1
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Verma S, Pathak AK, Rahman BMA. Review of Biosensors Based on Plasmonic-Enhanced Processes in the Metallic and Meta-Material-Supported Nanostructures. MICROMACHINES 2024; 15:502. [PMID: 38675314 PMCID: PMC11052336 DOI: 10.3390/mi15040502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Surface plasmons, continuous and cumulative electron vibrations confined to metal-dielectric interfaces, play a pivotal role in aggregating optical fields and energies on nanostructures. This confinement exploits the intrinsic subwavelength nature of their spatial profile, significantly enhancing light-matter interactions. Metals, semiconductors, and 2D materials exhibit plasmonic resonances at diverse wavelengths, spanning from ultraviolet (UV) to far infrared, dictated by their unique properties and structures. Surface plasmons offer a platform for various light-matter interaction mechanisms, capitalizing on the orders-of-magnitude enhancement of the electromagnetic field within plasmonic structures. This enhancement has been substantiated through theoretical, computational, and experimental studies. In this comprehensive review, we delve into the plasmon-enhanced processes on metallic and metamaterial-based sensors, considering factors such as geometrical influences, resonating wavelengths, chemical properties, and computational methods. Our exploration extends to practical applications, encompassing localized surface plasmon resonance (LSPR)-based planar waveguides, polymer-based biochip sensors, and LSPR-based fiber sensors. Ultimately, we aim to provide insights and guidelines for the development of next-generation, high-performance plasmonic technological devices.
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Affiliation(s)
- Sneha Verma
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Akhilesh Kumar Pathak
- Center for Smart Structures and Materials, Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA;
| | - B. M. Azizur Rahman
- School of Science and Technology, City University of London, London EC1V0HB, UK
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2
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Kemper U, Weizenmann N, Kielar C, Erbe A, Seidel R. Heavy Metal Stabilization of DNA Origami Nanostructures. NANO LETTERS 2024; 24:2429-2436. [PMID: 38363878 PMCID: PMC10905993 DOI: 10.1021/acs.nanolett.3c03751] [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: 09/29/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
DNA origami is a powerful tool to fold 3-dimensional DNA structures with nanometer precision. Its usage, however, is limited as high ionic strength, temperatures below ∼60 °C, and pH values between 5 and 10 are required to ensure the structural integrity of DNA origami nanostructures. Here, we demonstrate a simple and effective method to stabilize DNA origami nanostructures against harsh buffer conditions using [PdCl4]2-. It provided the stabilization of different DNA origami nanostructures against mechanical compression, temperatures up to 100 °C, double-distilled water, and pH values between 4 and 12. Additionally, DNA origami superstructures and bound cargos are stabilized with yields of up to 98%. To demonstrate the general applicability of our approach, we employed our protocol with a Pd metallization procedure at elevated temperatures. In the future, we think that our method opens up new possibilities for applications of DNA origami nanostructures beyond their usual reaction conditions.
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Affiliation(s)
- Ulrich Kemper
- Molecular
Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
| | - Nicole Weizenmann
- Molecular
Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
| | - Charlotte Kielar
- Institute
of Ion Beam Physics and Materials Research and Department of Nanoelectronics, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany
- Insitute
of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany
| | - Artur Erbe
- Institute
of Ion Beam Physics and Materials Research and Department of Nanoelectronics, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany
| | - Ralf Seidel
- Molecular
Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
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3
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Martynenko IV, Erber E, Ruider V, Dass M, Posnjak G, Yin X, Altpeter P, Liedl T. Site-directed placement of three-dimensional DNA origami. NATURE NANOTECHNOLOGY 2023; 18:1456-1462. [PMID: 37640908 DOI: 10.1038/s41565-023-01487-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023]
Abstract
The combination of lithographic methods with two-dimensional DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micrometre scale. Here we extend this concept to the third dimension by mounting three-dimensional DNA origami onto nanopatterned substrates, followed by silicification to provide hybrid DNA-silica structures exhibiting mechanical and chemical stability and achieving feature sizes in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to three-dimensionally position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated here with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and three-dimensionally patterned surfaces and integrated devices designed on the molecular level and reaching macroscopic dimensions.
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Affiliation(s)
- Irina V Martynenko
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
| | - Elisabeth Erber
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Veronika Ruider
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Gregor Posnjak
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Xin Yin
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Philipp Altpeter
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
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4
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Hanke M, Dornbusch D, Tomm E, Grundmeier G, Fahmy K, Keller A. Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants. NANOSCALE 2023; 15:16590-16600. [PMID: 37747200 DOI: 10.1039/d3nr02045b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The structural stability of DNA origami nanostructures in various chemical environments is an important factor in numerous applications, ranging from biomedicine and biophysics to analytical chemistry and materials synthesis. In this work, the stability of six different 2D and 3D DNA origami nanostructures is assessed in the presence of three different chaotropic salts, i.e., guanidinium sulfate (Gdm2SO4), guanidinium chloride (GdmCl), and tetrapropylammonium chloride (TPACl), which are widely employed denaturants. Using atomic force microscopy (AFM) to quantify nanostructural integrity, Gdm2SO4 is found to be the weakest and TPACl the strongest DNA origami denaturant, respectively. Despite different mechanisms of actions of the selected salts, DNA origami stability in each environment is observed to depend on DNA origami superstructure. This is especially pronounced for 3D DNA origami nanostructures, where mechanically more flexible designs show higher stability in both GdmCl and TPACl than more rigid ones. This is particularly remarkable as this general dependence has previously been observed under Mg2+-free conditions and may provide the possibility to optimize DNA origami design toward maximum stability in diverse chemical environments. Finally, it is demonstrated that melting temperature measurements may overestimate the stability of certain DNA origami nanostructures in certain chemical environments, so that such investigations should always be complemented by microscopic assessments of nanostructure integrity.
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Affiliation(s)
- Marcel Hanke
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Daniel Dornbusch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, Dresden 01328, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
| | - Emilia Tomm
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, Dresden 01328, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
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5
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Hong T, Zhou W, Tan S, Cai Z. A cooperation tale of biomolecules and nanomaterials in nanoscale chiral sensing and separation. NANOSCALE HORIZONS 2023; 8:1485-1508. [PMID: 37656443 DOI: 10.1039/d3nh00133d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The cooperative relationship between biomolecules and nanomaterials makes up a beautiful tale about nanoscale chiral sensing and separation. Biomolecules are considered a fabulous chirality 'donor' to develop chiral sensors and separation systems. Nature has endowed biomolecules with mysterious chirality. Various nanomaterials with specific physicochemical attributes can realize the transmission and amplification of this chirality. We focus on highlighting the advantages of combining biomolecules and nanomaterials in nanoscale chirality. To enhance the sensors' detection sensitivity, novel cooperation approaches between nanomaterials and biomolecules have attracted tremendous attention. Moreover, innovative biomolecule-based nanocomposites possess great importance in developing chiral separation systems with improved assay performance. This review describes the formation of a network based on nanomaterials and biomolecules mainly including DNA, proteins, peptides, amino acids, and polysaccharides. We hope this tale will record the perpetual relation between biomolecules and nanomaterials in nanoscale chirality.
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Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan 410013, China
- Academician Workstation, Changsha Medical University, Changsha 410219, China
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan 410013, China
- Jiangsu Dawning Pharmaceutical Co., Ltd, Changzhou, Jiangsu 213100, China
| | - Zhiqiang Cai
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.
- Jiangsu Dawning Pharmaceutical Co., Ltd, Changzhou, Jiangsu 213100, China
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6
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Zhang Y, Xu Z, Wen J, Zhao X, Gao R, Wang Y. Honeycomb-like Ag Nanocavity Array for SERS Observations Using Plasmon-Mediated Chemical Reactions. MICROMACHINES 2023; 14:1811. [PMID: 37893248 PMCID: PMC10609216 DOI: 10.3390/mi14101811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023]
Abstract
Organized two-dimensional polystyrene bead arrays perform ion etching, and protruding nanostructures are created on polystyrene beads due to the shadow effects from the ring beads, leading to nucleus selection and growth in Au nanostructure deposition. Ag nanostructures are prepared via plasmon-mediated chemical reactions (PMCRs), leading to the Ag nanocavity geometry of the honeycomb pattern when the etching time and Ag growth time are tuned. Due to the strong electromagnetic coupling, the Ag honeycomb-shaped nanocavity array works as the SERS substrate with high sensitivity and good repeatability, which is used to detect thiram pesticide residues with a concentration down to 10-9 M.
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Affiliation(s)
- Yongjun Zhang
- School of Material and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China; (Y.Z.)
| | - Zhen Xu
- School of Material and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China; (Y.Z.)
| | - Jiahong Wen
- The College of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Xiaoyu Zhao
- School of Material and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China; (Y.Z.)
- Zhejiang Laboratory, Hangzhou 311100, China
| | - Renxian Gao
- Department of Physics, Xiamen University, Xiamen 361005, China;
| | - Yaxin Wang
- School of Material and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China; (Y.Z.)
