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Barsanti L, Birindelli L, Sbrana F, Lombardi G, Gualtieri P. Advanced Microscopy Techniques for Molecular Biophysics. Int J Mol Sci 2023; 24:9973. [PMID: 37373120 DOI: 10.3390/ijms24129973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Though microscopy is most often intended as a technique for providing qualitative assessment of cellular and subcellular properties, when coupled with other instruments such as wavelength selectors, lasers, photoelectric devices and computers, it can perform a wide variety of quantitative measurements, which are demanding in establishing relationships between the properties and structures of biological material in all their spatial and temporal complexities. These combinations of instruments are a powerful approach to improve non-destructive investigations of cellular and subcellular properties (both physical and chemical) at a macromolecular scale resolution. Since many subcellular compartments in living cells are characterized by structurally organized molecules, this review deals with three advanced microscopy techniques well-suited for these kind of investigations, i.e., microspectrophotometry (MSP), super-resolution localization microscopy (SRLM) and holotomographic microscopy (HTM). These techniques can achieve an insight view into the role intracellular molecular organizations such as photoreceptive and photosynthetic structures and lipid bodies play in many cellular processes as well as their biophysical properties. Microspectrophotometry uses a set-up based on the combination of a wide-field microscope and a polychromator, which allows the measurement of spectroscopic features such as absorption spectra. Super resolution localization microscopy combines dedicated optics and sophisticated software algorithms to overcome the diffraction limit of light and allow the visualization of subcellular structures and dynamics in greater detail with respect to conventional optical microscopy. Holotomographic microscopy combines holography and tomography techniques into a single microscopy set-up, and allows 3D reconstruction by means of the phase separation of biomolecule condensates. This review is organized in sections, which for each technique describe some general aspects, a peculiar theoretical aspect, a specific experimental configuration and examples of applications (fish and algae photoreceptors, single labeled proteins and endocellular aggregates of lipids).
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Affiliation(s)
- Laura Barsanti
- Istituto di Biofisica, CNR, Via Moruzzi 1, 56124 Pisa, Italy
| | | | | | - Giovanni Lombardi
- Istituto di Scienza e Tecnologia dell'Informazione, CNR, Via Moruzzi 1, 56124 Pisa, Italy
| | - Paolo Gualtieri
- Istituto di Biofisica, CNR, Via Moruzzi 1, 56124 Pisa, Italy
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Kim WC, Moon H, Lee WS, Lim G, Choi GJ, Kang D, Lee H, Park NC. Investigation on achieving super-resolution by solid immersion lens based STED microscopy. OPTICS EXPRESS 2017; 25:16629-16642. [PMID: 28789164 DOI: 10.1364/oe.25.016629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
The feasibility of stimulated emission depletion (STED) microscopy using a solid immersion lens was investigated. First, the theoretical feasibility of the considered system is discussed based on a vectorial field algorithm that uses a stratified medium composed of a SIL air-gap and test sample. Using the simulation, we verified that evanescent waves with much higher spatial frequencies corresponding to the high numerical aperture in the air-gap can be utilized to achieve a higher resolution than a confocal fluorescent image without a depletion beam. The simulated expectation was supported by actual imaging on two types of samples: fluorescent beads with a 20 nm diameter and an actin sample with a filamentous structure. The lateral resolution of the system was determined to be 34 nm via the imaging results on the nano-beads. The system was quite promising for achieving nano-scale surface imaging of biological samples; an even higher resolution was achieved by adjusting the wavelength and the intensity of the depletion beam.
