1
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Power RM, Tschanz A, Zimmermann T, Ries J. Build and operation of a custom 3D, multicolor, single-molecule localization microscope. Nat Protoc 2024:10.1038/s41596-024-00989-x. [PMID: 38702387 DOI: 10.1038/s41596-024-00989-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/19/2024] [Indexed: 05/06/2024]
Abstract
Single-molecule localization microscopy (SMLM) enables imaging scientists to visualize biological structures with unprecedented resolution. Particularly powerful implementations of SMLM are capable of three-dimensional, multicolor and high-throughput imaging and can yield key biological insights. However, widespread access to these technologies is limited, primarily by the cost of commercial options and complexity of de novo development of custom systems. Here we provide a comprehensive guide for interested researchers who wish to establish a high-end, custom-built SMLM setup in their laboratories. We detail the initial configuration and subsequent assembly of the SMLM, including the instructions for the alignment of all the optical pathways, the software and hardware integration, and the operation of the instrument. We describe the validation steps, including the preparation and imaging of test and biological samples with structures of well-defined geometries, and assist the user in troubleshooting and benchmarking the system's performance. Additionally, we provide a walkthrough of the reconstruction of a super-resolved dataset from acquired raw images using the Super-resolution Microscopy Analysis Platform. Depending on the instrument configuration, the cost of the components is in the range US$95,000-180,000, similar to other open-source advanced SMLMs, and substantially lower than the cost of a commercial instrument. A builder with some experience of optical systems is expected to require 4-8 months from the start of the system construction to attain high-quality three-dimensional and multicolor biological images.
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Affiliation(s)
- Rory M Power
- EMBL Imaging Centre, EMBL Heidelberg, Heidelberg, Germany.
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Timo Zimmermann
- EMBL Imaging Centre, EMBL Heidelberg, Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany.
- Max Perutz Labs, Vienna Biocenter Campus, Vienna, Austria.
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Vienna, Austria.
- University of Vienna, Faculty of Physics, Vienna, Austria.
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2
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Nelson T, Vargas-Hernández S, Freire M, Cheng S, Gustavsson AK. Multimodal illumination platform for 3D single-molecule super-resolution imaging throughout mammalian cells. BIOMEDICAL OPTICS EXPRESS 2024; 15:3050-3063. [PMID: 38855669 PMCID: PMC11161355 DOI: 10.1364/boe.521362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 06/11/2024]
Abstract
Single-molecule super-resolution imaging is instrumental in investigating cellular architecture and organization at the nanoscale. Achieving precise 3D nanometric localization when imaging structures throughout mammalian cells, which can be multiple microns thick, requires careful selection of the illumination scheme in order to optimize the fluorescence signal to background ratio (SBR). Thus, an optical platform that combines different wide-field illumination schemes for target-specific SBR optimization would facilitate more precise 3D nanoscale studies of a wide range of cellular structures. Here, we demonstrate a versatile multimodal illumination platform that integrates the sectioning and background reduction capabilities of light sheet illumination with homogeneous, flat-field epi- and TIRF illumination. Using primarily commercially available parts, we combine the fast and convenient switching between illumination modalities with point spread function engineering to enable 3D single-molecule super-resolution imaging throughout mammalian cells. For targets directly at the coverslip, the homogenous intensity profile and excellent sectioning of our flat-field TIRF illumination scheme improves single-molecule data quality by providing low fluorescence background and uniform fluorophore blinking kinetics, fluorescence signal, and localization precision across the entire field of view. The increased contrast achieved with LS illumination, when compared with epi-illumination, makes this illumination modality an excellent alternative when imaging targets that extend throughout the cell. We validate our microscopy platform for improved 3D super-resolution imaging by two-color imaging of paxillin - a protein located in the focal adhesion complex - and actin in human osteosarcoma cells.
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Affiliation(s)
- Tyler Nelson
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
- Applied Physics Program, Rice University, 6100 Main St, Houston, TX 77005, USA
- Smalley-Curl Institute, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, 6100 Main St, Houston, TX 77005, USA
- Institute of Biosciences & Bioengineering, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Margareth Freire
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Siyang Cheng
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
- Applied Physics Program, Rice University, 6100 Main St, Houston, TX 77005, USA
- Smalley-Curl Institute, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
- Smalley-Curl Institute, Rice University, 6100 Main St, Houston, TX 77005, USA
- Institute of Biosciences & Bioengineering, Rice University, 6100 Main St, Houston, TX 77005, USA
- Department of Biosciences, Rice University, 6100 Main St, Houston, TX 77005, USA
- Department of Electrical and Computer Engineering, Rice University, 6100 Main St, Houston, TX 77005, USA
- Center for Nanoscale Imaging Sciences, Rice University, 6100 Main St, Houston, TX 77005, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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3
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Nelson T, Vargas-Hernández S, freire M, Cheng S, Gustavsson AK. Multimodal illumination platform for 3D single-molecule super-resolution imaging throughout mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.08.579549. [PMID: 38405960 PMCID: PMC10888752 DOI: 10.1101/2024.02.08.579549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Single-molecule super-resolution imaging is instrumental for investigating cellular architecture and organization at the nanoscale. Achieving precise 3D nanometric localization when imaging structures throughout mammalian cells, which can be multiple microns thick, requires careful selection of the illumination scheme in order to optimize the fluorescence signal to background ratio (SBR). Thus, an optical platform that combines different wide-field illumination schemes for target-specific SBR optimization would facilitate more precise, 3D nanoscale studies of a wide range of cellular structures. Here we demonstrate a versatile multimodal illumination platform that integrates the sectioning and background reduction capabilities of light sheet illumination with homogeneous, flat-field epi-and TIRF illumination. Using primarily commercially available parts, we combine the fast and convenient switching between illumination modalities with point spread function engineering to enable 3D single-molecule super-resolution imaging throughout mammalian cells. For targets directly at the coverslip, the homogenous intensity profile and excellent sectioning of our flat-field TIRF illumination scheme improves single-molecule data quality by providing low fluorescence background and uniform fluorophore blinking kinetics, fluorescence signal, and localization precision across the entire field of view. The increased contrast achieved with LS illumination, when compared with epi-illumination, makes this illumination modality an excellent alternative when imaging targets that extend throughout the cell. We validate our microscopy platform for improved 3D super-resolution imaging by two-color imaging of paxillin - a protein located in the focal adhesion complex - and actin in human osteosarcoma cells.
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Affiliation(s)
- Tyler Nelson
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
- Applied Physics Program, Rice University, 6100 Main St, Houston, TX 77005, USA
- Smalley-Curl Institute, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, 6100 Main St, Houston, TX 77005, USA
- Institute of Biosciences & Bioengineering, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Margareth freire
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Siyang Cheng
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
- Applied Physics Program, Rice University, 6100 Main St, Houston, TX 77005, USA
- Smalley-Curl Institute, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, 6100 Main St, Houston, TX 77005, USA
- Smalley-Curl Institute, Rice University, 6100 Main St, Houston, TX 77005, USA
- Institute of Biosciences & Bioengineering, Rice University, 6100 Main St, Houston, TX 77005, USA
- Department of Biosciences, Rice University, 6100 Main St, Houston, TX 77005, USA
- Department of Electrical and Computer Engineering, Rice University, 6100 Main St, Houston, TX 77005, USA
- Center for Nanoscale Imaging Sciences, Rice University, 6100 Main St, Houston, TX 77005, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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4
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Stein J, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM, Wu CK. Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.576943. [PMID: 38370628 PMCID: PMC10871237 DOI: 10.1101/2024.02.05.576943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
DNA-PAINT combined with total Internal Reflection Fluorescence (TIRF) microscopy enables the highest localization precisions, down to single nanometers in thin biological samples, due to TIRF's unique method for optical sectioning and attaining high contrast. However, most cellular targets elude the accessible TIRF range close to the cover glass and thus require alternative imaging conditions, affecting resolution and image quality. Here, we address this limitation by applying ultrathin physical cryosectioning in combination with DNA-PAINT. With "tomographic & kinetically-enhanced" DNA-PAINT (tokPAINT), we demonstrate the imaging of nuclear proteins with sub-3 nanometer localization precision, advancing the quantitative study of nuclear organization within fixed cells and mouse tissues at the level of single antibodies. We believe that ultrathin sectioning combined with the versatility and multiplexing capabilities of DNA-PAINT will be a powerful addition to the toolbox of quantitative DNA-based super-resolution microscopy in intracellular structural analyses of proteins, RNA and DNA in situ.