- Zhejiang Laboratory, Hangzhou 311100, China
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7
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Mao D, Liu L, Zhang C, Liu H, Mao C. Molecular Lithography on Silicon Wafers Guided by Porous, Extended Arrays of Small DNA Tiles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11782-11787. [PMID: 37562139 DOI: 10.1021/acs.langmuir.3c01422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Tile-based DNA self-assembly is a cost-effective fabrication method for large-scale nanopatterns. Herein, we report a protocol to directly assemble DNA 2D arrays on silicon wafers and then use the DNA nanostructures as molds to fabricate the corresponding nanostructures on the silicon wafers by hydrogen fluoride (HF) etching. Similar HF etching has been used with robust large DNA origami structures as templates. This work demonstrates that DNA nanostructures assembled from small tiles are sufficiently stable for this process. The resulting feature size (∼8.6 nm) approaches the sizes of e-beam lithography. While the reported method is parallel and inexpensive, e-beam lithography is a serial method and is expensive. We expect that this method will be very useful for preparing fine nanopatterns in large areas.
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Affiliation(s)
- Dake Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Longfei Liu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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8
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Pothineni BK, Grundmeier G, Keller A. Cation-dependent assembly of hexagonal DNA origami lattices on SiO 2 surfaces. NANOSCALE 2023; 15:12894-12906. [PMID: 37462427 DOI: 10.1039/d3nr02926c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
DNA origami nanostructures have emerged as functional materials for applications in various areas of science and technology. In particular, the transfer of the DNA origami shape into inorganic materials using established silicon lithography methods holds great promise for the fabrication of nanostructured surfaces for nanoelectronics and nanophotonics. Using ordered DNA origami lattices directly assembled on the oxidized silicon surface instead of single nanostructures would enable the fabrication of functional nanopatterned surfaces with macroscopic dimensions. Here, we thus investigate the assembly of hexagonal DNA lattices from DNA origami triangles on RCA-cleaned silicon wafers with hydroxylated surface oxide by time-lapse atomic force microscopy (AFM). Lattice assembly on the SiO2 surface is achieved by a competition of monovalent and divalent cations at elevated temperatures. Ca2+ is found to be superior to Mg2+ in promoting the assembly of ordered lattices, while the presence of Mg2+ rather results in DNA origami aggregation and multilayer formation at the comparably high Na+ concentrations of 200 to 600 mM. Furthermore, Na+ concentration and temperature have a similar effect on lattice order, so that a reduction of temperature can be compensated to some extent by an increase in Na+ concentration. However, even under optimized conditions, the DNA origami lattices assembled on the SiO2 surface exhibit a lower degree of order than equivalent lattices assembled on mica, which is attributed to a higher desorption rate of the DNA origami nanostructures. Even though this high desorption rate also complicates any post-assembly treatment, the formed DNA origami lattices could successfully be transferred into the dry state, which is an important prerequisite for further processing steps.
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Affiliation(s)
- Bhanu Kiran Pothineni
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
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9
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Li Z, Fan Q, Ye Z, Wu C, Wang Z, Yin Y. A magnetic assembly approach to chiral superstructures. Science 2023; 380:1384-1390. [PMID: 37384698 DOI: 10.1126/science.adg2657] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/22/2023] [Indexed: 07/01/2023]
Abstract
Colloidal assembly into chiral superstructures is usually accomplished with templating or lithographic patterning methods that are only applicable to materials with specific compositions and morphologies over narrow size ranges. Here, chiral superstructures can be rapidly formed by magnetically assembling materials of any chemical compositions at all scales, from molecules to nano- and microstructures. We show that a quadrupole field chirality is generated by permanent magnets caused by consistent field rotation in space. Applying the chiral field to magnetic nanoparticles produces long-range chiral superstructures controlled by field strength at the samples and orientation of the magnets. Transferring the chirality to any achiral molecules is enabled by incorporating guest molecules such as metals, polymers, oxides, semiconductors, dyes, and fluorophores into the magnetic nanostructures.
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Affiliation(s)
- Zhiwei Li
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Qingsong Fan
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Zuyang Ye
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Chaolumen Wu
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Zhongxiang Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Yadong Yin
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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10
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Kabusure KM, Piskunen P, Yang J, Linko V, Hakala TK. Raman enhancement in bowtie-shaped aperture-particle hybrid nanostructures fabricated with DNA-assisted lithography. NANOSCALE 2023; 15:8589-8596. [PMID: 37097163 DOI: 10.1039/d3nr00616f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We report on efficient surface-enhanced Raman spectroscopy (SERS) supporting substrates, which are based on deoxyribonucleic acid (DNA)-assisted lithography (DALI) and a layered configuration of materials. In detail, we used nanoscopic DNA origami bowtie templates to form hybrid nanostructures consisting of aligned silver bowtie-shaped particles and apertures of similar shape in a silver film. We hypothesized that this particular geometry could facilitate a four-fold advantage in Raman enhancement compared to common particle-based SERS substrates, and further, we verified these hypotheses experimentally and by finite difference time domain simulations. In summary, our DALI-fabricated hybrid structures suppress the background emission, allow emission predominantly from the areas of high field enhancement, and support additional resonances associated with the nanoscopic apertures. Finally, these nanoapertures also enhance the fields associated with the resonances of the underlying bowtie particles. The versatility and parallel nature of our DNA origami-based nanofabrication scheme and all of the above-mentioned features of the hybrid structures therefore make our optically resonant substrates attractive for various SERS-based applications.
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Affiliation(s)
- Kabusure M Kabusure
- Center for Photonics Sciences, University of Eastern Finland, Yliopistokatu 2, P.O. Box 111, FI-80101, Joensuu, Finland.
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
| | - Jiaqi Yang
- Center for Photonics Sciences, University of Eastern Finland, Yliopistokatu 2, P.O. Box 111, FI-80101, Joensuu, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia.
| | - Tommi K Hakala
- Center for Photonics Sciences, University of Eastern Finland, Yliopistokatu 2, P.O. Box 111, FI-80101, Joensuu, Finland.
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11
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Parikka JM, Järvinen H, Sokołowska K, Ruokolainen V, Markešević N, Natarajan AK, Vihinen-Ranta M, Kuzyk A, Tapio K, Toppari JJ. Creation of ordered 3D tubes out of DNA origami lattices. NANOSCALE 2023; 15:7772-7780. [PMID: 37057647 DOI: 10.1039/d2nr06001a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hierarchical self-assembly of nanostructures with addressable complexity has been a promising route for realizing novel functional materials. Traditionally, the fabrication of such structures on a large scale has been achievable using top-down methods but with the cost of complexity of the fabrication equipment versus resolution and limitation mainly to 2D structures. More recently bottom-up methods using molecules like DNA have gained attention due to the advantages of low fabrication costs, high resolution and simplicity in an extension of the methods to the third dimension. One of the more promising bottom-up techniques is DNA origami due to the robust self-assembly of arbitrarily shaped nanostructures with feature sizes down to a few nanometers. Here, we show that under specific ionic conditions of the buffer, the employed plus-shaped, blunt-ended Seeman tile (ST) origami forms elongated, ordered 2D lattices, which are further rolled into 3D tubes in solution. Imaging structures on a surface by atomic force microscopy reveals ribbon-like structures, with single or double layers of the origami lattice. Further studies of the double-layered structures in a liquid state by confocal microscopy and cryo-TEM revealed elongated tube structures with a relatively uniform width but with a varying length. Through meticulous study, we concluded that the assembly process of these 3D DNA origami tubes is heavily dependent on the concentration of both mono- and divalent cations. In particular, nickel seems to act as a trigger for the formation of the tubular assemblies in liquid.
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Affiliation(s)
- Johannes M Parikka
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Heini Järvinen
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Karolina Sokołowska
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Visa Ruokolainen
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, 40014 University of Jyväskylä, Finland
| | - Nemanja Markešević
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - Ashwin K Natarajan
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Maija Vihinen-Ranta
- University of Jyväskylä, Department of Biological and Environmental Science and Nanoscience Center, 40014 University of Jyväskylä, Finland
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Kosti Tapio
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
| | - J Jussi Toppari
- University of Jyväskylä, Department of Physics and Nanoscience Center, 40014 University of Jyväskylä, Finland.
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12
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Lolaico M, Blokhuizen S, Shen B, Wang Y, Högberg B. Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges. ACS NANO 2023; 17:6565-6574. [PMID: 36951760 PMCID: PMC10100577 DOI: 10.1021/acsnano.2c11982] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
In recent years, interest in wireframe DNA origami has increased, with different designs, software, and applications emerging at a fast pace. It is now possible to design a wide variety of shapes by starting with a 2D or 3D mesh and using different scaffold routing strategies. The design choices of the edges in wireframe structures can be important in some applications and have already been shown to influence the interactions between nanostructures and cells. In this work, we increase the alternatives for the design of A-trail routed wireframe DNA structures by using four-helix bundles (4HB). Our approach is based on the incorporation of additional helices to the edges of the wireframe structure to create a 4HB on a square lattice. We first developed the software for the design of these structures, followed by a demonstration of the successful design and folding of a library of structures, and then, finally, we investigated the higher mechanical rigidity of the reinforced structures. In addition, the routing of the scaffold allows us to easily incorporate these reinforced edges together with more flexible, single helix edges, thereby allowing the user to customize the desired stiffness of the structure. We demonstrated the successful folding of this type of hybrid structure and the different stiffnesses of the different parts of the nanostructures using a combination of computational and experimental techniques.
