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Cervantes-Salguero K, Gutiérrez Fosado YA, Megone W, Gautrot JE, Palma M. Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization. Molecules 2023; 28:molecules28093686. [PMID: 37175096 PMCID: PMC10180480 DOI: 10.3390/molecules28093686] [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: 03/03/2023] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
DNA is programmed to hierarchically self-assemble into superstructures spanning from nanometer to micrometer scales. Here, we demonstrate DNA nanosheets assembled out of a rationally designed flexible DNA unit (F-unit), whose shape resembles a Feynman diagram. F-units were designed to self-assemble in two dimensions and to display a high DNA density of hydrophobic moieties. oxDNA simulations confirmed the planarity of the F-unit. DNA nanosheets with a thickness of a single DNA duplex layer and with large coverage (at least 30 μm × 30 μm) were assembled from the liquid phase at the solid/liquid interface, as unambiguously evidenced by atomic force microscopy imaging. Interestingly, single-layer nanodiscs formed in solution at low DNA concentrations. DNA nanosheet superstructures were further assembled at liquid/liquid interfaces, as demonstrated by the fluorescence of a double-stranded DNA intercalator. Moreover, the interfacial mechanical properties of the nanosheet superstructures were measured as a response to temperature changes, demonstrating the control of interfacial shear mechanics based on DNA nanostructure engineering. The rational design of the F-unit, along with the presented results, provide an avenue toward the controlled assembly of reconfigurable/responsive nanosheets and membranes at liquid/liquid interfaces, to be potentially used in the characterization of biomechanical processes and materials transport.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | - William Megone
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Julien E Gautrot
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Matteo Palma
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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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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Zhu X, Yan X, Yang S, Wang Y, Wang S, Tian Y. DNA-Mediated Assembly of Carbon Nanomaterials. Chempluschem 2022; 87:e202200089. [PMID: 35589623 DOI: 10.1002/cplu.202200089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/26/2022] [Indexed: 02/18/2024]
Abstract
Carbon nanomaterials (CNMs) have attracted extensive attentions on account of their superior electrical, mechanical, optical, and biological properties. However, the dimensional limit and irregular arrangement have hampered their further application. It is necessary to find an easy, efficient and controllable way to assemble CNMs into well-ordered array. DNA nanotechnology, owning to the advantages of precise programmability, highly structural predictability and spatial addressability, has been widely applied in the assembly of CNMs. Summarizing the progress and achievements in this field will be of great value to related studies. Herein, based on the different dimensions of CNMs containing 0-dimensional (0D) carbon dots (CDs), fullerenes, 1-dimensional (1D) carbon nanotubes (CNTs) and 2-dimensional (2D) graphene, we introduced the conjugation strategies between DNA and CNMs, their different assembly methods and their applications. In addition, we also discuss the existing challenges and future opportunities in the field.
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Affiliation(s)
- Xurong Zhu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Xuehui Yan
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Sichang Yang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Yong Wang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Shuang Wang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Institute of Marine Biomedicine, Shenzhen Polytechnic, 518055, Shenzhen, P. R. China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
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Vittala SK, Zhao Y, Han D. Programmed Assembly of DNA Templates by Silver Nanowires. Chempluschem 2022; 87:e202100478. [PMID: 35014201 DOI: 10.1002/cplu.202100478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/20/2021] [Indexed: 12/16/2022]
Abstract
DNA origami templates are known to exhibit many advantages to integrate functional components at desirable locations for nanoelectronic applications. In order to immobilize conducting or semiconducting species in a bottom-up approach, the programmed assembly of DNA templates is of utmost necessity. This report demonstrates the silver nanowires enabled bridging of two linear DNA origami (DO) nanostructures by utilizing the host-guest interaction of biotin-STV and sequence-specific silver metallization of poly(dG-dC) DNA nanowires (in 10 % yield) using (dA)10 coated AgNPs (15 nm). The enzymatic synthesis of 750 bp, 1500 bp and 3000 bp bis-biotinylated poly(dG-dC), facile synthesis of 1 : 1 biotin-STV and silver-nanowire bridged DNA templates were characterized by gel electrophoresis, atomic force microscope imaging techniques. The strategy utilized here provides a method that can precisely connect heterogeneous templates towards bottom-up fabrication of practical nanoelectronics.