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Affiliation(s)
- Johannes Stein
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maria Ericsson
- Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Michel Nofal
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Lorenzo Magni
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Sarah Aufmkolk
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ryan B. McMillan
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Laura Breimann
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Jens Wohlmann
- Department of Biosciences, University of Oslo, Norway
| | - Laura Arguedas-Jimenez
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Peng Yin
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - George M. Church
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chao-Kng Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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5
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Zakomirnyi VI, Moroz A, Bhargava R, Rasskazov IL. Large Fluorescence Enhancement via Lossless All-Dielectric Spherical Mesocavities. ACS NANO 2024; 18:1621-1628. [PMID: 38157441 PMCID: PMC11064900 DOI: 10.1021/acsnano.3c09777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Nano- and microparticles are popular media to enhance optical signals, including fluorescence from a dye proximal to the particle. Here we show that homogeneous, lossless, all-dielectric spheres with diameters in the mesoscale range, between nano- (≲100 nm) and micro- (≳1 μm) scales, can offer surprisingly large fluorescence enhancements, up to F ∼ 104. With the absence of nonradiative Ohmic losses inherent to plasmonic particles, we show that F can increase, decrease or even stay the same with increasing intrinsic quantum yield q0, for suppressed, enhanced or intact radiative decay rates of a fluorophore, respectively. Further, the fluorophore may be located inside or outside the particle, providing additional flexibility and opportunities to design fit for purpose particles. The presented analysis with simple dielectric spheres should spur further interest in this less-explored scale of particles and experimental investigations to realize their potential for applications in imaging, molecular sensing, light coupling, and quantum information processing.
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Affiliation(s)
- Vadim I Zakomirnyi
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | | | - Rohit Bhargava
- Departments of Bioengineering, Electrical & Computer Engineering, Mechanical Science & Engineering, Chemical and Biomolecular Engineering and Chemistry, Cancer Center at Illinois, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Rames M, Kenison JP, Heineck D, Civitci F, Szczepaniak M, Zheng T, Shangguan J, Zhang Y, Tao K, Esener S, Nan X. Multiplexed and Millimeter-Scale Fluorescence Nanoscopy of Cells and Tissue Sections via Prism-Illumination and Microfluidics-Enhanced DNA-PAINT. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:817-830. [PMID: 38155726 PMCID: PMC10751790 DOI: 10.1021/cbmi.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/24/2023] [Accepted: 08/18/2023] [Indexed: 12/30/2023]
Abstract
Fluorescence nanoscopy has become increasingly powerful for biomedical research, but it has historically afforded a small field-of-view (FOV) of around 50 μm × 50 μm at once and more recently up to ∼200 μm × 200 μm. Efforts to further increase the FOV in fluorescence nanoscopy have thus far relied on the use of fabricated waveguide substrates, adding cost and sample constraints to the applications. Here we report PRism-Illumination and Microfluidics-Enhanced DNA-PAINT (PRIME-PAINT) for multiplexed fluorescence nanoscopy across millimeter-scale FOVs. Built upon the well-established prism-type total internal reflection microscopy, PRIME-PAINT achieves robust single-molecule localization with up to ∼520 μm × 520 μm single FOVs and 25-40 nm lateral resolutions. Through stitching, nanoscopic imaging over mm2 sample areas can be completed in as little as 40 min per target. An on-stage microfluidics chamber facilitates probe exchange for multiplexing and enhances image quality, particularly for formalin-fixed paraffin-embedded (FFPE) tissue sections. We demonstrate the utility of PRIME-PAINT by analyzing ∼106 caveolae structures in ∼1,000 cells and imaging entire pancreatic cancer lesions from patient tissue biopsies. By imaging from nanometers to millimeters with multiplexity and broad sample compatibility, PRIME-PAINT will be useful for building multiscale, Google-Earth-like views of biological systems.
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Affiliation(s)
- Matthew
J. Rames
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - John P. Kenison
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
| | - Daniel Heineck
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Fehmi Civitci
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
| | - Malwina Szczepaniak
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Ting Zheng
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
| | - Julia Shangguan
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Yujia Zhang
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Kai Tao
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Sadik Esener
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
| | - Xiaolin Nan
- Cancer
Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 South Moody Avenue, Portland, Oregon 97201, United States
- Program
in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 South Moody Avenue, Portland, Oregon 97201, United States
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7
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Niederauer C, Nguyen C, Wang-Henderson M, Stein J, Strauss S, Cumberworth A, Stehr F, Jungmann R, Schwille P, Ganzinger KA. Dual-color DNA-PAINT single-particle tracking enables extended studies of membrane protein interactions. Nat Commun 2023; 14:4345. [PMID: 37468504 DOI: 10.1038/s41467-023-40065-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
DNA-PAINT based single-particle tracking (DNA-PAINT-SPT) has recently significantly enhanced observation times in in vitro SPT experiments by overcoming the constraints of fluorophore photobleaching. However, with the reported implementation, only a single target can be imaged and the technique cannot be applied straight to live cell imaging. Here we report on leveraging this technique from a proof-of-principle implementation to a useful tool for the SPT community by introducing simultaneous live cell dual-color DNA-PAINT-SPT for quantifying protein dimerization and tracking proteins in living cell membranes, demonstrating its improved performance over single-dye SPT.
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Affiliation(s)
| | - Chikim Nguyen
- Autonomous Matter Department, AMOLF, Amsterdam, The Netherlands
| | | | - Johannes Stein
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Florian Stehr
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics, Ludwig Maximilian University, Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany
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8
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Stephen Li M, Tanyi Ako R, Sriram S, Fumeaux C, Withayachumnankul W. Terahertz metasurface for near-field beam conversion. OPTICS LETTERS 2023; 48:2202-2205. [PMID: 37058677 DOI: 10.1364/ol.487468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
A uniform illumination over a screen is crucial for terahertz imaging. As such, conversion from a Gaussian beam to a flattop beam becomes necessary. Most of the current beam conversion techniques rely on bulky multi-lens systems for collimated input and operate in the far-field. We present a single metasurface lens to efficiently convert a quasi-Gaussian beam from the near-field region of a WR-3.4 horn antenna to a flattop beam. The design process is divided into three sections to minimize simulation time, and the conventional Gerchberg-Saxton (GS) algorithm is supplemented with the Kirchhoff-Fresnel diffraction equation. Experimental validation confirms that a flattop beam with an efficiency of 80% has been achieved at 275 GHz. Such high-efficiency conversion is desirable for practical terahertz systems and the design approach can be generally used for beam shaping in the near-field.