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Affiliation(s)
- Marco Lolaico
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Sebbe Blokhuizen
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Boxuan Shen
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, P.O. Box 16100, 00076 Aalto, Finland
| | - Yang Wang
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Björn Högberg
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
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13
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Kemper U, Ye J, Poppitz D, Gläser R, Seidel R. DNA Mold-Based Fabrication of Palladium Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2206438. [PMID: 36960479 DOI: 10.1002/smll.202206438] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/03/2023] [Indexed: 06/18/2023]
Abstract
DNA origami molds allow a shape-controlled growth of metallic nanoparticles. So far, this approach is limited to gold and silver. Here, the fabrication of linear palladium nanostructures with controlled lengths and patterns is demonstrated. To obtain nucleation centers for a seeded growth, a synthesis procedure of palladium nanoparticles (PdNPs) using Bis(p-sulfonatophenyl)phenylphosphine (BSPP) both as reductant and stabilizer is developed to establish an efficient functionalization protocol of the particles with single-stranded DNA. Attaching the functionalized particles to complementary DNA strands inside DNA mold cavities supports subsequently a highly specific seeded palladium deposition. This provides rod-like PdNPs with diameters of 20-35 nm of grainy morphology. Using an annealing procedure and a post-reduction step with hydrogen, homogeneous palladium nanostructures can be obtained. With the adaptation of the procedure to palladium the capabilities of the mold-based tool-box are expanded. In the future, this may allow a facile adaptation of the mold approach to less noble metals including magnetic materials such as Ni and Co.
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Affiliation(s)
- Ulrich Kemper
- Molecular Biophysics group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Jingjing Ye
- Molecular Biophysics group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - David Poppitz
- Heterogeneous Catalysis, Institute of Chemical Technology, Universität Leipzig, 04103, Leipzig, Germany
| | - Roger Gläser
- Heterogeneous Catalysis, Institute of Chemical Technology, Universität Leipzig, 04103, Leipzig, Germany
| | - Ralf Seidel
- Molecular Biophysics group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
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14
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Korkos S, Arstila K, Tapio K, Kinnunen S, Toppari JJ, Sajavaara T. Elongation and plasmonic activity of embedded metal nanoparticles following heavy ion irradiation. RSC Adv 2023; 13:5851-5858. [PMID: 36816087 PMCID: PMC9932636 DOI: 10.1039/d3ra00573a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Shape modification of embedded nanoparticles by swift heavy ion (SHI) irradiation is an effective way to produce nanostructures with controlled size, shape, and orientation. In this study, randomly oriented gold nanorods embedded in SiO2 are shown to re-orient along the ion beam direction. The degree of orientation depends on the irradiation conditions and the nanorod's initial size. SHI irradiation was also applied to modify spherical metallic nanoparticles embedded in Al2O3. The results showed that they elongate due to the irradiation comparably to those embedded in SiO2. Metallic nanostructures embedded in dielectric matrices can exhibit localized surface plasmon (LSP) modes. The elongated nanoparticles investigated by means of dark-field spectroscopy showed two discrete peaks which correspond to longitudinal and transverse modes.
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Affiliation(s)
- Spyridon Korkos
- Accelerator Laboratory, Department of Physics, University of Jyväskylä P. O. Box 35 FI-40014 Jyvaskyla Finland .,Nanoscience Center and Department of Physics, University of Jyväskylä P. O. Box 35 FI-40014 Jyvaskyla Finland
| | - Kai Arstila
- Accelerator Laboratory, Department of Physics, University of Jyväskylä P. O. Box 35 FI-40014 Jyvaskyla Finland .,Nanoscience Center and Department of Physics, University of Jyväskylä P. O. Box 35 FI-40014 Jyvaskyla Finland
| | - Kosti Tapio
- Nanoscience Center and Department of Physics, University of Jyväskylä P. O. Box 35 FI-40014 Jyvaskyla Finland
| | - Sami Kinnunen
- Accelerator Laboratory, Department of Physics, University of Jyväskylä P. O. Box 35 FI-40014 Jyvaskyla Finland .,Nanoscience Center and Department of Physics, University of Jyväskylä P. O. Box 35 FI-40014 Jyvaskyla Finland
| | - J. Jussi Toppari
- Nanoscience Center and Department of Physics, University of JyväskyläP. O. Box 35FI-40014 JyvaskylaFinland
| | - Timo Sajavaara
- Accelerator Laboratory, Department of Physics, University of Jyväskylä P. O. Box 35 FI-40014 Jyvaskyla Finland .,Nanoscience Center and Department of Physics, University of Jyväskylä P. O. Box 35 FI-40014 Jyvaskyla Finland
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15
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Yu G, Xu Q, Lei Z, Lu Y, Xu W, Wu R. Novel polymeric platform produced by photodegradation‐induced rearrangement for a multifunctional negative photoresist. POLYM ADVAN TECHNOL 2023. [DOI: 10.1002/pat.5911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Gang Yu
- College of Chemistry and Chemical Engineering Hunan University Changsha People's Republic of China
| | - Qian Xu
- College of Chemistry and Chemical Engineering Hunan University Changsha People's Republic of China
- Academician Workstation Changsha Medical University Changsha People's Republic of China
| | - Zhiyou Lei
- College of Chemistry and Chemical Engineering Hunan University Changsha People's Republic of China
| | - Yanbing Lu
- College of Chemistry and Chemical Engineering Hunan University Changsha People's Republic of China
| | - Weijian Xu
- College of Chemistry and Chemical Engineering Hunan University Changsha People's Republic of China
| | - Ruoxi Wu
- Department of Water Science and Engineering, College of Civil Engineering Hunan University Changsha People's Republic of China
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16
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Parsons MF, Allan MF, Li S, Shepherd TR, Ratanalert S, Zhang K, Pullen KM, Chiu W, Rouskin S, Bathe M. 3D RNA-scaffolded wireframe origami. Nat Commun 2023; 14:382. [PMID: 36693871 PMCID: PMC9872083 DOI: 10.1038/s41467-023-36156-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.
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Affiliation(s)
- Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew F Allan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shanshan Li
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Inscripta, Inc., Boulder, CO, 80027, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Krista M Pullen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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17
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Ijäs H, Kostiainen MA, Linko V. Protein Coating of DNA Origami. Methods Mol Biol 2023; 2639:195-207. [PMID: 37166719 DOI: 10.1007/978-1-0716-3028-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA origami has emerged as a common technique to create custom two- (2D) and three-dimensional (3D) structures at the nanoscale. These DNA nanostructures have already proven useful in development of many biotechnological tools; however, there are still challenges that cast a shadow over the otherwise bright future of biomedical uses of these DNA objects. The rather obvious obstacles in harnessing DNA origami as drug-delivery vehicles and/or smart biodevices are related to their debatable stability in biologically relevant media, especially in physiological low-cation and endonuclease-rich conditions, relatively poor transfection rates, and, although biocompatible by nature, their unpredictable compatibility with the immune system. Here we demonstrate a technique for coating DNA origami with albumin proteins for enhancing their pharmacokinetic properties. To facilitate protective coating, a synthesized positively charged dendron was linked to bovine serum albumin (BSA) through a covalent maleimide-cysteine bonding, and then the purified dendron-protein conjugates were let to assemble on the negatively charged surface of DNA origami via electrostatic interaction. The resulted BSA-dendron conjugate-coated DNA origami showed improved transfection, high resistance against endonuclease digestion, and significantly enhanced immunocompatibility compared to bare DNA origami. Furthermore, our proposed coating strategy can be considered highly versatile as a maleimide-modified dendron serving as a synthetic DNA-binding domain can be linked to any protein with an available cysteine site.
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Affiliation(s)
- Heini Ijäs
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
- LIBER Center of Excellence, Aalto University, Aalto, Finland
- Ludwig-Maximilians-University, Munich, Germany
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, Aalto, Finland.
- Institute of Technology, University of Tartu, Tartu, Estonia.
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18
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An T, Wen J, Dong Z, Zhang Y, Zhang J, Qin F, Wang Y, Zhao X. Plasmonic Biosensors with Nanostructure for Healthcare Monitoring and Diseases Diagnosis. SENSORS (BASEL, SWITZERLAND) 2022; 23:445. [PMID: 36617043 PMCID: PMC9824517 DOI: 10.3390/s23010445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Nanophotonics has been widely utilized in enhanced molecularspectroscopy or mediated chemical reaction, which has major applications in the field of enhancing sensing and enables opportunities in developing healthcare monitoring. This review presents an updated overview of the recent exciting advances of plasmonic biosensors in the healthcare area. Manufacturing, enhancements and applications of plasmonic biosensors are discussed, with particular focus on nanolisted main preparation methods of various nanostructures, such as chemical synthesis, lithography, nanosphere lithography, nanoimprint lithography, etc., and describing their respective advances and challenges from practical applications of plasmon biosensors. Based on these sensing structures, different types of plasmonic biosensors are summarized regarding detecting cancer biomarkers, body fluid, temperature, gas and COVID-19. Last, the existing challenges and prospects of plasmonic biosensors combined with machine learning, mega data analysis and prediction are surveyed.