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Wang Y, Bai Z, Wang Q, Wang G. Experimental Investigations on Fluorescence Excitation and Depletion of Carbon Dots. J Fluoresc 2017; 27:1435-1441. [PMID: 28421321 DOI: 10.1007/s10895-017-2082-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/04/2017] [Indexed: 01/15/2023]
Abstract
Carbon dots (CDs) can be readily synthesized and utilized as attractive fluorescent probes for a variety of applications. In this study, we have synthesized CDs using a previously published method and characterized their photo-physical properties. The resultant CDs possess prominent photo-stability and short emission wavelength in the violet region. Our study reveals that CDs, with weak photo-bleaching, enable them to be employed to achieve high spatial resolution in stimulated emission depletion (STED) microscopy. The depletion efficiency can reach 60%. More importantly, the shorter excitation wavelength of CDs contributes to further improvement of resolution for STED microscopy. An excellent candidate for fluorophores, these CDs have potential to be used in super-resolution imaging for STED microscopy.
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Affiliation(s)
- Yunxia Wang
- Biomedical Engineering Program & Department of Mechanical Engineering, University of South Carolina, Columbia, SC, 29208, USA
| | - Zhenhua Bai
- Biomedical Engineering Program & Department of Mechanical Engineering, University of South Carolina, Columbia, SC, 29208, USA
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA.
| | - Guiren Wang
- Biomedical Engineering Program & Department of Mechanical Engineering, University of South Carolina, Columbia, SC, 29208, USA.
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Gao J, Yang X, Djekidel MN, Wang Y, Xi P, Zhang MQ. Developing bioimaging and quantitative methods to study 3D genome. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0065-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Wu HY, Huang YT, Shen PT, Lee H, Oketani R, Yonemaru Y, Yamanaka M, Shoji S, Lin KH, Chang CW, Kawata S, Fujita K, Chu SW. Ultrasmall all-optical plasmonic switch and its application to superresolution imaging. Sci Rep 2016; 6:24293. [PMID: 27063920 PMCID: PMC4827031 DOI: 10.1038/srep24293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/21/2016] [Indexed: 12/03/2022] Open
Abstract
Because of their exceptional local-field enhancement and ultrasmall mode volume, plasmonic components can integrate photonics and electronics at nanoscale, and active control of plasmons is the key. However, all-optical modulation of plasmonic response with nanometer mode volume and unity modulation depth is still lacking. Here we show that scattering from a plasmonic nanoparticle, whose volume is smaller than 0.001 μm3, can be optically switched off with less than 100 μW power. Over 80% modulation depth is observed, and shows no degradation after repetitive switching. The spectral bandwidth approaches 100 nm. The underlying mechanism is suggested to be photothermal effects, and the effective single-particle nonlinearity reaches nearly 10−9 m2/W, which is to our knowledge the largest record of metallic materials to date. As a novel application, the non-bleaching and unlimitedly switchable scattering is used to enhance optical resolution to λ/5 (λ/9 after deconvolution), with 100-fold less intensity requirement compared to similar superresolution techniques. Our work not only opens up a new field of ultrasmall all-optical control based on scattering from a single nanoparticle, but also facilitates superresolution imaging for long-term observation.
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Affiliation(s)
- Hsueh-Yu Wu
- Department of Physics, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Yen-Ta Huang
- Department of Physics, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Po-Ting Shen
- Department of Physics, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Hsuan Lee
- Department of Physics, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Ryosuke Oketani
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0851, Japan
| | - Yasuo Yonemaru
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0851, Japan
| | - Masahito Yamanaka
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0851, Japan
| | - Satoru Shoji
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0851, Japan
| | - Kung-Hsuan Lin
- Institute of Physics, Academia Sinica, 128 Sec. 2, Academia Rd., Nankang, Taipei 11529, Taiwan
| | - Chih-Wei Chang
- Center for Condensed Matter Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Satoshi Kawata
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0851, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0851, Japan
| | - Shi-Wei Chu
- Department of Physics, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan.,Molecular Imaging Center, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