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9
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Niederauer C, Seynen M, Zomerdijk J, Kamp M, Ganzinger KA. The K2: Open-source simultaneous triple-color TIRF microscope for live-cell and single-molecule imaging. HARDWAREX 2023; 13:e00404. [PMID: 36923558 PMCID: PMC10009532 DOI: 10.1016/j.ohx.2023.e00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Imaging the dynamics and interactions of biomolecules at the single-molecule level in live cells and reconstituted systems has generated unprecedented knowledge about the biomolecular processes underlying many cellular functions. To achieve the speed and sensitivity needed to detect and follow individual molecules, these experiments typically require custom-built microscopes or custom modifications of commercial systems. The costs of such single-molecule microscopes, their technical complexity and the lack of open-source documentation on how to build custom setups therefore limit the accessibility of single-molecule imaging techniques. To advance the adaptation of dynamic single-molecule imaging by a wider community, we present the "K2": an open-source, simultaneous triple-color total internal reflection fluorescence (TIRF) microscope specifically designed for live-cell and single-molecule imaging. We explain our design considerations and provide step-by-step building instructions, parts list and full CAD models. The modular design of this TIRF microscope allows users to customize it to their scientific and financial needs, or to re-use parts of our design to improve the capabilities of their existing setups without necessarily having to build a full copy of the K2 microscope.
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10
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Fazel M, Wester MJ, Schodt DJ, Cruz SR, Strauss S, Schueder F, Schlichthaerle T, Gillette JM, Lidke DS, Rieger B, Jungmann R, Lidke KA. High-precision estimation of emitter positions using Bayesian grouping of localizations. Nat Commun 2022; 13:7152. [PMID: 36418347 PMCID: PMC9684143 DOI: 10.1038/s41467-022-34894-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Single-molecule localization microscopy super-resolution methods rely on stochastic blinking/binding events, which often occur multiple times from each emitter over the course of data acquisition. Typically, the blinking/binding events from each emitter are treated as independent events, without an attempt to assign them to a particular emitter. Here, we describe a Bayesian method of inferring the positions of the tagged molecules by exploring the possible grouping and combination of localizations from multiple blinking/binding events. The results are position estimates of the tagged molecules that have improved localization precision and facilitate nanoscale structural insights. The Bayesian framework uses the localization precisions to learn the statistical distribution of the number of blinking/binding events per emitter and infer the number and position of emitters. We demonstrate the method on a range of synthetic data with various emitter densities, DNA origami constructs and biological structures using DNA-PAINT and dSTORM data. We show that under some experimental conditions it is possible to achieve sub-nanometer precision.
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Affiliation(s)
- Mohamadreza Fazel
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Michael J Wester
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
- Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM, USA
| | - David J Schodt
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Sebastian Restrepo Cruz
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - Sebastian Strauss
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Schueder
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thomas Schlichthaerle
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jennifer M Gillette
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Diane S Lidke
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands
| | - Ralf Jungmann
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA.
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA.
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11
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Koester AM, Szczepaniak M, Nan X. Fast and Multiplexed Super Resolution Imaging of Fixed and Immunostained Cells with DNA-PAINT-ERS. Curr Protoc 2022; 2:e618. [PMID: 36426921 PMCID: PMC9708096 DOI: 10.1002/cpz1.618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Recent advances in super resolution microscopy have enabled imaging at the 10-20 nm scale on a light microscope, providing unprecedented details of native biological structures and processes in intact and hydrated samples. Of the existing strategies, DNA points accumulation in imaging nanoscale topography (DNA-PAINT) affords convenient multiplexing, an important feature in interrogating complex biological systems. A practical limitation of DNA-PAINT, however, has been the slow imaging speed. In its original form, DNA-PAINT imaging of each target takes tens of minutes to hours to complete. To address this challenge, several improved implementations have been introduced. These include DNA-PAINT-ERS (where E = ethylene carbonate; R = repeat sequence; S = spacer), a set of strategies that leads to both accelerated DNA-PAINT imaging speed and improved image quality. With DNA-PAINT-ERS, imaging of typical cellular targets such as microtubules takes only 5-10 min. Importantly, DNA-PAINT-ERS also facilitates multiplexing and can be easily integrated into current workflows for fluorescence staining of biological samples. Here, we provide a detailed, step-by-step guide for fast and multiplexed DNA-PAINT-ERS imaging of fixed and immunostained cells grown on glass substrates as adherent monolayers. The protocol should be readily extended to biological samples of a different format (for example tissue sections) or staining mechanisms (for example using nanobodies). © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of probes for DNA-PAINT-ERS Basic Protocol 2: Sample preparation for imaging membrane targets with DNA-PAINT-ERS in fixed cells Alternate Protocol: Immunostaining of extracted U2OS cells Basic Protocol 3: Super resolution image acquisition and analysis.
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Affiliation(s)
- Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA
| | - Malwina Szczepaniak
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA
| | - Xiaolin Nan
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA
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12
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In vitro assembly, positioning and contraction of a division ring in minimal cells. Nat Commun 2022; 13:6098. [PMID: 36243816 PMCID: PMC9569390 DOI: 10.1038/s41467-022-33679-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/27/2022] [Indexed: 02/07/2023] Open
Abstract
Constructing a minimal machinery for autonomous self-division of synthetic cells is a major goal of bottom-up synthetic biology. One paradigm has been the E. coli divisome, with the MinCDE protein system guiding assembly and positioning of a presumably contractile ring based on FtsZ and its membrane adaptor FtsA. Here, we demonstrate the full in vitro reconstitution of this machinery consisting of five proteins within lipid vesicles, allowing to observe the following sequence of events in real time: 1) Assembly of an isotropic filamentous FtsZ network, 2) its condensation into a ring-like structure, along with pole-to-pole mode selection of Min oscillations resulting in equatorial positioning, and 3) onset of ring constriction, deforming the vesicles from spherical shape. Besides demonstrating these essential features, we highlight the importance of decisive experimental factors, such as macromolecular crowding. Our results provide an exceptional showcase of the emergence of cell division in a minimal system, and may represent a step towards developing a synthetic cell.
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13
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Čavka I, Power RM, Walsh D, Zimmermann T, Köhler S. Super-Resolution Microscopy of the Synaptonemal Complex within the Caenorhabditis elegans Germline. J Vis Exp 2022:10.3791/64363. [PMID: 36190293 PMCID: PMC7614930 DOI: 10.3791/64363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023] Open
Abstract
During meiosis, homologous chromosomes must recognize and adhere to one another to allow for their correct segregation. One of the key events that secures the interaction of homologous chromosomes is the assembly of the synaptonemal complex (SC) in meiotic prophase I. Even though there is little sequence homology between protein components within the SC among different species, the general structure of the SC has been highly conserved during evolution. In electron micrographs, the SC appears as a tripartite, ladder-like structure composed of lateral elements or axes, transverse filaments, and a central element. However, precisely identifying the localization of individual components within the complex by electron microscopy to determine the molecular structure of the SC remains challenging. By contrast, fluorescence microscopy allows for the identification of individual protein components within the complex. However, since the SC is only ~100 nm wide, its substructure cannot be resolved by diffraction-limited conventional fluorescence microscopy. Thus, determining the molecular architecture of the SC requires super-resolution light microscopy techniques such as structured illumination microscopy (SIM), stimulated-emission depletion (STED) microscopy, or single-molecule localization microscopy (SMLM). To maintain the structure and interactions of individual components within the SC, it is important to observe the complex in an environment that is close to its native environment in the germ cells. Therefore, we demonstrate an immunohistochemistry and imaging protocol that enables the study of the substructure of the SC in intact, extruded Caenorhabditis elegans germline tissue with SMLM and STED microscopy. Directly fixing the tissue to the coverslip reduces the movement of the samples during imaging and minimizes aberrations in the sample to achieve the high resolution necessary to visualize the substructure of the SC in its biological context.