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Affiliation(s)
- Tongge An
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Jiahong Wen
- The College of Electronics and Information, Hangzhou Dianzi University, Hangzhou 310018, China
- Shangyu Institute of Science and Engineering, Hangzhou Dianzi University, Shaoxing 312000, China
| | - Zhichao Dong
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Yongjun Zhang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Jian Zhang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Faxiang Qin
- Institute for Composites Science Innovation, School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Yaxin Wang
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Xiaoyu Zhao
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China
- Zhejiang Laboratory, Hangzhou 311100, China
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19
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Torres-Huerta AL, Antonio-Pérez A, García-Huante Y, Alcázar-Ramírez NJ, Rueda-Silva JC. Biomolecule-Based Optical Metamaterials: Design and Applications. BIOSENSORS 2022; 12:962. [PMID: 36354471 PMCID: PMC9688573 DOI: 10.3390/bios12110962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.
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Affiliation(s)
- Ana Laura Torres-Huerta
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Aurora Antonio-Pérez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Yolanda García-Huante
- Departamento de Ciencias Básicas, Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional (UPIITA-IPN), Mexico City 07340, Mexico
| | - Nayelhi Julieta Alcázar-Ramírez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Juan Carlos Rueda-Silva
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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20
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Luo S, Mancini A, Lian E, Xu W, Berté R, Li Y. Large Area Patterning of Highly Reproducible and Sensitive SERS Sensors Based on 10-nm Annular Gap Arrays. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3842. [PMID: 36364618 PMCID: PMC9655199 DOI: 10.3390/nano12213842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Applicable surface-enhanced Raman scattering (SERS) active substrates typically require low-cost patterning methodology, high reproducibility, and a high enhancement factor (EF) over a large area. However, the lack of reproducible, reliable fabrication for large area SERS substrates in a low-cost manner remains a challenge. Here, a patterning method based on nanosphere lithography and adhesion lithography is reported that allows massively parallel fabrication of 10-nm annular gap arrays on large areas. The arrays exhibit excellent reproducibility and high SERS performance, with an EF of up to 107. An effective wearable SERS contact lens for glucose detection is further demonstrated. The technique described here extends the range of SERS-active substrates that can be fabricated over large areas, and holds exciting potential for SERS-based chemical and biomedical detection.
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Affiliation(s)
- Sihai Luo
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Andrea Mancini
- Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig-Maximilians-Universität München, Königinstrasse 10, 80539 München, Germany
| | - Enkui Lian
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Wenqi Xu
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Rodrigo Berté
- Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig-Maximilians-Universität München, Königinstrasse 10, 80539 München, Germany
| | - Yi Li
- Chair in Hybrid Nanosystems, Nanoinstitute Munich, Faculty of Physics, Ludwig-Maximilians-Universität München, Königinstrasse 10, 80539 München, Germany
- School of Microelectronics, MOE Engineering Research Center of Integrated Circuits for Next Generation Communications, Southern University of Science and Technology, Shenzhen 518055, China
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21
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Abstract
Hierarchical assembly of programmable DNA frameworks─such as DNA origami─paves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems.
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Affiliation(s)
- Sofia Julin
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Adrian Keller
- Paderborn
University, Technical and Macromolecular
Chemistry, Warburger
Str. 100, 33098 Paderborn, Germany,
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland,LIBER
Center of Excellence, Aalto University, 00076 Aalto, Finland,
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22
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Manuguri S, Nguyen MK, Loo J, Natarajan AK, Kuzyk A. Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies. Bioconjug Chem 2022; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.
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Affiliation(s)
- Sesha Manuguri
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City 70000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City 756100, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Ashwin Karthick Natarajan
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,
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23
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Kabusure KM, Piskunen P, Yang J, Kataja M, Chacha M, Ojasalo S, Shen B, Hakala TK, Linko V. Optical characterization of DNA origami-shaped silver nanoparticles created through biotemplated lithography. NANOSCALE 2022; 14:9648-9654. [PMID: 35718875 DOI: 10.1039/d1nr06256e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Here, we study optically resonant substrates fabricated using the previously reported BLIN (biotemplated lithography of inorganic nanostructures) technique with single triangle and bowtie DNA origami as templates. We present the first optical characterization of BLIN-fabricated origami-shaped silver nanoparticle patterns on glass surfaces, comprising optical transmission measurements and surface-enhanced Raman spectroscopy. The formed nanoparticle patterns are examined by optical transmission measurements and used for surface enhanced Raman spectroscopy (SERS) of Rhodamine 6G (R6G) dye molecules. Polarization-resolved simulations reveal that the higher SERS enhancement observed for the bowties is primarily due to spectral overlap of the optical resonances with the Raman transitions of R6G. The results manifest the applicability of the BLIN method and substantiate its potential in parallel and high-throughput substrate manufacturing with engineered optical properties. While the results demonstrate the crucial role of the formed nanogaps for SERS, the DNA origami may enable even more complex nanopatterns for various optical applications.
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Affiliation(s)
- Kabusure M Kabusure
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
| | - Jiaqi Yang
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Mikko Kataja
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Mwita Chacha
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Tommi K Hakala
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
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24
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Sahu JK, Lone SA, Sadhu KK. Methionine-Controlled Impediment of Secondary Nucleation Leading to Nonclassical Growth within Self-Assembled De Novo Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5865-5873. [PMID: 35442695 DOI: 10.1021/acs.langmuir.2c00489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The conventional key steps for seed-mediated growth of noble metal nanostructures involve classical and nonclassical nucleation. Furthermore, the surface of the seed catalytically enhances the secondary nucleation involving Au+ to Au0 reduction, thus providing in-plane growth of the seed. In contrast to this well-established growth mechanism, herein, we report the unique case of a methionine (Met)-controlled seed-mediated growth reaction, which rather proceeds via impeding secondary nucleation in the presence of citrate-stabilized gold nanoparticles (AuNPs). The interaction between the freshly generated Au+ and the thioether group of Met in the medium restricts the secondary nucleation process of further seed-catalyzed Au+ reduction to Au0. This incomplete conversion of Au+, as confirmed by X-ray photoelectron spectroscopy, results in a significant enhancement of the zeta (ζ) potential even at low Met concentrations. Nucleation of in situ generated small-sized particles (nAuNPs) takes place on the parent seed surface followed by their segregation from the seed. The self-assembly process of these nAuNPs arises from the aurophilic interaction among the Au+. Furthermore, the time-dependent growth of smaller particles to larger-sized particles through assembly and merging within the same self-assembly validates the nonclassical growth. This strategy has been successfully extended toward the seed-mediated growth reaction of AuNPs in the presence of three bio-inspired decameric peptides having varying numbers of Met residues. The study confirms the nucleation strategy even in the presence of a single Met residue in the peptide and also the self-assembly of nucleated particles with increasing Met residues within the peptide.
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Affiliation(s)
- Jitendra K Sahu
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Shahbaz Ahmad Lone
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Kalyan K Sadhu
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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25
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Hui L, Chen C, Kim MA, Liu H. Fabrication of DNA-Templated Pt Nanostructures by Area-Selective Atomic Layer Deposition. ACS APPLIED MATERIALS & INTERFACES 2022; 14:16538-16545. [PMID: 35357800 DOI: 10.1021/acsami.2c02244] [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: 06/14/2023]
Abstract
We report the fabrication of DNA-templated Pt nanostructures by area-selective atomic layer deposition. A DNA-templated self-assembled monolayer was used to mediate the area-selective deposition of Pt. Using this approach, we demonstrated the fabrication of both single- and two-component nanostructure patterns, including Pt, TiO2/Pt, and Al2O3/Pt. These nanoscale patterns were used as hard masks for plasma deep etching of Si to fabricate anti-reflection surfaces. This work demonstrated a gas-phase, DNA-templated fabrication of metal nanostructures, which complements earlier work of solution-based DNA metallization. The nanostructures obtained here are useful for applications in nanoelectronics, nanophotonics, and surface engineering.
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Affiliation(s)
- Liwei Hui
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chen Chen
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Min A Kim
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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26
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Rahman BMA, Viphavakit C, Chitaree R, Ghosh S, Pathak AK, Verma S, Sakda N. Optical Fiber, Nanomaterial, and THz-Metasurface-Mediated Nano-Biosensors: A Review. BIOSENSORS 2022; 12:bios12010042. [PMID: 35049670 PMCID: PMC8773603 DOI: 10.3390/bios12010042] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 05/22/2023]
Abstract
The increasing use of nanomaterials and scalable, high-yield nanofabrication process are revolutionizing the development of novel biosensors. Over the past decades, researches on nanotechnology-mediated biosensing have been on the forefront due to their potential application in healthcare, pharmaceutical, cell diagnosis, drug delivery, and water and air quality monitoring. The advancement of nanoscale science relies on a better understanding of theory, manufacturing and fabrication practices, and the application specific methods. The topology and tunable properties of nanoparticles, a part of nanoscale science, can be changed by different manufacturing processes, which separate them from their bulk counterparts. In the recent past, different nanostructures, such as nanosphere, nanorods, nanofiber, core-shell nanoparticles, nanotubes, and thin films, have been exploited to enhance the detectability of labelled or label-free biological molecules with a high accuracy. Furthermore, these engineered-materials-associated transducing devices, e.g., optical waveguides and metasurface-based scattering media, widened the horizon of biosensors over a broad wavelength range from deep-ultraviolet to far-infrared. This review provides a comprehensive overview of the major scientific achievements in nano-biosensors based on optical fiber, nanomaterials and terahertz-domain metasurface-based refractometric, labelled and label-free nano-biosensors.
