1
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DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2024; 7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Po-An Lin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
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2
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Vecchioni S, Lu B, Livernois W, Ohayon YP, Yoder JB, Yang CF, Woloszyn K, Bernfeld W, Anantram MP, Canary JW, Hendrickson WA, Rothschild LJ, Mao C, Wind SJ, Seeman NC, Sha R. Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210938. [PMID: 37268326 DOI: 10.1002/adma.202210938] [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: 11/03/2022] [Revised: 03/06/2023] [Indexed: 06/04/2023]
Abstract
DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.
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Affiliation(s)
- Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Livernois
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, IL, 60439, USA
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Bernfeld
- Department of Chemistry, New York University, New York, NY, 10003, USA
- ASPIRE Program, King School, Stamford, CT, 06905, USA
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, CA, 94035, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Math, Columbia University, New York, NY, 10027, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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3
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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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4
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Rahmani P, Goodlad M, Zhang Y, Li Y, Ye T. One-Step Ligand-Exchange Method to Produce Quantum Dot-DNA Conjugates for DNA-Directed Self-Assembly. ACS APPLIED MATERIALS & INTERFACES 2022; 14:47359-47368. [PMID: 36219825 DOI: 10.1021/acsami.2c10580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To address the current challenges in making bright, stable, and small DNA-functionalized quantum dots (QDs), we have developed a one-step ligand-exchange method to produce QD-DNA conjugates from commonly available hydrophobic QDs. We show that by systematically adjusting the reaction conditions such as ligand-to-nanoparticle molar ratio, pH, and solvent composition, stable and highly photoluminescent water-soluble QD-DNA conjugates with relatively high ligand loadings can be produced. Moreover, by site specifically binding these QD-DNA conjugates to a DNA origami template, we demonstrate that these bioconjugates have sufficient colloidal stability for DNA-directed self-assembly. Fluorescence quenching by an adjacent gold nanoparticle (AuNP) was demonstrated. Such QD-AuNP dimers may serve as biosensors with improved sensitivity and reproducibility. Moreover, our simple method can facilitate the assembly of QDs into more complex superlattices and discrete clusters that may enable novel photophysical properties.
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Affiliation(s)
- Paniz Rahmani
- Department of Chemistry & Biochemistry, University of California, 5200 North Lake Road, Merced, California 95343, United States
| | - Melissa Goodlad
- Department of Chemistry & Biochemistry, University of California, 5200 North Lake Road, Merced, California 95343, United States
| | - Yehan Zhang
- Department of Chemistry & Biochemistry, University of California, 5200 North Lake Road, Merced, California 95343, United States
| | - Yichen Li
- Department of Materials and Biomaterials Science & Engineering, University of California, 5200 North Lake Road, Merced, California 95343, United States
| | - Tao Ye
- Department of Chemistry & Biochemistry, University of California, 5200 North Lake Road, Merced, California 95343, United States
- Department of Materials and Biomaterials Science & Engineering, University of California, 5200 North Lake Road, Merced, California 95343, United States
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5
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Cervantes-Salguero K, Freeley M, Gwyther REA, Jones DD, Chávez JL, Palma M. Single molecule DNA origami nanoarrays with controlled protein orientation. BIOPHYSICS REVIEWS 2022; 3:031401. [PMID: 38505279 PMCID: PMC10903486 DOI: 10.1063/5.0099294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/20/2022] [Indexed: 03/21/2024]
Abstract
The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.