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Affiliation(s)
- Ivana Čavka
- Cell Biology and Biophysics, European Molecular Biology Laboratory; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Rory M Power
- EMBL Imaging Centre, European Molecular Biology Laboratory
| | - Dietrich Walsh
- EMBL Imaging Centre, European Molecular Biology Laboratory
| | - Timo Zimmermann
- Cell Biology and Biophysics, European Molecular Biology Laboratory; EMBL Imaging Centre, European Molecular Biology Laboratory;
| | - Simone Köhler
- Cell Biology and Biophysics, European Molecular Biology Laboratory;
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14
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Hung ST, Cnossen J, Fan D, Siemons M, Jurriens D, Grußmayer K, Soloviev O, Kapitein LC, Smith CS. SOLEIL: single-objective lens inclined light sheet localization microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:3275-3294. [PMID: 35781973 PMCID: PMC9208595 DOI: 10.1364/boe.451634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
High-NA light sheet illumination can improve the resolution of single-molecule localization microscopy (SMLM) by reducing the background fluorescence. These approaches currently require custom-made sample holders or additional specialized objectives, which makes the sample mounting or the optical system complex and therefore reduces the usability of these approaches. Here, we developed a single-objective lens-inclined light sheet microscope (SOLEIL) that is capable of 2D and 3D SMLM in thick samples. SOLEIL combines oblique illumination with point spread function PSF engineering to enable dSTORM imaging in a wide variety of samples. SOLEIL is compatible with standard sample holders and off-the-shelve optics and standard high NA objectives. To accomplish optimal optical sectioning we show that there is an ideal oblique angle and sheet thickness. Furthermore, to show what optical sectioning delivers for SMLM we benchmark SOLEIL against widefield and HILO microscopy with several biological samples. SOLEIL delivers in 15 μm thick Caco2-BBE cells a 374% higher intensity to background ratio and a 54% improvement in the estimated CRLB compared to widefield illumination, and a 184% higher intensity to background ratio and a 20% improvement in the estimated CRLB compared to HILO illumination.
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Affiliation(s)
- Shih-Te Hung
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Jelmer Cnossen
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Daniel Fan
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Marijn Siemons
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Kristin Grußmayer
- Department of Bionanoscience and Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Oleg Soloviev
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Flexible Optical B.V., Polakweg 10-11, 2288 GG Rijswijk, Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Carlas S. Smith
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
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15
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Jabermoradi A, Yang S, Gobes MI, van Duynhoven JPM, Hohlbein J. Enabling single-molecule localization microscopy in turbid food emulsions. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A: MATHEMATICAL, PHYSICAL AND ENGINEERING SCIENCES 2022; 380:20200164. [PMID: 0 DOI: 10.1098/rsta.2020.0164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 08/20/2021] [Indexed: 05/19/2023]
Abstract
Turbidity poses a major challenge for the microscopic characterization of food systems. Local mismatches in refractive indices, for example, lead to significant image deterioration along sample depth. To mitigate the issue of turbidity and to increase the accessible optical resolution in food microscopy, we added adaptive optics (AO) and flat-field illumination to our previously published open microscopy framework, the miCube. In the detection path, we implemented AO via a deformable mirror to compensate aberrations and to modulate the emission wavefront enabling the engineering of point spread functions (PSFs) for single-molecule localization microscopy (SMLM) in three dimensions. As a model system for a non-transparent food colloid such as mayonnaise, we designed an oil-in-water emulsion containing the ferric ion binding protein phosvitin commonly present in egg yolk. We targeted phosvitin with fluorescently labelled primary antibodies and used PSF engineering to obtain two- and three-dimensional images of phosvitin covered oil droplets with sub 100 nm resolution. Our data indicated that phosvitin is homogeneously distributed at the interface. With the possibility to obtain super-resolved images in depth, our work paves the way for localizing biomacromolecules at heterogeneous colloidal interfaces in food emulsions.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
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Affiliation(s)
- Abbas Jabermoradi
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
| | - Suyeon Yang
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
| | - Martijn I. Gobes
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
| | - John P. M. van Duynhoven
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
- Unilever Global Foods Innovation Centre, Bronland 14, Wageningen 6708, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
- Microspectroscopy Research Facility, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
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16
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Lam JY, Wu Y, Dimou E, Zhang Z, Cheetham MR, Körbel M, Xia Z, Klenerman D, Danial JS. An economic, square-shaped flat-field illumination module for TIRF-based super-resolution microscopy. BIOPHYSICAL REPORTS 2022; 2:None. [PMID: 35299715 PMCID: PMC8914601 DOI: 10.1016/j.bpr.2022.100044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Super-resolution microscopy allows complex biological assemblies to be observed with remarkable resolution. However, the presence of uneven Gaussian-shaped illumination hinders its use in quantitative imaging or high-throughput assays. Methods developed to circumvent this problem are often expensive, hard to implement, or not applicable to total internal reflection fluorescence imaging. We herein demonstrate a cost-effective method to overcome these challenges using a small square-core multimodal optical fiber as the coupler. We characterize our method with synthetic, recombinant, and cellular systems imaged under total internal reflection fluorescence and highly inclined and laminated optical sheet illuminations to demonstrate its ability to produce highly uniform images under all conditions.
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Affiliation(s)
- Jeff Y.L. Lam
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, United Kingdom
| | - Yunzhao Wu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, United Kingdom
| | - Eleni Dimou
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, United Kingdom
| | - Ziwei Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Matthew R. Cheetham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, United Kingdom
| | - Markus Körbel
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Zengjie Xia
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, United Kingdom
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, United Kingdom
| | - John S.H. Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, United Kingdom
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17
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Abstract
Super-resolution microscopy techniques, and specifically single-molecule localization microscopy (SMLM), are approaching nanometer resolution inside cells and thus have great potential to complement structural biology techniques such as electron microscopy for structural cell biology. In this review, we introduce the different flavors of super-resolution microscopy, with a special emphasis on SMLM and MINFLUX (minimal photon flux). We summarize recent technical developments that pushed these localization-based techniques to structural scales and review the experimental conditions that are key to obtaining data of the highest quality. Furthermore, we give an overview of different analysis methods and highlight studies that used SMLM to gain structural insights into biologically relevant molecular machines. Ultimately, we give our perspective on what is needed to push the resolution of these techniques even further and to apply them to investigating dynamic structural rearrangements in living cells. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Sheng Liu
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
| | - Philipp Hoess
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
| | - Jonas Ries
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
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18
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Qutbuddin Y, Krohn JH, Brüggenthies GA, Stein J, Gavrilovic S, Stehr F, Schwille P. Design Features to Accelerate the Higher-Order Assembly of DNA Origami on Membranes. J Phys Chem B 2021; 125:13181-13191. [PMID: 34818013 PMCID: PMC8667037 DOI: 10.1021/acs.jpcb.1c07694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanotechnology often exploits DNA origami nanostructures assembled into even larger superstructures up to micrometer sizes with nanometer shape precision. However, large-scale assembly of such structures is very time-consuming. Here, we investigated the efficiency of superstructure assembly on surfaces using indirect cross-linking through low-complexity connector strands binding staple strand extensions, instead of connector strands binding to scaffold loops. Using single-molecule imaging techniques, including fluorescence microscopy and atomic force microscopy, we show that low sequence complexity connector strands allow formation of DNA origami superstructures on lipid membranes, with an order-of-magnitude enhancement in the assembly speed of superstructures. A number of effects, including suppression of DNA hairpin formation, high local effective binding site concentration, and multivalency are proposed to contribute to the acceleration. Thus, the use of low-complexity sequences for DNA origami higher-order assembly offers a very simple but efficient way of improving throughput in DNA origami design.