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Affiliation(s)
- B. M. Azizur Rahman
- School of Mathematics, Computer Science and Engineering, University of London, London EC1V 0HB, UK; (S.V.); (N.S.)
- Correspondence:
| | - Charusluk Viphavakit
- International School of Engineering and Intelligent Control Automation of Process Systems Research Unit, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand; (C.V.); (A.K.P.)
| | - Ratchapak Chitaree
- Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Souvik Ghosh
- Department of Electronic and Electrical Engineering, University College London, Gower St., London WC1E 6AE, UK;
| | - Akhilesh Kumar Pathak
- International School of Engineering and Intelligent Control Automation of Process Systems Research Unit, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand; (C.V.); (A.K.P.)
| | - Sneha Verma
- School of Mathematics, Computer Science and Engineering, University of London, London EC1V 0HB, UK; (S.V.); (N.S.)
| | - Natsima Sakda
- School of Mathematics, Computer Science and Engineering, University of London, London EC1V 0HB, UK; (S.V.); (N.S.)
- Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
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27
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Xie M, Hu Y, Yin J, Zhao Z, Chen J, Chao J. DNA Nanotechnology-Enabled Fabrication of Metal Nanomorphology. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9840131. [PMID: 35935136 PMCID: PMC9275100 DOI: 10.34133/2022/9840131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/24/2022] [Indexed: 11/09/2022]
Abstract
In recent decades, DNA nanotechnology has grown into a highly innovative and widely established field. DNA nanostructures have extraordinary structural programmability and can accurately organize nanoscale materials, especially in guiding the synthesis of metal nanomaterials, which have unique advantages in controlling the growth morphology of metal nanomaterials. This review started with the evolution in DNA nanotechnology and the types of DNA nanostructures. Next, a DNA-based nanofabrication technology, DNA metallization, was introduced. In this section, we systematically summarized the DNA-oriented synthesis of metal nanostructures with different morphologies and structures. Furthermore, the applications of metal nanostructures constructed from DNA templates in various fields including electronics, catalysis, sensing, and bioimaging were figured out. Finally, the development prospects and challenges of metal nanostructures formed under the morphology control by DNA nanotechnology were discussed.
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Affiliation(s)
- Mo Xie
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yang Hu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jue Yin
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Ziwei Zhao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jing Chen
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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28
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Heuer-Jungemann A, Linko V. Engineering Inorganic Materials with DNA Nanostructures. ACS CENTRAL SCIENCE 2021; 7:1969-1979. [PMID: 34963890 PMCID: PMC8704036 DOI: 10.1021/acscentsci.1c01272] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Indexed: 05/25/2023]
Abstract
Nucleic acid nanotechnology lays a foundation for the user-friendly design and synthesis of DNA frameworks of any desirable shape with extreme accuracy and addressability. Undoubtedly, such features make these structures ideal modules for positioning and organizing molecules and molecular components into complex assemblies. One of the emerging concepts in the field is to create inorganic and hybrid materials through programmable DNA templates. Here, we discuss the challenges and perspectives of such DNA nanostructure-driven materials science engineering and provide insights into the subject by introducing various DNA-based fabrication techniques including metallization, mineralization, lithography, casting, and hierarchical self-assembly of metal nanoparticles.
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Affiliation(s)
- Amelie Heuer-Jungemann
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Center
for Nanoscience, Ludwig-Maximilians University, 80539 Munich, Germany
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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29
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Liu D, Xue C. Plasmonic Coupling Architectures for Enhanced Photocatalysis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2005738. [PMID: 33891777 DOI: 10.1002/adma.202005738] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/05/2020] [Indexed: 06/12/2023]
Abstract
Plasmonic photocatalysis is a promising approach for solar energy transformation. Comparing with isolated metal nanoparticles, the plasmonic coupling architectures can provide further strengthened local electromagnetic field and boosted light-harvesting capability through optimal control over the composition, spacing, and orientation of individual nanocomponents. As such, when integrated with semiconductor photocatalysts, the coupled metal nanostructures can dramatically promote exciton generation and separation through plasmonic-coupling-driven charge/energy transfer toward superior photocatalytic efficiencies. Herein, the principles of the plasmonic coupling effect are presented and recent progress on the construction of plasmonic coupling architectures and their integration with semiconductors for enhanced photocatalytic reactions is summarized. In addition, the remaining challenges as to the rational design and utilization of plasmon coupling structures are elaborated, and some prospects to inspire new opportunities on the future development of plasmonic coupling structures for efficient and sustainable light-driven reactions are raised.
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Affiliation(s)
- Dong Liu
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Can Xue
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
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30
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Zhao Y, Zhang C, Yang L, Xu X, Xu R, Ma Q, Tang Q, Yang Y, Han D. Programmable and Site-Specific Patterning on DNA Origami Templates with Heterogeneous Condensation of Silver and Silica. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2103877. [PMID: 34636168 DOI: 10.1002/smll.202103877] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/15/2021] [Indexed: 06/13/2023]
Abstract
DNA origami has been widely used as a modular platform for condensation of functional molecules to assemble optical, electronic, and biological components. However, the heterogeneous condensation with greater diversities in chemical composition templated with DNA origami is still challenging. Herein, a programmable deposition method is developed to precisely condense silver-silica nanohybrids on DNA origami templates. First, the site-specific metallization of Ag is achieved by thiol group-initiated silver reduction at the designed areas of DNA origami. Next, cysteamine is used to selectively modify the condensed Ag surface with positively charged amino groups for creating an electronically different environment for site-specific placement of silica by a modified Stöber method. Using these strategies, customized patterning of both silver and silica on tubular and rectangular DNA origami nanostructures is successfully achieved with nanoscale spatial resolution. These findings will greatly facilitate the development of DNA nanotechnology-based bottom-up nanofabrication.
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Affiliation(s)
- Yumeng Zhao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Linlin Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Xuemei Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Rui Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Qian Ma
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Qian Tang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Yang Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
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31
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Semple M, Hryciw AC, Li P, Flaim E, Iyer AK. Patterning of Complex, Nanometer-Scale Features in Wide-Area Gold Nanoplasmonic Structures Using Helium Focused Ion Beam Milling. ACS APPLIED MATERIALS & INTERFACES 2021; 13:43209-43220. [PMID: 34472831 DOI: 10.1021/acsami.1c09295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Meeting the evolving demands of plasmonics research requires increasingly precise control over surface plasmon properties, which necessitates extremely fine nanopatterning, complex geometries, and/or long-range order. Nanoplasmonic metasurfaces are representative of a modern research area requiring intricate, high-fidelity features reproduced over areas of several free-space wavelengths, making them one of the most challenging fabrication problems in the field today. This work presents a systematic study of the helium focused ion beam milling of gold for nanoplasmonic metasurface applications, using as its example a nanoplasmonic metasurface based on an array of nanometer-scale plasmonic-wire-loaded subwavelength apertures in a gold film. At each step, the pattern variations are compared to simulation to predict the experimental outcome. Our results show that even in a practical fabrication environment, helium ion beam milling can be used to reliably pattern 10 nm features into gold with 1:5 aspect ratio in complex geometries over a wide area.
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Affiliation(s)
- Mitchell Semple
- Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Aaron C Hryciw
- nanoFAB Centre, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Peng Li
- nanoFAB Centre, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Eric Flaim
- nanoFAB Centre, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Ashwin K Iyer
- Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
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32
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Huang CM, Kucinic A, Johnson JA, Su HJ, Castro CE. Integrated computer-aided engineering and design for DNA assemblies. NATURE MATERIALS 2021; 20:1264-1271. [PMID: 33875848 DOI: 10.1038/s41563-021-00978-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 03/04/2021] [Indexed: 05/15/2023]
Abstract
Recently, DNA has been used to make nanodevices for a myriad of applications across fields including medicine, nanomanufacturing, synthetic biology, biosensing and biophysics. However, current DNA nanodevices rely primarily on geometric design, and it remains challenging to rationally design functional properties such as force-response or actuation behaviour. Here we report an iterative design pipeline for DNA assemblies that integrates computer-aided engineering based on coarse-grained molecular dynamics with a versatile computer-aided design approach that combines top-down automation with bottom-up control over geometry. This intuitive framework allows for rapid construction of large, multicomponent assemblies from three-dimensional models with finer control over the geometrical, mechanical and dynamical properties of the DNA structures in an automated manner. This approach expands the scope of structural complexity and enhances mechanical and dynamic design of DNA assemblies.
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Affiliation(s)
- Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA
| | - Anjelica Kucinic
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Joshua A Johnson
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Hai-Jun Su
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA.
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA.
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA.