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Yang X, Xie H, Alonas E, Liu Y, Chen X, Santangelo PJ, Ren Q, Xi P, Jin D. Mirror-enhanced super-resolution microscopy. LIGHT, SCIENCE & APPLICATIONS 2016; 5. [PMID: 27398242 PMCID: PMC4936537 DOI: 10.1038/lsa.2016.134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Axial excitation confinement beyond the diffraction limit is crucial to the development of next-generation, super-resolution microscopy. STimulated Emission Depletion (STED) nanoscopy offers lateral super-resolution using a donut-beam depletion, but its axial resolution is still over 500 nm. Total internal reflection fluorescence microscopy is widely used for single-molecule localization, but its ability to detect molecules is limited to within the evanescent field of ~ 100 nm from the cell attachment surface. We find here that the axial thickness of the point spread function (PSF) during confocal excitation can be easily improved to 110 nm by replacing the microscopy slide with a mirror. The interference of the local electromagnetic field confined the confocal PSF to a 110-nm spot axially, which enables axial super-resolution with all laser-scanning microscopes. Axial sectioning can be obtained with wavelength modulation or by controlling the spacer between the mirror and the specimen. With no additional complexity, the mirror-assisted excitation confinement enhanced the axial resolution six-fold and the lateral resolution two-fold for STED, which together achieved 19-nm resolution to resolve the inner rim of a nuclear pore complex and to discriminate the contents of 120 nm viral filaments. The ability to increase the lateral resolution and decrease the thickness of an axial section using mirror-enhanced STED without increasing the laser power is of great importance for imaging biological specimens, which cannot tolerate high laser power.
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Affiliation(s)
- Xusan Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
| | - Hao Xie
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Eric Alonas
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Yujia Liu
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
- Advanced Cytometry Labs, ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Macquarie University, Sydney, NSW 2109, Australia
| | - Xuanze Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
| | - Philip J Santangelo
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Qiushi Ren
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
| | - Peng Xi
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- Advanced Cytometry Labs, ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Macquarie University, Sydney, NSW 2109, Australia
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Dayong Jin
- Advanced Cytometry Labs, ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Macquarie University, Sydney, NSW 2109, Australia
- Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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Tressler C, Stolle M, Fradin C. Fluorescence correlation spectroscopy with a doughnut-shaped excitation profile as a characterization tool in STED microscopy. OPTICS EXPRESS 2014; 22:31154-31166. [PMID: 25607065 DOI: 10.1364/oe.22.031154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The resolution of stimulated emission depletion (STED) microscopes is ultimately limited by the quality of the doughnut-shaped illumination profile of the STED erase beam. We show here that in the focal plane this illumination profile is well approximated by an analytical expression - a difference of Gaussian functions, which tends towards a first order Laguerre-Gaussian profile in the case of a well aligned beam with a true zero-intensity central minimum. We further show that along the optical axis the maximum intensity profile is reasonably approximated by a Gaussian decay away from the focal plane. The result is a fully Gaussian analytical approximation of the three-dimensional point-spread function of STED erase beams. This allows the derivation of an analytical form for the autocorrelation function of the fluorescence generated by fluorophore diffusion through the STED depletion volume. We verified this form to be correct by performing fluorescence correlation spectroscopy (FCS) experiments in solutions of the dye Alexa Fluor 532. Since the quality of the illumination profile is reflected in the shape of the autocorrelation function, we propose that fluctuation analysis can be used as a tool to assess the quality of STED erase beams.
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Chen X, Xi P. Hundred-thousand light holes push nanoscopy to go parallel. Microsc Res Tech 2014; 78:8-10. [PMID: 25212875 DOI: 10.1002/jemt.22434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 05/14/2014] [Accepted: 08/25/2014] [Indexed: 11/10/2022]
Abstract
With the application of the elements of all major super-resolution techniques including stimulated emission depletion, structure illumination microscopy, and photo-activated localization microscopy, the incoherent crossed standing-wave microscopy achieves parallel super-resolution imaging.
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Affiliation(s)
- Xuanze Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
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Yang X, Tzeng YK, Zhu Z, Huang Z, Chen X, Liu Y, Chang HC, Huang L, Li WD, Xi P. Sub-diffraction imaging of nitrogen-vacancy centers in diamond by stimulated emission depletion and structured illumination. RSC Adv 2014. [DOI: 10.1039/c3ra47240j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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