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Affiliation(s)
- Yusuf Qutbuddin
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Jan-Hagen Krohn
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.,Exzellenzcluster ORIGINS, Boltzmannstrasse 2, D-85748 Garching, Germany
| | - Gereon A Brüggenthies
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Johannes Stein
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Svetozar Gavrilovic
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Florian Stehr
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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19
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Stein J, Stehr F, Jungmann R, Schwille P. Calibration-free counting of low molecular copy numbers in single DNA-PAINT localization clusters. BIOPHYSICAL REPORTS 2021; 1:100032. [PMID: 36425461 PMCID: PMC9680712 DOI: 10.1016/j.bpr.2021.100032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 06/16/2023]
Abstract
Single-molecule localization microscopy (SMLM) has revolutionized light microscopy by enabling optical resolution down to a few nanometer. Yet, localization precision commonly does not suffice to visually resolve single subunits in molecular assemblies or multimeric complexes. Because each targeted molecule contributes localizations during image acquisition, molecular counting approaches to reveal the target copy numbers within localization clusters have been persistently proposed since the early days of SMLM, most of which rely on preliminary knowledge of the dye photophysics or on a calibration to a reference. Previously, we developed localization-based fluorescence correlation spectroscopy (lbFCS) as an absolute ensemble counting approach for the SMLM-variant DNA-PAINT (points accumulation for imaging in nanoscale topography), for the first time, to our knowledge, circumventing the necessity for reference calibrations. Here, we present an extended concept termed lbFCS+, which allows absolute counting of copy numbers for individual localization clusters in a single DNA-PAINT image. In lbFCS+, absolute counting of fluorescent loci contained in individual nanoscopic volumes is achieved via precise measurement of the local hybridization rates of the fluorescently labeled oligonucleotides ("imagers") employed in DNA-PAINT imaging. In proof-of-principle experiments on DNA origami nanostructures, we demonstrate the ability of lbFCS+ to truthfully determine molecular copy numbers and imager association and dissociation rates in well-separated localization clusters containing up to 10 docking strands. For N ≤ 4 target molecules, lbFCS+ is even able to resolve integers, providing the potential to study the composition of up to tetrameric molecular complexes. Furthermore, we show that lbFCS+ allows resolving heterogeneous binding dynamics, enabling the distinction of stochastically generated and a priori indistinguishable DNA assemblies. Beyond advancing quantitative DNA-PAINT imaging, we believe that lbFCS+ could find promising applications ranging from biosensing to DNA computing.
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Affiliation(s)
- Johannes Stein
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Stehr
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics, Ludwig Maximilian University, Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany
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20
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Masullo LA, Szalai AM, Lopez LF, Stefani FD. Fluorescence nanoscopy at the sub-10 nm scale. Biophys Rev 2021; 13:1101-1112. [PMID: 35059030 PMCID: PMC8724505 DOI: 10.1007/s12551-021-00864-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
Fluorescence nanoscopy represented a breakthrough for the life sciences as it delivers 20-30 nm resolution using far-field fluorescence microscopes. This resolution limit is not fundamental but imposed by the limited photostability of fluorophores under ambient conditions. This has motivated the development of a second generation of fluorescence nanoscopy methods that aim to deliver sub-10 nm resolution, reaching the typical size of structural proteins and thus providing true molecular resolution. In this review, we present common fundamental aspects of these nanoscopies, discuss the key experimental factors that are necessary to fully exploit their capabilities, and discuss their current and future challenges.
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Affiliation(s)
- Luciano A. Masullo
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Alan M. Szalai
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucía F. Lopez
- Departamento de Física, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando D. Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
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21
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Herdly L, Janin P, Bauer R, van de Linde S. Tunable Wide-Field Illumination and Single-Molecule Photoswitching with a Single MEMS Mirror. ACS PHOTONICS 2021; 8:2728-2736. [PMID: 34553004 PMCID: PMC8447260 DOI: 10.1021/acsphotonics.1c00843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Homogeneous illumination in single-molecule localization microscopy (SMLM) is key for the quantitative analysis of super-resolution images. Therefore, different approaches for flat-field illumination have been introduced as alternative to the conventional Gaussian illumination. Here, we introduce a single microelectromechanical systems (MEMS) mirror as a tunable and cost-effective device for adapting wide-field illumination in SMLM. In flat-field mode the MEMS allowed for consistent SMLM metrics across the entire field of view. Employing single-molecule photoswitching, we developed a simple yet powerful routine to benchmark different illumination schemes on the basis of local emitter brightness and ON-state lifetime. Moreover, we propose that tuning the MEMS beyond optimal flat-field conditions enables to study the kinetics of photoswitchable fluorophores within a single acquisition.
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Affiliation(s)
- Lucas Herdly
- Department
of Physics, SUPA, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Paul Janin
- Department
of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Ralf Bauer
- Department
of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, Scotland, United Kingdom
| | - Sebastian van de Linde
- Department
of Physics, SUPA, University of Strathclyde, Glasgow, Scotland, United Kingdom
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22
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Xue B, Zhou C, Qin Y, Li Y, Sun Y, Chang L, Shao S, Li Y, Zhang M, Sun C, He R, Peter Su Q, Sun Y. PN-ImTLSM facilitates high-throughput low background single-molecule localization microscopy deep in the cell. BIOPHYSICS REPORTS 2021; 7:313-325. [PMID: 37287761 PMCID: PMC10233473 DOI: 10.52601/bpr.2021.210014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/15/2021] [Indexed: 06/09/2023] Open
Abstract
When imaging the nucleus structure of a cell, the out-of-focus fluorescence acts as background and hinders the detection of weak signals. Light-sheet fluorescence microscopy (LSFM) is a wide-field imaging approach which has the best of both background removal and imaging speed. However, the commonly adopted orthogonal excitation/detection scheme is hard to be applied to single-cell imaging due to steric hindrance. For LSFMs capable of high spatiotemporal single-cell imaging, the complex instrument design and operation largely limit their throughput of data collection. Here, we propose an approach for high-throughput background-free fluorescence imaging of single cells facilitated by the Immersion Tilted Light Sheet Microscopy (ImTLSM). ImTLSM is based on a light-sheet projected off the optical axis of a water immersion objective. With the illumination objective and the detection objective placed opposingly, ImTLSM can rapidly patrol and optically section multiple individual cells while maintaining single-molecule detection sensitivity and resolution. Further, the simplicity and robustness of ImTLSM in operation and maintenance enables high-throughput image collection to establish background removal datasets for deep learning. Using a deep learning model to train the mapping from epi-illumination images to ImTLSM illumination images, namely PN-ImTLSM, we demonstrated cross-modality fluorescence imaging, transforming the epi-illumination image to approach the background removal performance obtained with ImTLSM. We demonstrated that PN-ImTLSM can be generalized to large-field homogeneous illumination imaging, thereby further improving the imaging throughput. In addition, compared to commonly used background removal methods, PN-ImTLSM showed much better performance for areas where the background intensity changes sharply in space, facilitating high-density single-molecule localization microscopy. In summary, PN-ImTLSM paves the way for background-free fluorescence imaging on ordinary inverted microscopes.
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Affiliation(s)
- Boxin Xue
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Caiwei Zhou
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yizhi Qin
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yongzheng Li
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yuao Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Lei Chang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Shipeng Shao
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- Beijing Institute of Heart Lung and Blood Vessel Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Yongliang Li
- Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Chaoying Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Renxi He
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Qian Peter Su
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- School of Future Technology, Peking University, Beijing 100871, China
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23
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Tyson J, Hu K, Zheng S, Kidd P, Dadina N, Chu L, Toomre D, Bewersdorf J, Schepartz A. Extremely Bright, Near-IR Emitting Spontaneously Blinking Fluorophores Enable Ratiometric Multicolor Nanoscopy in Live Cells. ACS CENTRAL SCIENCE 2021; 7:1419-1426. [PMID: 34471685 PMCID: PMC8393207 DOI: 10.1021/acscentsci.1c00670] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 05/16/2023]
Abstract
New bright, photostable, emission-orthogonal fluorophores that blink without toxic additives are needed to enable multicolor, live-cell, single-molecule localization microscopy (SMLM). Here we report the design, synthesis, and biological evaluation of Yale676sb, a photostable, near-IR-emitting fluorophore that achieves these goals in the context of an exceptional quantum yield (0.59). When used alongside HMSiR, Yale676sb enables simultaneous, live-cell, two-color SMLM of two intracellular organelles (ER + mitochondria) with only a single laser and no chemical additives.