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Affiliation(s)
- K. Cervantes-Salguero
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - M. Freeley
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - R. E. A. Gwyther
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - D. D. Jones
- Division of Molecular Biosciences, School of Biosciences, Main Building, Cardiff University, Cardiff, Wales, United Kingdom
| | - J. L. Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright Patterson Air Force Base, Dayton, Ohio 45433-7901, USA
| | - M. Palma
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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6
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Barad HN, Kwon H, Alarcón-Correa M, Fischer P. Large Area Patterning of Nanoparticles and Nanostructures: Current Status and Future Prospects. ACS NANO 2021; 15:5861-5875. [PMID: 33830726 PMCID: PMC8155328 DOI: 10.1021/acsnano.0c09999] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 04/02/2021] [Indexed: 05/05/2023]
Abstract
Nanoparticles possess exceptional optical, magnetic, electrical, and chemical properties. Several applications, ranging from surfaces for optical displays and electronic devices, to energy conversion, require large-area patterns of nanoparticles. Often, it is crucial to maintain a defined arrangement and spacing between nanoparticles to obtain a consistent and uniform surface response. In the majority of the established patterning methods, the pattern is written and formed, which is slow and not scalable. Some parallel techniques, forming all points of the pattern simultaneously, have therefore emerged. These methods can be used to quickly assemble nanoparticles and nanostructures on large-area substrates into well-ordered patterns. Here, we review these parallel methods, the materials that have been processed by them, and the types of particles that can be used with each method. We also emphasize the maximal substrate areas that each method can pattern and the distances between particles. Finally, we point out the advantages and disadvantages of each method, as well as the challenges that still need to be addressed to enable facile, on-demand large-area nanopatterning.
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Affiliation(s)
- Hannah-Noa Barad
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany
| | - Hyunah Kwon
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany
| | - Mariana Alarcón-Correa
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany
| | - Peer Fischer
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany
- Institute
of Physical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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7
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Cervantes-Salguero K, Freeley M, Chávez JL, Palma M. Single-molecule DNA origami aptasensors for real-time biomarker detection. J Mater Chem B 2021; 8:6352-6356. [PMID: 32716449 DOI: 10.1039/d0tb01291b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Here we report the use of DNA nanostructures as platforms to monitor the inherent conformational changes of aptamers upon analyte binding, with single-molecule resolution and real-time capability. An aptasensor designed to sense cortisol was found to suffer from instability in solution, but this was reconciled via a rational design of a single-molecule sensing platform. In this regard, DNA origami was employed to immobilise individual aptasensors on a glass surface and to ensure adequate interaction with their environment, for single-molecule analysis. The strategy presented here can be applied to any aptamer obtained by the destabilisation of a duplex in a SELEX process, and hence employed in the rational design of single-molecule biosensors.
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Affiliation(s)
- Keitel Cervantes-Salguero
- School of Biological and Chemical Sciences and Materials Research Institute, Queen Mary University of London, London, UK.
| | - Mark Freeley
- School of Biological and Chemical Sciences and Materials Research Institute, Queen Mary University of London, London, UK.
| | - Jorge L Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright Patterson Air Force Base, Dayton, Ohio, USA.
| | - Matteo Palma
- School of Biological and Chemical Sciences and Materials Research Institute, Queen Mary University of London, London, UK.
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8
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Constructing Large 2D Lattices Out of DNA-Tiles. Molecules 2021; 26:molecules26061502. [PMID: 33801952 PMCID: PMC8000633 DOI: 10.3390/molecules26061502] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.
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9
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Amoroso G, Sapelkin A, Ye Q, Araullo-Peters V, Cecconello A, Fernandez G, Palma M. DNA-driven dynamic assembly of MoS 2 nanosheets. Faraday Discuss 2021; 227:233-244. [PMID: 33404023 DOI: 10.1039/c9fd00118b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Controlling the assembly of molybdenum disulfide (MoS2) layers into static and dynamic superstructures can impact on their use in optoelectronics, energy, and drug delivery. Toward this goal, we present a strategy to drive the assembly of MoS2 layers via the hybridization of complementary DNA linkers. By functionalizing the MoS2 surface with thiolated DNA, MoS2 nanosheets were assembled into mulitlayered superstructures, and the complementary DNA strands were used as linkers. A disassembly process was triggered by the formation of an intramolecular i-motif structure at a cystosine-rich sequence in the DNA linker at acidic pH values. We tested the versatility of our approach by driving the disassembly of the MoS2 superstructures through a different DNA-based mechanism, namely strand displacement. This study demonstrates how DNA can be employed to drive the static and dynamic assembly of MoS2 nanosheets in aqueous solution.