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33
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Liu W, Wang J, Xu X, Zhao C, Xu X, Weiss PS. Single-Step Dual-Layer Photolithography for Tunable and Scalable Nanopatterning. ACS NANO 2021; 15:12180-12188. [PMID: 34170108 DOI: 10.1021/acsnano.1c03703] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Conventional photolithography, due to its scalability, robustness, and straightforward processes, has been widely applied to micro- and nanostructure manufacturing in electronics, optics, and biology. However, optical diffraction limits the ultimate resolution of conventional photolithography, which hinders its potential in nanoscale patterning for broader applications. Here, we introduce a derivative of conventional photolithography for nanoscale patterning called dual-layer photolithography (DLPL), which is based on the controlled exposure and development of overlapping positive and negative photoresists. In a typical experiment, substrates are sequentially coated by two layers of photoresists (both positive and negative). Then, we purposefully control the exposure time to generate slightly larger features in the positive photoresist than those in the negative photoresist. After development, their overlapping areas become the final features, which outline the original features. We demonstrate line widths down to 300 nm here, which can be readily improved with more precise control. By adjusting the lithography parameters and material deposition, the feature sizes, shapes (e.g., rings, numbers, letters), line widths (300-900 nm), and materials (e.g., SiO2, Cr, and Ag) of these features can be independently controlled. Combined with anisotropic etching, more complex three-dimensional nanostructures can be fabricated as well, as we demonstrate here with Si. We further fabricate photodetectors as an example application to show that these nanostructures fabricated by DLPL can be used to promote light-trapping MAPbI3 perovskite films to achieve good photoelectric properties. This strategy is not limited to ultraviolet photolithography and may also be incorporated into other energetic beam-based lithographic approaches, including deep and extreme ultraviolet photolithographies and electron beam lithography, to enhance their resolution.
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Affiliation(s)
- Wenfei Liu
- California NanoSystems Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jiabao Wang
- Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Key Laboratory of D&A for Metal-Functional Materials, School of Materials Science & Engineering, & Institute for Advanced Study, Tongji University, Shanghai 201804, China
| | - Xiuzhen Xu
- Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Key Laboratory of D&A for Metal-Functional Materials, School of Materials Science & Engineering, & Institute for Advanced Study, Tongji University, Shanghai 201804, China
| | - Chuanzhen Zhao
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Xiaobin Xu
- Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Key Laboratory of D&A for Metal-Functional Materials, School of Materials Science & Engineering, & Institute for Advanced Study, Tongji University, Shanghai 201804, China
| | - Paul S Weiss
- California NanoSystems Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Bioengineering and Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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34
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Ye J, Aftenieva O, Bayrak T, Jain A, König TAF, Erbe A, Seidel R. Complex Metal Nanostructures with Programmable Shapes from Simple DNA Building Blocks. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2100381. [PMID: 34085729 DOI: 10.1002/adma.202100381] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Advances in DNA nanotechnology allow the design and fabrication of highly complex DNA structures, uisng specific programmable interactions between smaller nucleic acid building blocks. To convey this concept to the fabrication of metallic nanoparticles, an assembly platform is developed based on a few basic DNA structures that can serve as molds. Programming specific interactions between these elements allows the assembly of mold superstructures with a range of different geometries. Subsequent seeded growth of gold within the mold cavities enables the synthesis of complex metal structures including tightly DNA-caged particles, rolling-pin- and dumbbell-shaped particles, as well as T-shaped and loop particles with high continuity. The method further supports the formation of higher-order assemblies of the obtained metal geometries. Based on electrical and optical characterizations, it is expected that the developed platform is a valuable tool for a self-assembly-based fabrication of nanoelectronic and nanooptic devices.
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Affiliation(s)
- Jingjing Ye
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01069, Dresden, Germany
| | - Olha Aftenieva
- Leibniz-Institut für Polymerforschung Dresden e. V., Hohe Straße 6, 01069, Dresden, Germany
| | - Türkan Bayrak
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01069, Dresden, Germany
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328, Dresden, Germany
| | - Archa Jain
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328, Dresden, Germany
- Faculty of Electrical Engineering and Information Technology, Chair of Nanoelectronics Technologies, Technische Universität Chemnitz, 09107, Chemnitz, Germany
| | - Tobias A F König
- Leibniz-Institut für Polymerforschung Dresden e. V., Hohe Straße 6, 01069, Dresden, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01069, Dresden, Germany
| | - Artur Erbe
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01069, Dresden, Germany
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328, Dresden, Germany
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, Helmholtzstraße 18, 01069, Dresden, Germany
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35
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Pang C, Aryal BR, Ranasinghe DR, Westover TR, Ehlert AEF, Harb JN, Davis RC, Woolley AT. Bottom-Up Fabrication of DNA-Templated Electronic Nanomaterials and Their Characterization. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1655. [PMID: 34201888 PMCID: PMC8306176 DOI: 10.3390/nano11071655] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/30/2022]
Abstract
Bottom-up fabrication using DNA is a promising approach for the creation of nanoarchitectures. Accordingly, nanomaterials with specific electronic, photonic, or other functions are precisely and programmably positioned on DNA nanostructures from a disordered collection of smaller parts. These self-assembled structures offer significant potential in many domains such as sensing, drug delivery, and electronic device manufacturing. This review describes recent progress in organizing nanoscale morphologies of metals, semiconductors, and carbon nanotubes using DNA templates. We describe common substrates, DNA templates, seeding, plating, nanomaterial placement, and methods for structural and electrical characterization. Finally, our outlook for DNA-enabled bottom-up nanofabrication of materials is presented.
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Affiliation(s)
- Chao Pang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - Basu R. Aryal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - Dulashani R. Ranasinghe
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - Tyler R. Westover
- Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602, USA; (T.R.W.); (R.C.D.)
| | - Asami E. F. Ehlert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
| | - John N. Harb
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA;
| | - Robert C. Davis
- Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602, USA; (T.R.W.); (R.C.D.)
| | - Adam T. Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (C.P.); (B.R.A.); (D.R.R.); (A.E.F.E.)
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36
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Xin Y, Shen B, Kostiainen MA, Grundmeier G, Castro M, Linko V, Keller A. Scaling Up DNA Origami Lattice Assembly. Chemistry 2021; 27:8564-8571. [PMID: 33780583 PMCID: PMC8252642 DOI: 10.1002/chem.202100784] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 12/31/2022]
Abstract
The surface-assisted hierarchical assembly of DNA origami nanostructures is a promising route to fabricate regular nanoscale lattices. In this work, the scalability of this approach is explored and the formation of a homogeneous polycrystalline DNA origami lattice at the mica-electrolyte interface over a total surface area of 18.75 cm2 is demonstrated. The topological analysis of more than 50 individual AFM images recorded at random locations over the sample surface showed only minuscule and random variations in the quality and order of the assembled lattice. The analysis of more than 450 fluorescence microscopy images of a quantum dot-decorated DNA origami lattice further revealed a very homogeneous surface coverage over cm2 areas with only minor boundary effects at the substrate edges. At total DNA costs of € 0.12 per cm2 , this large-scale nanopatterning technique holds great promise for the fabrication of functional surfaces.
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Affiliation(s)
- Yang Xin
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| | - Boxuan Shen
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Mauri A. Kostiainen
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Guido Grundmeier
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| | - Mario Castro
- Grupo Interdisciplinar de Sistemas Complejos and Instituto de Investigación TecnológicaUniversidad Pontificia Comillas de MadridMadrid28015Spain
| | - Veikko Linko
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
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Zhang Y, Qu ZB, Jiang C, Liu Y, Pradeep Narayanan R, Williams D, Zuo X, Wang L, Yan H, Liu H, Fan C. Prescribing Silver Chirality with DNA Origami. J Am Chem Soc 2021; 143:8639-8646. [DOI: 10.1021/jacs.1c00363] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yinan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Center for Molecular Design and Biomimetics, The Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Zhi-bei Qu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chu Jiang
- School of Chemical Science and Engineering, Shanghai Research Institute for Intelligent Autonomous Systems, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, Shanghai 200092, China
| | - Yingying Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Raghu Pradeep Narayanan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Dewight Williams
- Eyring Materials Center, Office of Knowledge Enterprise Development, Arizona State University, Tempe, Arizona 85281, United States
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lihua Wang
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Huajie Liu
- School of Chemical Science and Engineering, Shanghai Research Institute for Intelligent Autonomous Systems, Key Laboratory of Advanced Civil Engineering Materials of Ministry of Education, Tongji University, Shanghai 200092, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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Shen J, Sun W, Liu D, Schaus T, Yin P. Three-dimensional nanolithography guided by DNA modular epitaxy. NATURE MATERIALS 2021; 20:683-690. [PMID: 33846583 DOI: 10.1038/s41563-021-00930-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Lithographic scaling of periodic three-dimensional patterns is critical for advancing scalable nanomanufacturing. Current state-of-the-art quadruple patterning or extreme-ultraviolet lithography produce a line pitch down to around 30 nm, which might be further scaled to sub-20 nm through complex post-fabrication processes. Herein, we report the use of three-dimensional (3D) DNA nanostructures to scale the line pitch down to 16.2 nm, around 50% smaller than state-of-the-art results. We use a DNA modular epitaxy approach to fabricate 3D DNA masks with prescribed structural parameters (geometry, pitch and critical dimensions) along a designer assembly pathway. Single-run reactive ion etching then transfers the DNA patterns to a Si substrate at a lateral critical dimension of 7 nm and a vertical critical dimension of 2 nm. The nanolithography guided by DNA modular epitaxy achieves a smaller pitch than the projected values for advanced technology nodes in field-effect transistors, and provides a potential complement to the existing lithographic tools for advanced 3D nanomanufacturing.