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Affiliation(s)
- Jonathan Tyson
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Kevin Hu
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Department
of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Shuai Zheng
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Phylicia Kidd
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
| | - Neville Dadina
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ling Chu
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Derek Toomre
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Nanobiology
Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Joerg Bewersdorf
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Department
of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
- Kavli
Institute for Neuroscience, Yale School
of Medicine, New Haven, Connecticut 06510, United States
- Nanobiology
Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Alanna Schepartz
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States
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24
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Shetty RM, Brady SR, Rothemund PWK, Hariadi RF, Gopinath A. Bench-Top Fabrication of Single-Molecule Nanoarrays by DNA Origami Placement. ACS NANO 2021; 15:11441-11450. [PMID: 34228915 PMCID: PMC9701110 DOI: 10.1021/acsnano.1c01150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Large-scale nanoarrays of single biomolecules enable high-throughput assays while unmasking the underlying heterogeneity within ensemble populations. Until recently, creating such grids which combine the advantages of microarrays and single-molecule experiments (SMEs) has been particularly challenging due to the mismatch between the size of these molecules and the resolution of top-down fabrication techniques. DNA origami placement (DOP) combines two powerful techniques to address this issue: (i) DNA origami, which provides a ∼100 nm self-assembled template for single-molecule organization with 5 nm resolution and (ii) top-down lithography, which patterns these DNA nanostructures, transforming them into functional nanodevices via large-scale integration with arbitrary substrates. Presently, this technique relies on state-of-the-art infrastructure and highly trained personnel, making it prohibitively expensive for researchers. Here, we introduce a cleanroom-free, $1 benchtop technique to create meso-to-macro-scale DNA origami nanoarrays using self-assembled colloidal nanoparticles, thereby circumventing the need for top-down fabrication. We report a maximum yield of 74%, 2-fold higher than the statistical limit of 37% imposed on non-specific molecular loading alternatives. Furthermore, we provide a proof-of-principle for the ability of this nanoarray platform to transform traditionally low-throughput, stochastic, single-molecule assays into high-throughput, deterministic ones, without compromising data quality. Our approach has the potential to democratize single-molecule nanoarrays and demonstrates their utility as a tool for biophysical assays and diagnostics.
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Affiliation(s)
- Rishabh M. Shetty
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, Arizona 85287, United States; School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sarah R. Brady
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, Arizona 85287, United States
| | - Paul W. K. Rothemund
- Department of Bioengineering, Computational and Mathematical Sciences, and Computation and Neural Systems, California Institute of Technology, Pasadena, California 91125, United States
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25
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Vladimirova YV, Zadkov VN. Quantum Optics in Nanostructures. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1919. [PMID: 34443750 PMCID: PMC8398959 DOI: 10.3390/nano11081919] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 01/27/2023]
Abstract
This review is devoted to the study of effects of quantum optics in nanostructures. The mechanisms by which the rates of radiative and nonradiative decay are modified are considered in the model of a two-level quantum emitter (QE) near a plasmonic nanoparticle (NP). The distributions of the intensity and polarization of the near field around an NP are analyzed, which substantially depend on the polarization of the external field and parameters of plasmon resonances of the NP. The effects of quantum optics in the system NP + QE plus external laser field are analyzed-modification of the resonance fluorescence spectrum of a QE in the near field, bunching/antibunching phenomena, quantum statistics of photons in the spectrum, formation of squeezed states of light, and quantum entangled states in these systems.
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Affiliation(s)
- Yulia V. Vladimirova
- Department of Physics and Quantum Technology Centre, Lomonosov Moscow State University, 119991 Moscow, Russia
- Faculty of Physics, Higher School of Economics, Old Basmannya 21/4, 105066 Moscow, Russia;
| | - Victor N. Zadkov
- Faculty of Physics, Higher School of Economics, Old Basmannya 21/4, 105066 Moscow, Russia;
- Institute of Spectroscopy of the Russian Academy of Sciences, Fizicheskaya Str. 5, Troitsk, 108840 Moscow, Russia
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26
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Tracking single particles for hours via continuous DNA-mediated fluorophore exchange. Nat Commun 2021; 12:4432. [PMID: 34290254 PMCID: PMC8295357 DOI: 10.1038/s41467-021-24223-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/07/2021] [Indexed: 01/13/2023] Open
Abstract
Monitoring biomolecules in single-particle tracking experiments is typically achieved by employing fixed organic dyes or fluorescent fusion proteins linked to a target of interest. However, photobleaching typically limits observation times to merely a few seconds, restricting downstream statistical analysis and observation of rare biological events. Here, we overcome this inherent limitation via continuous fluorophore exchange using DNA-PAINT, where fluorescently-labeled oligonucleotides reversibly bind to a single-stranded DNA handle attached to the target molecule. Such versatile and facile labeling allows uninterrupted monitoring of single molecules for extended durations. We demonstrate the power of our approach by observing DNA origami on membranes for tens of minutes, providing perspectives for investigating cellular processes on physiologically relevant timescales. The length of single-particle tracking experiments are limited due to photobleaching. Here the authors achieve long-term single-particle tracking with continuous fluorophore exchange in DNA-PAINT and use this to observe DNA origami on lipid bilayers for tens of minutes.
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27
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Berry K, Taormina M, Maltzer Z, Turner K, Gorham M, Nguyen T, Serafin R, Nicovich PR. Characterization of a fiber-coupled EvenField illumination system for fluorescence microscopy. OPTICS EXPRESS 2021; 29:24349-24362. [PMID: 34614682 DOI: 10.1364/oe.430440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Fluorescence microscopy benefits from spatially and temporally homogeneous illumination with the illumination area matched to the shape and size of the camera sensor. Fiber-coupled illumination schemes have the added benefit of straightforward and robust alignment and ease of installation compared to free-space coupled illumination. Commercial and open-source fiber-coupled, homogenized illumination schemes have recently become available to the public; however, there have been no published comparisons of speckle reduction schemes to date. We characterize three different multimode fibers in combination with two laser speckle reduction devices and compare spatial and temporal profiles to a commercial unit. This work yields a new design, the EvenField Illuminator, which is freely available for researchers to integrate into their own imaging systems.
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28
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Van den Eynde R, Vandenberg W, Hugelier S, Bouwens A, Hofkens J, Müller M, Dedecker P. Self-contained and modular structured illumination microscope. BIOMEDICAL OPTICS EXPRESS 2021; 12:4414-4422. [PMID: 34457422 PMCID: PMC8367227 DOI: 10.1364/boe.423492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 06/13/2023]
Abstract
We present a modular implementation of structured illumination microscopy (SIM) that is fast, largely self-contained and that can be added onto existing fluorescence microscopes. Our strategy, which we call HIT-SIM, can theoretically deliver well over 50 super-resolved images per second and is readily compatible with existing acquisition software packages. We provide a full technical package consisting of schematics, a list of components and an alignment scheme that provides detailed specifications and assembly instructions. We illustrate the performance of the instrument by imaging optically large samples containing sequence-specifically stained DNA fragments.
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Affiliation(s)
| | - Wim Vandenberg
- Lab for Nanobiology, Department of Chemistry, KU Leuven, Belgium
| | - Siewert Hugelier
- Lab for Nanobiology, Department of Chemistry, KU Leuven, Belgium
| | - Arno Bouwens
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Belgium
- Perseus Biomics BV, Tienen, Belgium
| | - Johan Hofkens
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Belgium
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Marcel Müller
- Lab for Nanobiology, Department of Chemistry, KU Leuven, Belgium
- Present adress: Faculty of Physics, Bielefeld University, Germany
| | - Peter Dedecker
- Lab for Nanobiology, Department of Chemistry, KU Leuven, Belgium
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29
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Danial JSH, Klenerman D. Single molecule imaging of protein aggregation in Dementia: Methods, insights and prospects. Neurobiol Dis 2021; 153:105327. [PMID: 33705938 PMCID: PMC8039184 DOI: 10.1016/j.nbd.2021.105327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/21/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
The aggregation of misfolded proteins is a fundamental pathology in neurodegeneration which remains poorly understood due to its exceptional complexity and lack of appropriate characterization tools that can probe the role of the low concentrations of heterogeneous protein aggregates formed during the progression of the disease. In this review, we explain the principles underlying the operation of single molecule microscopy, an imaging method that can resolve molecules one-by-one, its application to imaging and characterizing individual protein aggregates in human samples and in vitro as well as the important questions in neurobiology this has answered and can answer.
