1
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White D, Smith MA, Chanda B, Goldsmith RH. Strategies for Overcoming the Single-Molecule Concentration Barrier. ACS MEASUREMENT SCIENCE AU 2023; 3:239-257. [PMID: 37600457 PMCID: PMC10436376 DOI: 10.1021/acsmeasuresciau.3c00002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 08/22/2023]
Abstract
Fluorescence-based single-molecule approaches have helped revolutionize our understanding of chemical and biological mechanisms. Unfortunately, these methods are only suitable at low concentrations of fluorescent molecules so that single fluorescent species of interest can be successfully resolved beyond background signal. The application of these techniques has therefore been limited to high-affinity interactions despite most biological and chemical processes occurring at much higher reactant concentrations. Fortunately, recent methodological advances have demonstrated that this concentration barrier can indeed be broken, with techniques reaching concentrations as high as 1 mM. The goal of this Review is to discuss the challenges in performing single-molecule fluorescence techniques at high-concentration, offer applications in both biology and chemistry, and highlight the major milestones that shatter the concentration barrier. We also hope to inspire the widespread use of these techniques so we can begin exploring the new physical phenomena lying beyond this barrier.
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Affiliation(s)
- David
S. White
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Mackinsey A. Smith
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Baron Chanda
- Center
for
Investigation of Membrane Excitability Diseases, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Randall H. Goldsmith
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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2
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Messina TC, Srijanto BR, Collier CP, Kravchenko II, Richards CI. Gold Ion Beam Milled Gold Zero-Mode Waveguides. NANOMATERIALS 2022; 12:nano12101755. [PMID: 35630978 PMCID: PMC9147361 DOI: 10.3390/nano12101755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 12/02/2022]
Abstract
Zero-mode waveguides (ZMWs) are widely used in single molecule fluorescence microscopy for their enhancement of emitted light and the ability to study samples at physiological concentrations. ZMWs are typically produced using photo or electron beam lithography. We report a new method of ZMW production using focused ion beam (FIB) milling with gold ions. We demonstrate that ion-milled gold ZMWs with 200 nm apertures exhibit similar plasmon-enhanced fluorescence seen with ZMWs fabricated with traditional techniques such as electron beam lithography.
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Affiliation(s)
- Troy C. Messina
- Department of Physics, Berea College, 101 Chestnut Street, Berea, KY 40404, USA
- Correspondence: ; Tel.: +1-859-985-3326
| | - Bernadeta R. Srijanto
- Center for Nanophase Materials Science, Oak Ridge National Labs, Oak Ridge, TN 37831, USA; (B.R.S.); (C.P.C.); (I.I.K.)
| | - Charles Patrick Collier
- Center for Nanophase Materials Science, Oak Ridge National Labs, Oak Ridge, TN 37831, USA; (B.R.S.); (C.P.C.); (I.I.K.)
| | - Ivan I. Kravchenko
- Center for Nanophase Materials Science, Oak Ridge National Labs, Oak Ridge, TN 37831, USA; (B.R.S.); (C.P.C.); (I.I.K.)