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Affiliation(s)
- Giuseppe Amoroso
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
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10
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Hawkes W, Huang D, Reynolds P, Hammond L, Ward M, Gadegaard N, Marshall JF, Iskratsch T, Palma M. Probing the nanoscale organisation and multivalency of cell surface receptors: DNA origami nanoarrays for cellular studies with single-molecule control. Faraday Discuss 2020; 219:203-219. [PMID: 31314021 DOI: 10.1039/c9fd00023b] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nanoscale organisation of receptor ligands has become an important approach to study the clustering behaviour of cell-surface receptors. Biomimetic substrates fabricated via different nanopatterning strategies have so far been applied to investigate specific integrins and cell types, but without multivalent control. Here we use DNA origami to surpass the limits of current approaches and fabricate nanoarrays to study different cell adhesion processes, with nanoscale spatial resolution and single-molecule control. Notably, DNA nanostructures enable the display of receptor ligands in a highly customisable manner, with modifiable parameters including ligand number, ligand spacing and most importantly, multivalency. To test the adaptability and robustness of the system we combined it with focused ion beam and electron-beam lithography nanopatterning to additionally control the distance between the origami structures (i.e. receptor clusters). Moreover, we demonstrate how the platform can be used to interrogate two different biological questions: (1) the cooperative effect of integrin and growth factor receptor in cancer cell spreading, and (2) the role of integrin clustering in cardiomyocyte adhesion and maturation. Thereby we find previously unknown clustering behaviour of different integrins, further outlining the importance for such customisable platforms for future investigations of specific receptor organisation at the nanoscale.
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Affiliation(s)
- William Hawkes
- Randall Centre of Cell and Molecular Biophysics, King's College London, UK
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11
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Son J, Roh H, Shin HY, Park KW, Park C, Park H, Lee C, Kwak J, Jung BJ, Lee JK. Photo-cleavable perfluoroalkylated copolymers for tailoring quantum dot thin films. Polym Chem 2020. [DOI: 10.1039/d0py01017k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report the synthesis, operating mechanism, and application of a copolymer that reveals increasing solubility in fluorous solvents by photolysis.
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Affiliation(s)
- Jongchan Son
- Department of Polymer Science and Engineering
- Inha University
- Incheon 22212
- Republic of Korea
| | - Heebum Roh
- Department of Electrical and Computer Engineering
- Inter-University Semiconductor Research Center
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Han Young Shin
- Department of Materials Science and Engineering
- University of Seoul
- Seoul 02504
- Republic of Korea
| | - Keun-Woo Park
- Department of Polymer Science and Engineering
- Inha University
- Incheon 22212
- Republic of Korea
| | - Chunhee Park
- Department of Polymer Science and Engineering
- Inha University
- Incheon 22212
- Republic of Korea
| | - Hanbit Park
- Department of Polymer Science and Engineering
- Inha University
- Incheon 22212
- Republic of Korea
| | - Changhee Lee
- Department of Electrical and Computer Engineering
- Inter-University Semiconductor Research Center
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Jeonghun Kwak
- Department of Electrical and Computer Engineering
- Inter-University Semiconductor Research Center
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Byung Jun Jung
- Department of Materials Science and Engineering
- University of Seoul
- Seoul 02504
- Republic of Korea
| | - Jin-Kyun Lee
- Department of Polymer Science and Engineering
- Inha University
- Incheon 22212
- Republic of Korea
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12
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Zhang P, Wang F, Liu W, Mao X, Hao C, Zhang Y, Fan C, Hu J, Wang L, Li B. Quantitative Measurement of Spatial Effects of DNA Origami on Molecular Binding Reactions Detected using Atomic Force Microscopy. ACS APPLIED MATERIALS & INTERFACES 2019; 11:21973-21981. [PMID: 31117423 DOI: 10.1021/acsami.9b01691] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA origami is a ubiquitous nanostructure that can be used as a universal scaffold for constructing molecular motors, nanosensors, nanodrugs, and optical devices. Understanding the inherent heterogeneity of DNA origami structures is crucial for optimizing the design of high-efficiency nanosized-devices. Here, we investigated the spatial effects of the DNA origami on binding reactions using atomic force microscopy. Protein complexes formed more efficiently at the vertex and rim than on the surface of the DNA origami; surprisingly, the maximum difference in biotin-streptavidin binding efficiency was over 80%, and the change in the binding rate was approximately 40-fold, suggesting the presence of distinct microenvironments at different locations of the DNA origami. Our findings are not only useful for the potential applications of the DNA origami, but also for clarifying differences in nanomaterials caused by nonuniform distribution or defects.