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Affiliation(s)
- John S H Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom.
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom.
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30
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Mau A, Friedl K, Leterrier C, Bourg N, Lévêque-Fort S. Fast widefield scan provides tunable and uniform illumination optimizing super-resolution microscopy on large fields. Nat Commun 2021; 12:3077. [PMID: 34031402 PMCID: PMC8144377 DOI: 10.1038/s41467-021-23405-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
Non-uniform illumination limits quantitative analyses of fluorescence imaging techniques. In particular, single molecule localization microscopy (SMLM) relies on high irradiances, but conventional Gaussian-shaped laser illumination restricts the usable field of view to around 40 µm × 40 µm. We present Adaptable Scanning for Tunable Excitation Regions (ASTER), a versatile illumination technique that generates uniform and adaptable illumination. ASTER is also highly compatible with optical sectioning techniques such as total internal reflection fluorescence (TIRF). For SMLM, ASTER delivers homogeneous blinking kinetics at reasonable laser power over fields-of-view up to 200 µm × 200 µm. We demonstrate that ASTER improves clustering analysis and nanoscopic size measurements by imaging nanorulers, microtubules and clathrin-coated pits in COS-7 cells, and β2-spectrin in neurons. ASTER's sharp and quantitative illumination paves the way for high-throughput quantification of biological structures and processes in classical and super-resolution fluorescence microscopies.
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Affiliation(s)
- Adrien Mau
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, Orsay, France
- Abbelight, Cachan, France
| | - Karoline Friedl
- Abbelight, Cachan, France
- Aix-Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | | | | | - Sandrine Lévêque-Fort
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, Orsay, France.
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31
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Cheng X, Yin W. Probing Biosensing Interfaces With Single Molecule Localization Microscopy (SMLM). Front Chem 2021; 9:655324. [PMID: 33996750 PMCID: PMC8117217 DOI: 10.3389/fchem.2021.655324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/16/2021] [Indexed: 11/23/2022] Open
Abstract
Far field single molecule localization microscopy (SMLM) has been established as a powerful tool to study biological structures with resolution far below the diffraction limit of conventional light microscopy. In recent years, the applications of SMLM have reached beyond traditional cellular imaging. Nanostructured interfaces are enriched with information that determines their function, playing key roles in applications such as chemical catalysis and biological sensing. SMLM enables detailed study of interfaces at an individual molecular level, allowing measurements of reaction kinetics, and detection of rare events not accessible to ensemble measurements. This paper provides an update to the progress made to the use of SMLM in characterizing nanostructured biointerfaces, focusing on practical aspects, recent advances, and emerging opportunities from an analytical chemistry perspective.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory for Modern Optical Instrumentations, National Engineering Research Center of Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Wei Yin
- Core Facilities, School of Medicine, Zhejiang University, Hangzhou, China
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32
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DNA hybridisation kinetics using single-molecule fluorescence imaging. Essays Biochem 2021; 65:27-36. [PMID: 33491734 PMCID: PMC8056036 DOI: 10.1042/ebc20200040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023]
Abstract
Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about the process which are still unknown. Prior to the invention of single-molecule microscopy, DNA hybridisation experiments were conducted at the ensemble level, and thus it was impossible to directly observe individual hybridisation events and understand fully the kinetics of DNA hybridisation. In this mini-review, recent single-molecule fluorescence-based studies of DNA hybridisation are discussed, particularly for short nucleic acids, to gain more insight into the kinetics of DNA hybridisation. As well as looking at single-molecule studies of intrinsic and extrinsic factors affecting DNA hybridisation kinetics, the influence of the methods used to detect hybridisation of single DNAs is considered. Understanding the kinetics of DNA hybridisation not only gives insight into an important biological process but also allows for further advancements in the growing field of nucleic acid biotechnology.
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33
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Hummert J, Tashev SA, Herten DP. An update on molecular counting in fluorescence microscopy. Int J Biochem Cell Biol 2021; 135:105978. [PMID: 33865985 DOI: 10.1016/j.biocel.2021.105978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/14/2021] [Accepted: 04/08/2021] [Indexed: 01/18/2023]
Abstract
Quantitative assessment of protein complexes, such as receptor clusters in the context of cellular signalling, has become a pressing objective in cell biology. The advancements in the field of single molecule fluorescence microscopy have led to different approaches for counting protein copy numbers in various cellular structures. This has resulted in an increasing interest in robust calibration protocols addressing photophysical properties of fluorescent labels and the effect of labelling efficiencies. Here, we want to give an update on recent methods for protein counting with a focus on novel calibration protocols. In this context, we discuss different types of calibration samples and identify some of the challenges arising in molecular counting experiments. Some recently published applications offer potential approaches to tackle these challenges.
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Affiliation(s)
- Johan Hummert
- College of Medical and Dental Sciences & School of Chemistry, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, UK
| | - Stanimir Asenov Tashev
- College of Medical and Dental Sciences & School of Chemistry, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, UK
| | - Dirk-Peter Herten
- College of Medical and Dental Sciences & School of Chemistry, University of Birmingham, Birmingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, UK.
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34
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Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 253] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
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Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
- ;
;
;
;
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
- ;
;
;
;
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
- ;
;
;
;
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- ;
;
;
;
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
- ;
;
;
;
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35
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Wang Q, Chen X, Li X, Song D, Yang J, Yu H, Li Z. 2'-Fluoroarabinonucleic Acid Nanostructures as Stable Carriers for Cellular Delivery in the Strongly Acidic Environment. ACS APPLIED MATERIALS & INTERFACES 2020; 12:53592-53597. [PMID: 33206496 DOI: 10.1021/acsami.0c11684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA nanotechnology is powerful in constructing programmable nanostructures with distinct dimensions, sizes, and shapes. However, natural DNA molecules are prone to nuclease degradation, thus limiting the in vivo applications of such DNA nanostructures. 2'-Fluoroarabinonucleic acid (FANA) is a chemically modified oligonucleotide with similar base pairing properties to DNA and exhibits superior physical and chemical stabilities. In this work, FANA molecules were used to construct double crossover nanostructures, and it was demonstrated that incorporation of FANA conferred nucleic acid nanostructures with increased thermal stability and stronger nuclease resistance. More importantly, FANA nanostructures were able to maintain the structural integrity in the strongly acidic environment (pH 1.2). Last, such FANA nanostructures functioned well in acting as stable carriers of small-molecule cargoes for cellular delivery in simulated gastric fluid, while the DNA counterparts were mostly degraded. Collectively, these results demonstrated that FANA self-assembly was not only a substantial complement to the structural DNA nanotechnology but also an appealing molecular tool for in vivo biomedical applications.