| | - Christopher I. Richards
- Department of Chemistry, University of Kentucky, 209 Chemistry-Physics Building, Lexington, KY 40202, USA;
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3
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Baek S, Han D, Kwon SR, Sundaresan V, Bohn PW. Electrochemical Zero-Mode Waveguide Potential-Dependent Fluorescence of Glutathione Reductase at Single-Molecule Occupancy. Anal Chem 2022; 94:3970-3977. [PMID: 35213143 PMCID: PMC8904319 DOI: 10.1021/acs.analchem.1c05091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding functional states of individual redox enzymes is important because electron-transfer reactions are fundamental to life, and single-enzyme molecules exhibit molecule-to-molecule heterogeneity in their properties, such as catalytic activity. Zero-mode waveguides (ZMW) constitute a powerful tool for single-molecule studies, enabling investigations of binding reactions up to the micromolar range due to the ability to trap electromagnetic radiation in zeptoliter-scale observation volumes. Here, we report the potential-dependent fluorescence dynamics of single glutathione reductase (GR) molecules using a bimodal electrochemical ZMW (E-ZMW), where a single-ring electrode embedded in each of the nanopores of an E-ZMW array simultaneously serves to control electrochemical potential and to confine optical radiation within the nanopores. Here, the redox state of GR is manipulated using an external potential control of the Au electrode in the presence of a redox mediator, methyl viologen (MV). Redox-state transitions in GR are monitored by correlating electrochemical and spectroscopic signals from freely diffusing MV/GR in 60 zL effective observation volumes at single GR molecule average pore occupancy, ⟨n⟩ ∼ 0.8. Fluorescence intensities decrease (increase) at reducing (oxidizing) potentials for MV due to the MV-mediated control of the GR redox state. The spectroelectrochemical response of GR to the enzyme substrate, i.e., glutathione disulfide (GSSG), shows that GSSG promotes GR oxidation via enzymatic reduction. The capabilities of E-ZMWs to probe spectroelectrochemical phenomena in zL-scale-confined environments show great promise for the study of single-enzyme reactions and can be extended to important technological applications, such as those in molecular diagnostics.
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Affiliation(s)
- Seol Baek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Donghoon Han
- Department of Chemistry, The Catholic University of Korea, Bucheon, Gyeonggi-do 14662, South Korea
| | - Seung-Ryong Kwon
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, South Korea
| | - Vignesh Sundaresan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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4
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Iizuka R, Yamazaki H, Uemura S. Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies. Biophys Physicobiol 2022; 19:e190032. [DOI: 10.2142/biophysico.bppb-v19.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/26/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Hirohito Yamazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
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5
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Patra S, Claude JB, Naubron JV, Wenger J. Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled in zero-mode waveguides. Nucleic Acids Res 2021; 49:12348-12357. [PMID: 34791437 PMCID: PMC8643622 DOI: 10.1093/nar/gkab1002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 11/14/2022] Open
Abstract
G-quadruplexes (GQs), a non-canonical form of DNA, are receiving a huge interest as target sites for potential applications in antiviral and anticancer drug treatments. The biological functions of GQs can be controlled by specifically binding proteins known as GQs binding proteins. Some of the GQs binding proteins contain an arginine and glycine-rich sequence known as RGG peptide. Despite the important role of RGG, the GQs-RGG interaction remains poorly understood. By single molecule measurements, the interaction dynamics can be determined in principle. However, the RGG-GQs interaction occurs at micromolar concentrations, making conventional single-molecule experiments impossible with a diffraction-limited confocal microscope. Here, we use a 120 nm zero-mode waveguide (ZMW) nanoaperture to overcome the diffraction limit. The combination of dual-color fluorescence cross-correlation spectroscopy (FCCS) with FRET is used to unveil the interaction dynamics and measure the association and dissociation rates. Our data show that the RGG-GQs interaction is predominantly driven by electrostatics but that a specific affinity between the RGG sequence and the GQs structure is preserved. The single molecule approach at micromolar concentration is the key to improve our understanding of GQs function and develop its therapeutic applications by screening a large library of GQs-targeting peptides and proteins.