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Affiliation(s)
- Jie Shen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Wei Sun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Di Liu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas Schaus
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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Ijäs H, Shen B, Heuer-Jungemann A, Keller A, Kostiainen M, Liedl T, Ihalainen JA, Linko V. Unraveling the interaction between doxorubicin and DNA origami nanostructures for customizable chemotherapeutic drug release. Nucleic Acids Res 2021; 49:3048-3062. [PMID: 33660776 PMCID: PMC8034656 DOI: 10.1093/nar/gkab097] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/27/2021] [Accepted: 02/03/2021] [Indexed: 12/11/2022] Open
Abstract
Doxorubicin (DOX) is a common drug in cancer chemotherapy, and its high DNA-binding affinity can be harnessed in preparing DOX-loaded DNA nanostructures for targeted delivery and therapeutics. Although DOX has been widely studied, the existing literature of DOX-loaded DNA-carriers remains limited and incoherent. Here, based on an in-depth spectroscopic analysis, we characterize and optimize the DOX loading into different 2D and 3D scaffolded DNA origami nanostructures (DONs). In our experimental conditions, all DONs show similar DOX binding capacities (one DOX molecule per two to three base pairs), and the binding equilibrium is reached within seconds, remarkably faster than previously acknowledged. To characterize drug release profiles, DON degradation and DOX release from the complexes upon DNase I digestion was studied. For the employed DONs, the relative doses (DOX molecules released per unit time) may vary by two orders of magnitude depending on the DON superstructure. In addition, we identify DOX aggregation mechanisms and spectral changes linked to pH, magnesium, and DOX concentration. These features have been largely ignored in experimenting with DNA nanostructures, but are probably the major sources of the incoherence of the experimental results so far. Therefore, we believe this work can act as a guide to tailoring the release profiles and developing better drug delivery systems based on DNA-carriers.
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Affiliation(s)
- Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Amelie Heuer-Jungemann
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, P.O. Box 15100, 00076 Aalto, Finland
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Janne A Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, P.O. Box 15100, 00076 Aalto, Finland
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Abstract
Structural DNA nanotechnology is a pioneering biotechnology that presents the opportunity to engineer DNA-based hardware that will mediate a profound interface to the nanoscale. To date, an enormous library of shaped 3D DNA nanostructures have been designed and assembled. Moreover, recent research has demonstrated DNA nanostructures that are not only static but can exhibit specific dynamic motion. DNA nanostructures have thus garnered significant research interest as a template for pursuing shape and motion-dependent nanoscale phenomena. Potential applications have been explored in many interdisciplinary areas spanning medicine, biosensing, nanofabrication, plasmonics, single-molecule chemistry, and facilitating biophysical studies. In this review, we begin with a brief overview of general and versatile design techniques for 3D DNA nanostructures as well as some techniques and studies that have focused on improving the stability of DNA nanostructures in diverse environments, which is pivotal for its reliable utilization in downstream applications. Our main focus will be to compile a wide body of existing research on applications of 3D DNA nanostructures that demonstrably rely on the versatility of their mechanical design. Furthermore, we frame reviewed applications into three primary categories, namely encapsulation, surface templating, and nanomechanics, that we propose to be archetypal shape- or motion-related functions of DNA nanostructures found in nanoscience applications. Our intent is to identify core concepts that may define and motivate specific directions of progress in this field as we conclude the review with some perspectives on the future.
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41
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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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Winogradoff D, Li P, Joshi H, Quednau L, Maffeo C, Aksimentiev A. Chiral Systems Made from DNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003113. [PMID: 33717850 PMCID: PMC7927625 DOI: 10.1002/advs.202003113] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/13/2020] [Indexed: 05/05/2023]
Abstract
The very chemical structure of DNA that enables biological heredity and evolution has non-trivial implications for the self-organization of DNA molecules into larger assemblies and provides limitless opportunities for building functional nanostructures. This progress report discusses the natural organization of DNA into chiral structures and recent advances in creating synthetic chiral systems using DNA as a building material. How nucleic acid chirality naturally comes into play in a diverse array of situations is considered first, at length scales ranging from an individual nucleotide to entire chromosomes. Thereafter, chiral liquid crystal phases formed by dense DNA mixtures are discussed, including the ongoing efforts to understand their origins. The report then summarizes recent efforts directed toward building chiral structures, and other structures of complex topology, using the principle of DNA self-assembly. Discussed last are existing and proposed functional man-made nanostructures designed to either probe or harness DNA's chirality, from plasmonics and spintronics to biosensing.
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Affiliation(s)
- David Winogradoff
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Pin‐Yi Li
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Himanshu Joshi
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Lauren Quednau
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Christopher Maffeo
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Aleksei Aksimentiev
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
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Liang L, Zheng P, Zhang C, Barman I. A Programmable DNA-Silicification-Based Nanocavity for Single-Molecule Plasmonic Sensing. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2005133. [PMID: 33458901 PMCID: PMC8275373 DOI: 10.1002/adma.202005133] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/23/2020] [Indexed: 05/19/2023]
Abstract
Plasmonic nanocavities are highly desirable for optical sensing because of their singular ability to confine light into deep subwavelength volumes. Yet, it remains profoundly challenging to fabricate structurally resilient nanocavities with high fidelity, and to obtain direct, noninvasive visualization of the plasmonic hotspots within such constructs. Herein, highly precise and robust nanocavities, entitled DNA-silicified template for Raman optical beacon (DNA-STROBE), are engineered by using silicified DNA scaffolds for spatial organization of discrete plasmonic nanoparticles. In addition to substantially enhancing structural stability and chemical inertness, DNA silicification significantly improves nanogap control, resulting simultaneously in large and controlled local electromagnetic field enhancement. The ultrasmall mode volume of the DNA-STROBE constructs promotes single-molecule occupancy enabling surface-enhanced Raman spectroscopy (SERS) observations of single-molecule activity even at elevated background concentration, significantly relaxing the restrictive pico- to nanomolar molecular concentration condition typically required for such investigations. Additionally, leveraging super-resolution SERS measurements allows noninvasive and diffraction-unlimited spatial profiling of otherwise unresolvable plasmonic hotspots. The highly programmable and reproducible nature of the DNA-STROBE, coupled with its quantitative label-free molecular readouts, provides a versatile platform with applications across the spectrum of nanophotonics and biomedical sciences.
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Affiliation(s)
- Le Liang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Peng Zheng
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Chi Zhang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
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44
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Sokolov PA, Ramazanov RR, Rolich VI, Popova MA, Shalygin VE, Kasyanenko NA. Stabilization of DNA by sodium and magnesium ions during the synthesis of DNA-bridged gold nanoparticles. NANOTECHNOLOGY 2021; 32:045604. [PMID: 33045696 DOI: 10.1088/1361-6528/abc037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanostructures synthesized using DNA-conjugated gold nanoparticles have a wide range of applications in the field of biosensorics. The stability of the DNA duplex plays a critical role as it determines the final geometry of these nanostructures. The main way to control DNA stability is to maintain a high ionic strength of the buffer solution; at the same time, high salt concentrations lead to an aggregation of nanoparticles. In this study, by means of the instrumentality of DNA-bridged seeds using tris(hydroxymethyl)aminomethane as a soft reducing agent the dumbbell-like gold nanoparticles up to 35 nm were synthesized with a high concentration of sodium ions of up to 100 mM and magnesium ions up to 1 mM. We also examined at the atomic level the details of the effect of the gold nanoparticle surface, as well as Na+ and Mg2+ ions, on the stability of nucleotide pairs located in close proximity to the grafting site.
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Affiliation(s)
- Petr A Sokolov
- St. Petersburg University, 7/9 Universitetskaya Emb., St. Petersburg, 199034, Russia
| | - Ruslan R Ramazanov
- St. Petersburg University, 7/9 Universitetskaya Emb., St. Petersburg, 199034, Russia
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoy Prospect V.O. 31, St. Petersburg, 199004, Russia
| | - Valeriy I Rolich
- St. Petersburg University, 7/9 Universitetskaya Emb., St. Petersburg, 199034, Russia
| | - Maria A Popova
- St. Petersburg University, 7/9 Universitetskaya Emb., St. Petersburg, 199034, Russia
| | - Vyacheslav E Shalygin
- St. Petersburg University, 7/9 Universitetskaya Emb., St. Petersburg, 199034, Russia
| | - Nina A Kasyanenko
- St. Petersburg University, 7/9 Universitetskaya Emb., St. Petersburg, 199034, Russia
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45
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Ohannesian N, Misbah I, Lin SH, Shih WC. Plasmonic nano-aperture label-free imaging (PANORAMA). Nat Commun 2020; 11:5805. [PMID: 33199716 PMCID: PMC7670455 DOI: 10.1038/s41467-020-19678-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022] Open
Abstract
Label-free optical imaging of nanoscale objects faces fundamental challenges. Techniques based on propagating surface plasmon resonance (SPR) and localized surface plasmon resonance (LSPR) have shown promises. However, challenges remain to achieve diffraction-limited resolution and better surface localization in SPR imaging. LSPR imaging with dark-field microscopy on metallic nanostructures suffers from low light throughput and insufficient imaging capacity. Here we show ultra-near-field index modulated PlAsmonic NanO-apeRture lAbel-free iMAging (PANORAMA) which uniquely relies on unscattered light to detect sub-100 nm dielectric nanoparticles. PANORAMA provides diffraction-limited resolution, higher surface sensitivity, and wide-field imaging with dense spatial sampling. Its system is identical to a standard bright-field microscope with a lamp and a camera – no laser or interferometry is needed. In a parallel fashion, PANORAMA can detect, count and size individual dielectric nanoparticles beyond 25 nm, and dynamically monitor their distance to the plasmonic surface at millisecond timescale. Here, the authors report on an imaging method based on localized surface plasmon resonance excitation, employing gold nanodisk arrays as substrates that enable imaging of transparent dielectric particles of several sizes. They demonstrate the ability to detect and image particles smaller than the diffraction limit at 25 nm with standard bright-field imaging.