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Affiliation(s)
- Ping Zhang
- Division of Physical Biology & Bioimaging Centre, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Wenjing Liu
- Division of Physical Biology & Bioimaging Centre, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xiuhai Mao
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Changchun Hao
- Laboratory of Biophysics and Biomedicine, College of Physics and Information Technology , Shaanxi Normal University , Xi'an 710062 , China
| | - Yi Zhang
- Division of Physical Biology & Bioimaging Centre, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Centre, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Jun Hu
- Division of Physical Biology & Bioimaging Centre, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Centre, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
| | - Bin Li
- Division of Physical Biology & Bioimaging Centre, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
- Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , China
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13
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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14
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Huang D, Patel K, Perez-Garrido S, Marshall JF, Palma M. DNA Origami Nanoarrays for Multivalent Investigations of Cancer Cell Spreading with Nanoscale Spatial Resolution and Single-Molecule Control. ACS NANO 2019; 13:728-736. [PMID: 30588806 DOI: 10.1021/acsnano.8b08010] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We present a strategy for the fabrication of biomimetic nanoarrays, based on the use of DNA origami, that permits the multivalent investigation of ligand-receptor molecule interactions in cancer cell spreading, with nanoscale spatial resolution and single-molecule control. We employed DNA origami to control the nanoscale spatial organization of integrin- and epidermal growth factor (EGF)-binding ligands that modulate epidermal cancer cell behavior. By organizing these multivalent DNA nanostructures in nanoarray configurations on nanopatterned surfaces, we demonstrated the cooperative behavior of integrin and EGF ligands in the spreading of human cutaneous melanoma cells: this cooperation was shown to depend on both the number and ratio of the selective ligands employed. Notably, the multivalent biochips we have developed allowed for this cooperative effect to be demonstrated with single-molecule control and nanoscale spatial resolution. By and large, the platform presented here is of general applicability for the study, with molecular control, of different multivalent interactions governing biological processes from the function of cell-surface receptors to protein-ligand binding and pathogen inhibition.