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Affiliation(s)
- Satyajit Patra
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013 Marseille, France
| | - Jean-Benoît Claude
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013 Marseille, France
| | - Jean-Valère Naubron
- Aix Marseille Univ, CNRS, Centrale Marseille, FSCM – Spectropole, 13013 Marseille, France
| | - Jérome Wenger
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013 Marseille, France
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6
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Takahashi S, Oshige M, Katsura S. DNA Manipulation and Single-Molecule Imaging. Molecules 2021; 26:1050. [PMID: 33671359 PMCID: PMC7922115 DOI: 10.3390/molecules26041050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/22/2022] Open
Abstract
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan;
| | - Masahiko Oshige
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
| | - Shinji Katsura
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
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7
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Perotto S, Biagini C, Hubarevich A, Tantussi F, De Angelis F. Toward all on chip optical detection in the few molecule regime. Biosens Bioelectron 2020; 169:112600. [PMID: 32971342 DOI: 10.1016/j.bios.2020.112600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/04/2020] [Accepted: 09/06/2020] [Indexed: 10/23/2022]
Abstract
Integrated optics devices are one of the most promising technologies in many fields such as biosensing, optical monitoring, and portable devices. They provide several advantages such as unique sensitivity and the possibility of the well-established and developed silicon photonics technology. However some challenges still remain open, as the implementation of multiplex assay able to reach the single particle sensitivity. In this context, we propose a new design for a Si-based photonic structure that enables the realization of on chip sub-wavelength optical sources. The idea is based on the insertion of opportunely designed nanometric holes in the photonic circuit, which are available for analyte detection with high efficiency. We propose three different configurations in which both excitation and detection are obtained through the same waveguide thus simplifying the detection scheme and potentially enabling multiplexed detection. We proved the high confinement of the electromagnetic field in the holes both by theoretical modelling and spectroscopic measurements. We investigate the possibility of inserting an arbitrary number of optical sources by using a resonator and evaluate advantages and drawbacks of resonating and non-resonating solutions. Finally, we report the proof-of-concept experiment, where detection sensitivity down to single Quantum Dots is obtained by combining the novel design with fluorescence-based techniques. Importantly, the presented results are achieved by a simple modification of photonic sensing chips which are already on the market thus having an excellent translational perspective.
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Affiliation(s)
- Sara Perotto
- Istituto Italiano di Tecnologia, via Morego 30, I-16159 Genova, Italy; Department of Physics, Politecnico di Milano, Milan, Italy
| | - Claudio Biagini
- Istituto Italiano di Tecnologia, via Morego 30, I-16159 Genova, Italy; Università degli Studi di Genova, via Balbi 5, I-16126 Genova, Italy
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8
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Calabrase W, Bishop LDC, Dutta C, Misiura A, Landes CF, Kisley L. Transforming Separation Science with Single-Molecule Methods. Anal Chem 2020; 92:13622-13629. [PMID: 32936608 DOI: 10.1021/acs.analchem.0c02572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Empirical optimization of the multiscale parameters underlying chromatographic and membrane separations leads to enormous resource waste and production costs. A bottom-up approach to understand the physical phenomena underlying challenges in separations is possible with single-molecule observations of solute-stationary phase interactions. We outline single-molecule fluorescence techniques that can identify key interactions under ambient conditions. Next, we describe how studying increasingly complex samples heightens the relevance of single-molecule results to industrial applications. Finally, we illustrate how separation methods that have not been studied at the single-molecule scale can be advanced, using chiral chromatography as an example case. We hope new research directions based on a molecular approach to separations will emerge based on the ideas, technologies, and open scientific questions presented in this Perspective.