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Affiliation(s)
- Nareg Ohannesian
- Department of Electrical and Computer Engineering, University of Houston, 4800 Calhoun Road, Houston, TX, 77204, USA
| | - Ibrahim Misbah
- Department of Electrical and Computer Engineering, University of Houston, 4800 Calhoun Road, Houston, TX, 77204, USA
| | - Steven H Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Wei-Chuan Shih
- Department of Electrical and Computer Engineering, University of Houston, 4800 Calhoun Road, Houston, TX, 77204, USA. .,Department of Biomedical Engineering, University of Houston, 4800 Calhoun Road, Houston, TX, 77204, USA. .,Department of Chemistry, University of Houston, 4800 Calhoun Road, Houston, TX, 77204, USA. .,Program of Materials Science and Engineering, University of Houston, 4800 Calhoun Road, Houston, TX, 77204, USA.
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46
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Ramakrishnan S, Subramaniam S, Kielar C, Grundmeier G, Stewart AF, Keller A. Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures. Molecules 2020; 25:molecules25215099. [PMID: 33153073 PMCID: PMC7663122 DOI: 10.3390/molecules25215099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 12/30/2022] Open
Abstract
Immobile Holliday junctions represent not only the most fundamental building block of structural DNA nanotechnology but are also of tremendous importance for the in vitro investigation of genetic recombination and epigenetics. Here, we present a detailed study on the room-temperature assembly of immobile Holliday junctions with the help of the single-strand annealing protein Redβ. Individual DNA single strands are initially coated with protein monomers and subsequently hybridized to form a rigid blunt-ended four-arm junction. We investigate the efficiency of this approach for different DNA/protein ratios, as well as for different DNA sequence lengths. Furthermore, we also evaluate the potential of Redβ to anneal sticky-end modified Holliday junctions into hierarchical assemblies. We demonstrate the Redβ-mediated annealing of Holliday junction dimers, multimers, and extended networks several microns in size. While these hybrid DNA–protein nanostructures may find applications in the crystallization of DNA–protein complexes, our work shows the great potential of Redβ to aid in the synthesis of functional DNA nanostructures under mild reaction conditions.
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Affiliation(s)
- Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (S.R.); (C.K.); (G.G.)
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Sivaraman Subramaniam
- Biotechnology Center, Department of Genomics, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany; (S.S.); (A.F.S.)
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany
| | - Charlotte Kielar
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (S.R.); (C.K.); (G.G.)
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (S.R.); (C.K.); (G.G.)
| | - A. Francis Stewart
- Biotechnology Center, Department of Genomics, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany; (S.S.); (A.F.S.)
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (S.R.); (C.K.); (G.G.)
- Correspondence:
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47
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Ranasinghe DR, Aryal BR, Westover TR, Jia S, Davis RC, Harb JN, Schulman R, Woolley AT. Seeding, Plating and Electrical Characterization of Gold Nanowires Formed on Self-Assembled DNA Nanotubes. Molecules 2020; 25:E4817. [PMID: 33092123 PMCID: PMC7587963 DOI: 10.3390/molecules25204817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
Self-assembly nanofabrication is increasingly appealing in complex nanostructures, as it requires fewer materials and has potential to reduce feature sizes. The use of DNA to control nanoscale and microscale features is promising but not fully developed. In this work, we study self-assembled DNA nanotubes to fabricate gold nanowires for use as interconnects in future nanoelectronic devices. We evaluate two approaches for seeding, gold and palladium, both using gold electroless plating to connect the seeds. These gold nanowires are characterized electrically utilizing electron beam induced deposition of tungsten and four-point probe techniques. Measured resistivity values for 15 successfully studied wires are between 9.3 × 10-6 and 1.2 × 10-3 Ωm. Our work yields new insights into reproducible formation and characterization of metal nanowires on DNA nanotubes, making them promising templates for future nanowires in complex electronic circuitry.
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Affiliation(s)
- Dulashani R. Ranasinghe
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (D.R.R.); (B.R.A.)
| | - Basu R. Aryal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (D.R.R.); (B.R.A.)
| | - Tyler R. Westover
- Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602, USA; (T.R.W.); (R.C.D.)
| | - Sisi Jia
- Johns Hopkins Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA; (S.J.); (R.S.)
| | - Robert C. Davis
- Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602, USA; (T.R.W.); (R.C.D.)
| | - John N. Harb
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA;
| | - Rebecca Schulman
- Johns Hopkins Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA; (S.J.); (R.S.)
| | - Adam T. Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA; (D.R.R.); (B.R.A.)
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48
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Shen B, Piskunen P, Nummelin S, Liu Q, Kostiainen MA, Linko V. Advanced DNA Nanopore Technologies. ACS APPLIED BIO MATERIALS 2020; 3:5606-5619. [DOI: 10.1021/acsabm.0c00879] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Qing Liu
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
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Ferhan AR, Yoon BK, Jeon WY, Cho NJ. Biologically interfaced nanoplasmonic sensors. NANOSCALE ADVANCES 2020; 2:3103-3114. [PMID: 36134263 PMCID: PMC9418064 DOI: 10.1039/d0na00279h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/26/2020] [Indexed: 05/30/2023]
Abstract
Understanding biointerfacial processes is crucial in various fields across fundamental and applied biology, but performing quantitative studies via conventional characterization techniques remains challenging due to instrumentation as well as analytical complexities and limitations. In order to accelerate translational research and address current challenges in healthcare and medicine, there is an outstanding need to develop surface-sensitive technologies with advanced measurement capabilities. Along this line, nanoplasmonic sensing has emerged as a powerful tool to quantitatively study biointerfacial processes owing to its high spatial resolution at the nanoscale. Consequently, the development of robust biological interfacing strategies becomes imperative to maximize its characterization potential. This review will highlight and discuss the critical role of biological interfacing within the context of constructing nanoplasmonic sensing platforms for biointerfacial science applications. Apart from paving the way for the development of highly surface-sensitive characterization tools that will spur fundamental biological interaction studies and improve the overall understanding of biological processes, the basic principles behind biointerfacing strategies presented in this review are also applicable to other fields that involve an interface between an inorganic material and a biological system.
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Affiliation(s)
- Abdul Rahim Ferhan
- School of Materials Science and Engineering, Nanyang Technological University 50 Nanyang Avenue 639798 Singapore
| | - Bo Kyeong Yoon
- School of Materials Science and Engineering, Nanyang Technological University 50 Nanyang Avenue 639798 Singapore
- School of Chemical Engineering, Sungkyunkwan University Suwon 16419 Republic of Korea
| | - Won-Yong Jeon
- School of Chemical Engineering, Sungkyunkwan University Suwon 16419 Republic of Korea
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University 50 Nanyang Avenue 639798 Singapore
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Park SM, Park G, Cha YJ, Yoon DK. Generation of 2D DNA Microstructures via Topographic Control and Shearing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2002449. [PMID: 32686286 DOI: 10.1002/smll.202002449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/07/2020] [Indexed: 06/11/2023]
Abstract
2D DNA microstructures are fabricated by applying the shear force to the DNA solution on the microchannels. The "U"-like textures of DNA are clearly observed when the mechanical shearing is applied on the aqueous DNA sample under the topographic confinement, in which the shearing direction is perpendicular to the grooves. The optical textures of U-like microstructures are directly observed by polarized optical microscopy (POM) and laser scanning fluorescent confocal polarizing microscopy (FCPM). The DNA microstructures can be modified by varying the width, showing the multiple U-patterns along with channel direction due to the synergistic interaction between the elastic behavior of DNA chains and topographic boundary condition. The resultant microstructures can be used to align rod-like liquid crystals (LCs) to generate alternatively oriented nematic phase and tilted focal conic domains (FCDs) in the smectic A phase. It is believed that this approach can suggest a hint to use to DNA materials for organizing multiscale hierarchical structures of soft- and biomaterials.
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Affiliation(s)
- Soon Mo Park
- Graduate School of Nanoscience and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - Geonhyeong Park
- Graduate School of Nanoscience and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - Yun Jeong Cha
- Graduate School of Nanoscience and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - Dong Ki Yoon
- Graduate School of Nanoscience and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Department of Chemistry and KINC, KAIST, Daejeon, 34141, Republic of Korea
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