tile assembly, scaffolded origami and DNA bricks, have been developed to design and produce 1D, 2D, and 3D architectures with sophisticated morphologies. Moreover, the spatial addressability of DNA nanostructures and sequence-dependent recognition enable functional elements to be precisely positioned and allow for the control of chemical and biochemical processes. The spatial arrangement of heterogeneous components using DNA nanostructures as the templates will aid in the fabrication of functional materials that are difficult to produce using other methods and can address scientific and technical challenges in interdisciplinary research. For example, plasmonic nanoparticles can be assembled into well-defined configurations with high resolution limit while exhibiting desirable collective behaviors, such as near-field enhancement. Conducting metallic or polymer patterns can be synthesized site-specifically on DNA nanostructures to form various controllable geometries, which could be used for electronic nanodevices. Biomolecules can be arranged into organized networks to perform programmable biological functionalities, such as distance-dependent enzyme-cascade activities. DNA nanostructures can carry multiple cytoactive molecules and cell-targeting groups simultaneously to address medical issues such as targeted therapy and combined administration. In this Account, we describe recent advances in the functionalization of DNA nanostructures in different fashions based on our research efforts in nanophotonics, nanoelectronics, and nanomedicine. We show that DNA origami nanostructures can guide the assembly of achiral, spherical, metallic nanoparticles into nature-mimicking chiral geometries through hybridization between complementary DNA strands on the surface of nanoparticles and DNA scaffolds, to generate circular dichroism (CD) response in the visible light region. We also show that DNA nanostructures, on which a HRP-mimicking DNAzyme acts as the catalyst, can direct the site-selective growth of conductive polymer nanomaterials with template configuration-dependent doping behaviors. We demonstrate that DNA origami nanostructures can act as an anticancer-drug carrier, loading drug through intercalation, and can effectively circumvent the drug resistance of cultured cancer cells. Finally, we show a label-free strategy for probing the location and stability of DNA origami nanocarriers in cellular environments by docking turn-off fluorescence dyes in DNA double helices. These functionalizations require further improvement and expansion for realistic applications. We discuss the future opportunities and challenges of DNA based assemblies. We expect that DNA nanostructures as engineering materials will stimulate the development of multidisciplinary and interdisciplinary research.
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Affiliation(s)
- Zhen-Gang Wang
- National Center for NanoScience and Technology, No. 11
BeiYiTiao, ZhongGuanCun, Beijing, 100190 China
| | - Baoquan Ding
- National Center for NanoScience and Technology, No. 11
BeiYiTiao, ZhongGuanCun, Beijing, 100190 China
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41
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DNA from natural sources in design of functional devices. Methods 2014; 67:105-15. [DOI: 10.1016/j.ymeth.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 02/20/2014] [Accepted: 03/02/2014] [Indexed: 01/01/2023] Open
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Nguyen T, Håkansson P, Edge R, Collison D, Goodman BA, Burns JR, Stulz E. EPR based distance measurement in Cu-porphyrin–DNA. NEW J CHEM 2014. [DOI: 10.1039/c4nj00673a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Measurement of EPR spectra of Cu-porphyrin–DNA reveals intermolecular interactions between the DNA strands with average distances of 6.5–8.9 Å.
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Affiliation(s)
- ThaoNguyen Nguyen
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Pär Håkansson
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Ruth Edge
- School of Chemistry and Photon Science Institute
- The University of Manchester
- Manchester, UK
| | - David Collison
- School of Chemistry and Photon Science Institute
- The University of Manchester
- Manchester, UK
| | - Bernard A. Goodman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
- Guangxi University
- Nanning 530005, China
| | - Jonathan R. Burns
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Eugen Stulz
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
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