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Affiliation(s)
- William Calabrase
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Logan D C Bishop
- Department of Chemistry, Rice University, Houston, Texas 77251, United States
| | - Chayan Dutta
- Department of Chemistry, Rice University, Houston, Texas 77251, United States
| | - Anastasiia Misiura
- Department of Chemistry, Rice University, Houston, Texas 77251, United States
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, Texas 77251, United States.,Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77251, United States.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77251, United States.,Smalley-Curl Institute, Rice University, Houston, Texas 77251, United States
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106, United States.,Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
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9
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Al Masud A, Martin WE, Moonschi FH, Park SM, Srijanto BR, Graham KR, Collier CP, Richards CI. Mixed metal zero-mode guides (ZMWs) for tunable fluorescence enhancement. NANOSCALE ADVANCES 2020; 2:1894-1903. [PMID: 36132495 PMCID: PMC9419232 DOI: 10.1039/c9na00641a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/25/2020] [Indexed: 05/28/2023]
Abstract
Zero-mode waveguides (ZMWs) are capable of modifying fluorescence emission through interactions with surface plasmon modes leading to either plasmon-enhanced fluorescence or quenching. Enhancement requires spectral overlap of the plasmon modes with the absorption or emission of the fluorophore. Thus, enhancement is limited to fluorophores in resonance with metals (e.g. Al, Au, Ag) used for ZMWs. The ability to tune interactions to match a wider range of fluorophores across the visible spectra would significantly extend the utility of ZMWs. We fabricated ZMWs composed of aluminum and gold individually and also in mixtures of three different ratios, (Al : Au; 75 : 25, 50 : 50, 25 : 75). We characterized the effect of mixed-metal ZMWs on single-molecule emission for a range fluorophores across the visible spectrum. Mixed metal ZMWs exhibited a shift in the spectral range where they exhibited the maximum fluorescence enhancement allowing us to match the emission of fluorophores that were nonresonant with single metal ZMWs. We also compared the effect of mixed-metal ZMWs on the photophysical properties of fluorescent molecules due to metal-molecule interactions. We quantified changes in fluorescence lifetimes and photostability that were dependent on the ratio of Au and Al. Tuning the enhancement properties of ZMWs by changing the ratio of Au and Al allowed us to match the fluorescence of fluorophores that emit in different regions of the visible spectrum.
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Affiliation(s)
- Abdullah Al Masud
- Department of Chemistry, University of Kentucky Lexington KY 40506 USA
| | - W Elliott Martin
- Department of Chemistry, University of Kentucky Lexington KY 40506 USA
| | - Faruk H Moonschi
- Department of Physiology, School of Medicine, University of Kentucky KY 40506 USA
| | - So Min Park
- Department of Chemical and Materials Engineering, Univ. of Kentucky 40506 USA
| | - Bernadeta R Srijanto
- Center for Nanophase Materials Sciences, Oakridge National Lab Oakridge TN 37831 USA
| | - Kenneth R Graham
- Department of Chemistry, University of Kentucky Lexington KY 40506 USA
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oakridge National Lab Oakridge TN 37831 USA
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10
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Chen KY, Jamiolkowski RM, Tate AM, Fiorenza SA, Pfeil SH, Goldman YE. Fabrication of Zero Mode Waveguides for High Concentration Single Molecule Microscopy. J Vis Exp 2020:10.3791/61154. [PMID: 32478723 PMCID: PMC9020539 DOI: 10.3791/61154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In single molecule fluorescence enzymology, background fluorescence from labeled substrates in solution often limits fluorophore concentration to pico- to nanomolar ranges, several orders of magnitude less than many physiological ligand concentrations. Optical nanostructures called zero mode waveguides (ZMWs), which are 100-200 nm in diameter apertures fabricated in a thin conducting metal such as aluminum or gold, allow imaging of individual molecules at micromolar concentrations of fluorophores by confining visible light excitation to zeptoliter effective volumes. However, the need for expensive and specialized nanofabrication equipment has precluded the widespread use of ZMWs. Typically, nanostructures such as ZMWs are obtained by direct writing using electron beam lithography, which is sequential and slow. Here, colloidal, or nanosphere, lithography is used as an alternative strategy to create nanometer-scale masks for waveguide fabrication. This report describes the approach in detail, with practical considerations for each phase. The method allows thousands of aluminum or gold ZMWs to be made in parallel, with final waveguide diameters and depths of 100-200 nm. Only common lab equipment and a thermal evaporator for metal deposition are required. By making ZMWs more accessible to the biochemical community, this method can facilitate the study of molecular processes at cellular concentrations and rates.