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Affiliation(s)
- Da Huang
- School of Biological and Chemical Sciences, Materials Research Institute, Institute of Bioengineering , Queen Mary University of London , Mile End Road , London E1 4NS , United Kingdom
| | - Ketan Patel
- Barts Cancer Institute, Cancer Research UK Centre of Excellence , Queen Mary University of London , Charterhouse Square , London EC1M 6BQ , United Kingdom
| | - Sandra Perez-Garrido
- School of Biological and Chemical Sciences, Materials Research Institute, Institute of Bioengineering , Queen Mary University of London , Mile End Road , London E1 4NS , United Kingdom
- Barts Cancer Institute, Cancer Research UK Centre of Excellence , Queen Mary University of London , Charterhouse Square , London EC1M 6BQ , United Kingdom
| | - John F Marshall
- Barts Cancer Institute, Cancer Research UK Centre of Excellence , Queen Mary University of London , Charterhouse Square , London EC1M 6BQ , United Kingdom
| | - Matteo Palma
- School of Biological and Chemical Sciences, Materials Research Institute, Institute of Bioengineering , Queen Mary University of London , Mile End Road , London E1 4NS , United Kingdom
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15
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Freeley M, Attanzio A, Cecconello A, Amoroso G, Clement P, Fernandez G, Gesuele F, Palma M. Tuning the Coupling in Single-Molecule Heterostructures: DNA-Programmed and Reconfigurable Carbon Nanotube-Based Nanohybrids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1800596. [PMID: 30356926 PMCID: PMC6193148 DOI: 10.1002/advs.201800596] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/27/2018] [Indexed: 06/08/2023]
Abstract
Herein a strategy is presented for the assembly of both static and stimuli-responsive single-molecule heterostructures, where the distance and electronic coupling between an individual functional nanomoiety and a carbon nanostructure are tuned via the use of DNA linkers. As proof of concept, the formation of 1:1 nanohybrids is controlled, where single quantum dots (QDs) are tethered to the ends of individual carbon nanotubes (CNTs) in solution with DNA interconnects of different lengths. Photoluminescence investigations-both in solution and at the single-hybrid level-demonstrate the electronic coupling between the two nanostructures; notably this is observed to progressively scale, with charge transfer becoming the dominant process as the linkers length is reduced. Additionally, stimuli-responsive CNT-QD nanohybrids are assembled, where the distance and hence the electronic coupling between an individual CNT and a single QD are dynamically modulated via the addition and removal of potassium (K+) cations; the system is further found to be sensitive to K+ concentrations from 1 pM to 25 × 10-3 m. The level of control demonstrated here in modulating the electronic coupling of reconfigurable single-molecule heterostructures, comprising an individual functional nanomoiety and a carbon nanoelectrode, is of importance for the development of tunable molecular optoelectronic systems and devices.
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Affiliation(s)
- Mark Freeley
- School of Biological and Chemical SciencesMaterials Research Instituteand Institute of BioengineeringQueen Mary University of LondonMile End RoadLondonE1 4NSUK
| | - Antonio Attanzio
- School of Biological and Chemical SciencesMaterials Research Instituteand Institute of BioengineeringQueen Mary University of LondonMile End RoadLondonE1 4NSUK
| | - Alessandro Cecconello
- School of Biological and Chemical SciencesMaterials Research Instituteand Institute of BioengineeringQueen Mary University of LondonMile End RoadLondonE1 4NSUK
| | - Giuseppe Amoroso
- School of Biological and Chemical SciencesMaterials Research Instituteand Institute of BioengineeringQueen Mary University of LondonMile End RoadLondonE1 4NSUK
- Organisch‐Chemisches InstitutWestfälische Wilhelms‐Universität MünsterCorrensstrasse 4048149MünsterGermany
| | - Pierrick Clement
- School of Biological and Chemical SciencesMaterials Research Instituteand Institute of BioengineeringQueen Mary University of LondonMile End RoadLondonE1 4NSUK
| | - Gustavo Fernandez
- Organisch‐Chemisches InstitutWestfälische Wilhelms‐Universität MünsterCorrensstrasse 4048149MünsterGermany
| | - Felice Gesuele
- Department of PhysicsUniversity of Naples “Federico II”Via Cintia, 26 Ed. 680126NapoliItaly
| | - Matteo Palma
- School of Biological and Chemical SciencesMaterials Research Instituteand Institute of BioengineeringQueen Mary University of LondonMile End RoadLondonE1 4NSUK
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16
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Kumari S, Solanki A, Mandal S, Subramanyam D, Das P. Creation of Linear Carbon Dot Array with Improved Optical Properties through Controlled Covalent Conjugation with DNA. Bioconjug Chem 2018; 29:1500-1504. [PMID: 29634254 DOI: 10.1021/acs.bioconjchem.8b00173] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Controlled conjugation of fluorescent carbon dots (CDs) with DNA and subsequent fabrication of the CDs into an array through hybridization mediated self-assembly in the solution phase is reported. Covalent conjugation of CD with DNA and the subsequent array formation change the mobility of the CD-DNA array in gel electrophoresis and HPLC significantly. Interspatial distance in the CD-DNA array is tuned by the DNA sequence length and maintained at ∼8 ± 0.3 nm as revealed by electron microscopy studies. An increase in fluorescence lifetime by ∼2 ns was observed for the CD-DNA array compared to a solitary CD, vis-á-vis better imaging prospects of HEK293 cells by the former. Thus, the array displays improved fluorescence and unhindered cell penetration.