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Affiliation(s)
- Sandeepa K Vittala
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Yumeng Zhao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Da Han
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
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Saraswathi SK, Karunakaran V, Maiti KK, Joseph J. DNA Condensation Triggered by the Synergistic Self-Assembly of Tetraphenylethylene-Viologen Aggregates and CT-DNA. Front Chem 2021; 9:716771. [PMID: 34368086 PMCID: PMC8341308 DOI: 10.3389/fchem.2021.716771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 06/24/2021] [Indexed: 01/24/2023] Open
Abstract
Development of small organic chromophores as DNA condensing agents, which explore supramolecular interactions and absorbance or fluorescence-based tracking of condensation and gene delivery processes, is in the initial stages. Herein, we report the synthesis and electrostatic/groove binding interaction-directed synergistic self-assembly of the aggregates of two viologen-functionalized tetraphenylethylene (TPE-V) molecules with CT-DNA and subsequent concentration-dependent DNA condensation process. TPE-V molecules differ in their chemical structure according to the number of viologen units. Photophysical and morphological studies have revealed the interaction of the aggregates of TPE-V in Tris buffer with CT-DNA, which transforms the fibrous network structure of CT-DNA to partially condensed beads-on-a-string-like arrangement with TPE-V aggregates as beads via electrostatic and groove binding interactions. Upon further increasing the concentration of TPE-V, the "beads-on-a-string"-type assembly of TPE-V/CT-DNA complex changes to completely condensed compact structures with 40-50 nm in diameter through the effective charge neutralization process. Enhancement in the melting temperature of CT-DNA, quenching of the fluorescence emission of ethidium bromide/CT-DNA complex, and the formation of induced CD signal in the presence of TPE-V molecules support the observed morphological changes and thereby verify the DNA condensation abilities of TPE-V molecules. Decrease in the hydrodynamic size, increase in the zeta potential value with the addition of TPE-V molecules to CT-DNA, failure of TPE-V/cucurbit(8)uril complex to condense CT-DNA, and the enhanced DNA condensation ability of TPE-V2 with two viologen units compared to TPE-V1 with a single viologen unit confirm the importance of positively charged viologen units in the DNA condensation process. Initial cytotoxicity analysis on A549 cancer and WI-38 normal cells revealed that these DNA condensing agents are non-toxic in nature and hence could be utilized in further cellular delivery studies.
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Affiliation(s)
- Sajena Kanangat Saraswathi
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Varsha Karunakaran
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kaustabh Kumar Maiti
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Joshy Joseph
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Long K, Liu Y, Li Y, Wang W. Self-assembly of trigonal building blocks into nanostructures: molecular design and biomedical applications. J Mater Chem B 2021; 8:6739-6752. [PMID: 32686806 DOI: 10.1039/d0tb01128b] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Trigonal molecules have a special triskelion structure similar to clathrin protein, providing great inspiration for constructing artificial nanoassemblies. To date, various synthetic trigonal conjugates have been designed for supramolecular self-assembly, which have demonstrated versatile and controllable self-assembly ability in materials science. Here we will review the design of trigonal (sometimes called three-legged, tripodal, C3-symmetric, or triskelion) building blocks that can self-assemble into various nanostructures and discuss the biomedical applications of the self-assembled nanomaterials.
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Affiliation(s)
- Kaiqi Long
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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Saraswathi SK, Vittala SK, Manayani MK, Joseph J. Sequence programmed DNA three-way junctions for templated assembly of fluorescent silver nanoclusters. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 207:111886. [DOI: 10.1016/j.jphotobiol.2020.111886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/17/2020] [Accepted: 04/24/2020] [Indexed: 12/23/2022]
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Vittala SK, Han D. DNA-Guided Assemblies toward Nanoelectronic Applications. ACS APPLIED BIO MATERIALS 2020; 3:2702-2722. [PMID: 35025404 DOI: 10.1021/acsabm.9b01178] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandeepa Kulala Vittala
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Da Han
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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