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Affiliation(s)
- Kevin Y Chen
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania
| | - Ryan M Jamiolkowski
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania
| | - Alyssa M Tate
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania
| | | | | | - Yale E Goldman
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania;
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11
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Fu K, Kwon SR, Han D, Bohn PW. Single Entity Electrochemistry in Nanopore Electrode Arrays: Ion Transport Meets Electron Transfer in Confined Geometries. Acc Chem Res 2020; 53:719-728. [PMID: 31990518 PMCID: PMC8020881 DOI: 10.1021/acs.accounts.9b00543] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Electrochemical measurements conducted in confined volumes provide a powerful and direct means to address scientific questions at the nexus of nanoscience, biotechnology, and chemical analysis. How are electron transfer and ion transport coupled in confined volumes and how does understanding them require moving beyond macroscopic theories? Also, how do these coupled processes impact electrochemical detection and processing? We address these questions by studying a special type of confined-volume architecture, the nanopore electrode array, or NEA, which is designed to be commensurate in size with physical scaling lengths, such as the Debye length, a concordance that offers performance characteristics not available in larger scale structures.The experiments described here depend critically on carefully constructed nanoscale architectures that can usefully control molecular transport and electrochemical reactivity. We begin by considering the experimental constraints that guide the design and fabrication of zero-dimensional nanopore arrays with multiple embedded electrodes. These zero-dimensional structures are nearly ideal for exploring how permselectivity and unscreened ion migration can be combined to amplify signals and improve selectivity by enabling highly efficient redox cycling. Our studies also highlight the benefits of arrays, in that molecules escaping from a single nanopore are efficiently captured by neighboring pores and returned to the population of active redox species being measured, benefits that arise from coupling ion accumulation and migration. These tools for manipulating redox species are well-positioned to explore single molecule and single particle electron transfer events through spectroelectrochemistry, studies which are enabled by the electrochemical zero-mode waveguide (ZMW), a special hybrid nanophotonic/nanoelectronic architecture in which the lower ring electrode of an NEA nanopore functions both as a working electrode to initiate electron transfer reactions and as the optical cladding layer of a ZMW. While the work described here is largely exploratory and fundamental, we believe that the development of NEAs will enable important applications that emerge directly from the unique coupled transport and electron-transfer capabilities of NEAs, including in situ molecular separation and detection with external stimuli, redox-based electrochemical rectification in individually encapsulated nanopores, and coupled sorters and analyzers for nanoparticles.
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Affiliation(s)
- Kaiyu Fu
- Department of Radiology, Stanford University, Stanford, CA, 94306
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94306
| | - Seung-Ryong Kwon
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Donghoon Han
- Department of Chemistry, The Catholic University of Korea, Bucheon, Gyeonggi-do, 14662 Republic of Korea
| | - Paul W. Bohn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
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12
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Crouch GM, Oh C, Fu K, Bohn PW. Tunable optical metamaterial-based sensors enabled by closed bipolar electrochemistry. Analyst 2019; 144:6240-6246. [PMID: 31538160 PMCID: PMC8030654 DOI: 10.1039/c9an01137d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enabled by the proliferation of nanoscale fabrication techniques required to create spatially-repeating, sub-wavelength structures to manipulate the behavior of visible-wavelength radiation, optical metamaterials are of increasing interest. Here we develop and characterize a chemical sensing approach based on electrochemical tuning of the optical response function of large-area, inexpensive nanoaperture metamaterials at visible and near-IR wavelengths. Nanosphere lithography is used to create an ordered array of sub-wavelength apertures in a Au film. The spacing of these apertures is established during fabrication, based on the size of the polystyrene nanospheres. Tunable shifts in the transmission spectrum can be produced post-fabrication by electrodeposition of a dissimilar metal, Ag, using the nanoaperture film as one electrode in a 2-electrode closed bipolar electrochemical (CBE) cell, altering hole size, film thickness, and film composition while maintaining hole spacing dictated by the original pattern. Optical transmission spectra acquired under galvanostatic conditions can be expressed as a linear combination of the initial and final (saturated) spectra, and the resulting response function exhibits a sigmoidal response with respect to the amount of charge (or metal) deposited. This architecture is then used to perform optical coulometry of model analytes in a CBE-based analyte-reporter dual cell device, thus expanding the capability of CBE-based sensors. Increasing the exposed electrode area of the analyte cell increases the response of the device, while modifying the circuit resistance alters the balance between sensitivity and dynamic range. These tunable nanoaperture metamaterials exhibit enhanced sensitivity compared to CBE electrochromic reporter cells to the μM to nM concentration range, suggesting further avenues for development of CBE-based chemical sensors as well as application to inexpensive, point-of-care diagnostic devices.