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Affiliation(s)
- Sonam Kumari
- Department of Chemistry , IIT Patna, Bihta , Patna 801103 , India
| | - Apurv Solanki
- National Centre for Cell Science , Pune 411007 , Maharashtra , India
| | - Saptarshi Mandal
- Department of Chemistry , IIT Patna, Bihta , Patna 801103 , India
| | - Deepa Subramanyam
- National Centre for Cell Science , Pune 411007 , Maharashtra , India
| | - Prolay Das
- Department of Chemistry , IIT Patna, Bihta , Patna 801103 , India
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17
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Huang D, Freeley M, Palma M. Single-Molecule Patterning via DNA Nanostructure Assembly: A Reusable Platform. Methods Mol Biol 2018; 1811:231-251. [PMID: 29926457 DOI: 10.1007/978-1-4939-8582-1_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here we describe a facile strategy of general applicability for controlling the immobilization of individual nanomoieties on nanopatterned surfaces with single-molecule control. We combine the ability of DNA nanostructures as programmable platforms, with a one-step Focused Ion Beam nanopatterning, to demonstrate the controlled immobilization of DNA origami functionalized with individual quantum dots (QDs) at predesigned positions on glass coverslips and silicon substrates. Remarkably, the platform developed is reusable after a simple cleaning process, and can be designed to display different geometrical arrangements.
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Affiliation(s)
- Da Huang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Mark Freeley
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Matteo Palma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
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18
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Plénat T, Yoshizawa S, Fourmy D. DNA-Guided Delivery of Single Molecules into Zero-Mode Waveguides. ACS APPLIED MATERIALS & INTERFACES 2017; 9:30561-30566. [PMID: 28825461 DOI: 10.1021/acsami.7b11953] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Zero-mode waveguides (ZMWs) are powerful analytical tools corresponding to optical nanostructures fabricated in a thin metallic film capable of confining an excitation volume to the range of attoliters. This small volume of confinement allows single-molecule fluorescence experiments to be performed at physiologically relevant concentrations of fluorescently labeled biomolecules. Exactly one molecule to be studied must be attached at the floor of the ZMW for signal detection and analysis; however, the massive parallelism of these nanoarrays suffers from a Poissonian-limited distribution of these biomolecules. To date, there is no method available that provides full single-molecule occupancy of massively arrayed ZMWs. Here we report the performance of a DNA-guided method that uses steric exclusion properties of large DNA molecules to bias the Poissonian-limited delivery of single molecules. Non-Poissonian statistics were obtained with DNA molecules that contain a free-biotinylated extremity for efficient binding to the floor of the ZMW, which resulted in a decrease of accessibility for a second molecule. Both random-coiled and condensed DNA conformations drove non-Poissonian single-molecule delivery into ZMW arrays. The results suggest that an optimal balance between the rigidity and flexibility of the macromolecule is critical for favorable accessibility and single occupancy. The optimized method provides a means for full exploitation of these massively parallelized analytical tools.
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Affiliation(s)
- Thomas Plénat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif-sur-Yvette Cedex, France
| | - Satoko Yoshizawa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif-sur-Yvette Cedex, France
| | - Dominique Fourmy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif-sur-Yvette Cedex, France
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