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Affiliation(s)
- Garrison M Crouch
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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13
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Zambrana-Puyalto X, Ponzellini P, Maccaferri N, Tessarolo E, Pelizzo MG, Zhang W, Barbillon G, Lu G, Garoli D. A hybrid metal-dielectric zero mode waveguide for enhanced single molecule detection. Chem Commun (Camb) 2019; 55:9725-9728. [PMID: 31355377 DOI: 10.1039/c9cc04118d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We fabricated hybrid metal-dielectric nanoslots and measured their optical response at three different wavelengths. The nanostructure is fabricated on a bilayer film formed by the sequential deposition of silicon and gold on a transparent substrate. The optical characterization is done via fluorescence spectroscopy measurements. We characterized the fluorescence enhancement, as well as the lifetime and the detection volume reduction for each wavelength. We observe that the hybrid metal-dielectric nanoslots behave as enhanced zero mode waveguides in the near-infrared spectral region. Their detection volume is such that they can perform enhanced single-molecule detection at tens of μM. We compared their behavior with that of a golden ZMW, and we demonstrated that the dielectric silicon layer improves both the optical performance and the stability of the device.
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Affiliation(s)
| | - Paolo Ponzellini
- Istituto Italiano di Tecnologia, Via Morego 30, 16136 Genova, Italy.
| | - Nicolò Maccaferri
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | | | | | - Weidong Zhang
- State Key Laboratory for Mesoscopic Physics & Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
| | | | - Guowei Lu
- State Key Laboratory for Mesoscopic Physics & Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
| | - Denis Garoli
- Istituto Italiano di Tecnologia, Via Morego 30, 16136 Genova, Italy.
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14
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Abstract
Optical biosensors are defined as portable optical devices that use biorecognition molecules to interrogate a sample for the presence of a target. The capabilities of optical biosensors have expanded rapidly with advances in miniature optical components and molecular engineering. Biosensors to meet the needs in health and environmental monitoring and food safety have become commercially available, with many more in the pipeline. We review the innovative approaches to overcoming existing hurdles to practical biosensor designs and explore potential areas for future breakthroughs in optical biosensor technology.
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Affiliation(s)
- Frances S Ligler
- Joint Department of Biomedical Engineering , University of North Carolina at Chapel Hill and North Carolina State University and the North Carolina State University Comparative Medicine Institute , Raleigh , North Carolina 27695-7115 , United States
| | - J Justin Gooding
- School of Chemistry, The Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology , The University of New South Wales , Sydney 2052 , Australia
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15
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Han D, Crouch GM, Chao Z, Fullerton-Shirey SK, Go DB, Bohn PW. Nanopore-Templated Silver Nanoparticle Arrays Photopolymerized in Zero-Mode Waveguides. Front Chem 2019; 7:216. [PMID: 31024900 PMCID: PMC6467962 DOI: 10.3389/fchem.2019.00216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/19/2019] [Indexed: 12/27/2022] Open
Abstract
In situ fabrication of nanostructures within a solid-polymer electrolyte confined to subwavelength-diameter nanoapertures is a promising approach for producing nanomaterials for nanophotonic and chemical sensing applications. The solid-polymer electrolyte can be patterned by lithographic photopolymerization of poly(ethylene glycol) diacrylate (PEGDA)-based silver cation (Ag+)-containing polyelectrolyte. Here, we present a new method for fabricating nanopore-templated Ag nanoparticle (AgNP) arrays by in situ photopolymerization using a zero-mode waveguide (ZMW) array to simultaneously template embedded AgNPs and control the spatial distribution of the optical field used for photopolymerization. The approach starts with an array of nanopores fabricated by sequential layer-by-layer deposition and focused ion beam milling. These structures have an optically transparent bottom, allowing access of the optical radiation to the attoliter-volume ZMW region to photopolymerize a PEGDA monomer solution containing AgNPs and Ag+. The electric field intensity distribution is calculated for various ZMW optical cladding layer thicknesses using finite-element simulations, closely following the light-blocking efficiency of the optical cladding layer. The fidelity of the polyelectrolyte nanopillar pattern was optimized with respect to experimental conditions, including the presence or absence of Ag+ and AgNPs and the concentrations of PEGDA and Ag+. The self-templated approach for photopatterning high-resolution photolabile polyelectrolyte nanostructures directly within a ZMW array could lead to a new class of metamaterials formed by embedding metal nanoparticles within a dielectric in a well-defined spatial array.
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Affiliation(s)
- Donghoon Han
- Department of Chemistry, The Catholic University of Korea, Bucheon, South Korea
| | - Garrison M. Crouch
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Zhongmou Chao
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Susan K. Fullerton-Shirey
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - David B. Go
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, United States
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Paul W. Bohn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, United States
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
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Kim JY, Han D, Crouch GM, Kwon SR, Bohn PW. Capture of Single Silver Nanoparticles in Nanopore Arrays Detected by Simultaneous Amperometry and Surface-Enhanced Raman Scattering. Anal Chem 2019; 91:4568-4576. [PMID: 30860812 PMCID: PMC8083125 DOI: 10.1021/acs.analchem.8b05748] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The attoliter volumes and confinement abilities of zero-dimensional nanopore-electrode arrays (NEAs) hold considerable promise for examining the behavior of single nanoparticles. In this work, we use surface-enhanced Raman scattering (SERS) in tandem with amperometry in order to monitor single Ag Raman-sentinel nanoparticles transported to and captured in single nanopores. To that end, highly ordered solid-state NEAs were fabricated to contain periodic arrays of nanopores, each housing a single recessed Au-ring electrode. These were used to electrostatically capture and trap single silver nanoparticles (AgNPs) functionalized with the electrochemically stable Raman reporter, 1,4-bis(2-methylstyryl)benzene (bis-MSB). Transport and capture of the bis-MSB-tagged AgNPs in the nanopores was followed by simultaneous amperometry and SERS signals characteristic of AgNP oxidation and enhanced Raman scattering by bis-MSB at silver-gold hot spots, respectively. The frequency and magnitude of oxidation-current spikes increased with stepwise increases in DC voltage, and characteristic bis-MSB SERS spectra were observed. Under AC excitation, on the other hand, two distinctly different types of SERS signals were observed, independent of frequency and amplitude: (1) strong, transient (<10 s) spectra and (2) slow (>100 s) monotonically diminishing spectra. We hypothesize that the former behavior results from AgNP aggregates, whereas the latter occurs as a result of multiple incomplete AgNP-oxidation events in succession. These results show that attoliter-volume NEAs are competent for acquiring concurrent SERS spectra and for amperometry of single nanoparticles and that together these measurements can illuminate the collision dynamics of nanoparticles in confined environments.
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Affiliation(s)
- Ju-Young Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Donghoon Han
- Department of Chemistry, The Catholic University of Korea, Bucheon-si, Gyeonggi-do, 14662, Republic of Korea
| | - Garrison M. Crouch
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Seung-Ryong Kwon
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
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