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Affiliation(s)
- Qian Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaoxing Chen
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xintong Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, Jiangsu 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, Jiangsu 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jintao Yang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, Jiangsu 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hanyang Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, Jiangsu 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zhe Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, China
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36
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Lee S, Batjikh I, Kang SH. Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy. SENSORS (BASEL, SWITZERLAND) 2020; 20:E6667. [PMID: 33233370 PMCID: PMC7700606 DOI: 10.3390/s20226667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/14/2020] [Accepted: 11/20/2020] [Indexed: 12/27/2022]
Abstract
The natural characteristics of deoxyribonucleic acid (DNA) enable its advanced applications in nanotechnology as a special tool that can be detected by high-resolution imaging with precise localization. Super-resolution (SR) microscopy enables the examination of nanoscale molecules beyond the diffraction limit. With the development of SR microscopy methods, DNA nanostructures can now be optically assessed. Using the specific binding of fluorophores with their target molecules, advanced single-molecule localization microscopy (SMLM) has been expanded into different fields, allowing wide-range detection at the single-molecule level. This review discusses the recent progress in the SR imaging of DNA nano-objects using SMLM techniques, such as direct stochastic optical reconstruction microscopy, binding-activated localization microscopy, and point accumulation for imaging nanoscale topography. Furthermore, we discuss their advantages and limitations, present applications, and future perspectives.
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Affiliation(s)
| | | | - Seong Ho Kang
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Korea; (S.L.); (I.B.)
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37
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Schueder F, Unterauer EM, Ganji M, Jungmann R. DNA-Barcoded Fluorescence Microscopy for Spatial Omics. Proteomics 2020; 20:e1900368. [PMID: 33030780 DOI: 10.1002/pmic.201900368] [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: 04/14/2020] [Revised: 07/24/2020] [Indexed: 12/18/2022]
Abstract
Innovation in genomics, transcriptomics, and proteomics research has created a plethora of state-of-the-art techniques such as nucleic acid sequencing and mass-spectrometry-based proteomics with paramount impact in the life sciences. While current approaches yield quantitative abundance analysis of biomolecules on an almost routine basis, coupling this high content to spatial information in a single cell and tissue context is challenging. Here, current implementations of spatial omics are discussed and recent developments in the field of DNA-barcoded fluorescence microscopy are reviewed. Light is shed on the potential of DNA-based imaging techniques to provide a comprehensive toolbox for spatial genomics and transcriptomics and discuss current challenges, which need to be overcome on the way to spatial proteomics using high-resolution fluorescence microscopy.
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Affiliation(s)
- Florian Schueder
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Eduard M Unterauer
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Mahipal Ganji
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Ralf Jungmann
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
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38
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Civitci F, Shangguan J, Zheng T, Tao K, Rames M, Kenison J, Zhang Y, Wu L, Phelps C, Esener S, Nan X. Fast and multiplexed superresolution imaging with DNA-PAINT-ERS. Nat Commun 2020; 11:4339. [PMID: 32859909 PMCID: PMC7455722 DOI: 10.1038/s41467-020-18181-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) facilitates multiplexing in superresolution microscopy but is practically limited by slow imaging speed. To address this issue, we propose the additions of ethylene carbonate (EC) to the imaging buffer, sequence repeats to the docking strand, and a spacer between the docking strand and the affinity agent. Collectively termed DNA-PAINT-ERS (E = EC, R = Repeating sequence, and S = Spacer), these strategies can be easily integrated into current DNA-PAINT workflows for both accelerated imaging speed and improved image quality through optimized DNA hybridization kinetics and efficiency. We demonstrate the general applicability of DNA-PAINT-ERS for fast, multiplexed superresolution imaging using previously validated oligonucleotide constructs with slight modifications.
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Affiliation(s)
- Fehmi Civitci
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Julia Shangguan
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Ting Zheng
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Kai Tao
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Matthew Rames
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - John Kenison
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
| | - Ying Zhang
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Lei Wu
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA
- Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Rd., Wuhan, 430079, Hubei, China
| | - Carey Phelps
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Sadik Esener
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA
| | - Xiaolin Nan
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S. Moody Ave., Portland, OR, 97201, USA.
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, 2730 S. Moody Ave., Portland, OR, 97201, USA.
- Department of Biomedical Engineering, Oregon Health and Science University, 3303 S. Bond Ave., Portland, OR, 97239, USA.
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39
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Ibrahim KA, Mahecic D, Manley S. Characterization of flat-fielding systems for quantitative microscopy. OPTICS EXPRESS 2020; 28:22036-22048. [PMID: 32752472 DOI: 10.1364/oe.395900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Optical flat-fielding systems, such as field-mapping or integration-based beam shapers, are used to transform nonuniform illumination into uniform illumination. Thus, flat-fielding paves the way for imaging that is independent of position within a field of view and enables more quantitative analysis. Here, we characterize and compare three systems for homogenizing both widefield and multifocal illumination. Our analysis includes two refractive field-mapping beam shapers: PiShaper and TopShape, as well as one integration-based: Köhler integrator. The comparison is based on figures of merit including ISO-standard values, such as the plateau uniformity and edge steepness, transmission efficiency, stability of the beams along propagation and multifocal intensity, pitch, and point width. By characterizing and comparing existing beam shapers, we facilitate the choice of the appropriate flat-fielding solution and increase their accessibility for different applications.
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40
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Xu F, Ma D, MacPherson KP, Liu S, Bu Y, Wang Y, Tang Y, Bi C, Kwok T, Chubykin AA, Yin P, Calve S, Landreth GE, Huang F. Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval. Nat Methods 2020; 17:531-540. [PMID: 32371980 PMCID: PMC7289454 DOI: 10.1038/s41592-020-0816-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Single-molecule localization microscopy is a powerful tool for visualizing subcellular structures, interactions and protein functions in biological research. However, inhomogeneous refractive indices inside cells and tissues distort the fluorescent signal emitted from single-molecule probes, which rapidly degrades resolution with increasing depth. We propose a method that enables the construction of an in situ 3D response of single emitters directly from single-molecule blinking datasets, and therefore allows their locations to be pinpointed with precision that achieves the Cramér-Rao lower bound and uncompromised fidelity. We demonstrate this method, named in situ PSF retrieval (INSPR), across a range of cellular and tissue architectures, from mitochondrial networks and nuclear pores in mammalian cells to amyloid-β plaques and dendrites in brain tissues and elastic fibers in developing cartilage of mice. This advancement expands the routine applicability of super-resolution microscopy from selected cellular targets near coverslips to intra- and extracellular targets deep inside tissues.
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Affiliation(s)
- Fan Xu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Donghan Ma
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Kathryn P MacPherson
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Ye Bu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Yu Tang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| | - Cheng Bi
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Tim Kwok
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
| | - Alexander A Chubykin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | - Gary E Landreth
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA. .,Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA. .,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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41
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Abstract
Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from super-resolution imaging to long-term real-time observation of living organisms. In this review, we discuss current fluorescence imaging techniques in terms of the use of tailored or structured light for the sample illumination and fluorescence detection, providing a clear overview of their working principles and capabilities.
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Affiliation(s)
- Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Jinhan Ren
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
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42
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Stein J, Stehr F, Schueler P, Blumhardt P, Schueder F, Mücksch J, Jungmann R, Schwille P. Toward Absolute Molecular Numbers in DNA-PAINT. NANO LETTERS 2019; 19:8182-8190. [PMID: 31535868 PMCID: PMC6856960 DOI: 10.1021/acs.nanolett.9b03546] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/16/2019] [Indexed: 05/17/2023]
Abstract
Single-molecule localization microscopy (SMLM) has revolutionized optical microscopy, extending resolution down to the level of individual molecules. However, the actual counting of molecules relies on preliminary knowledge of the blinking behavior of individual targets or on a calibration to a reference. In particular for biological applications, great care has to be taken because a plethora of factors influence the quality and applicability of calibration-dependent approaches to count targets in localization clusters particularly in SMLM data obtained from heterogeneous samples. Here, we present localization-based fluorescence correlation spectroscopy (lbFCS) as the first absolute molecular counting approach for DNA-points accumulation for imaging in nanoscale topography (PAINT) microscopy and, to our knowledge, for SMLM in general. We demonstrate that lbFCS overcomes the limitation of previous DNA-PAINT counting and allows the quantification of target molecules independent of the localization cluster density. In accordance with the promising results of our systematic proof-of-principle study on DNA origami structures as idealized targets, lbFCS could potentially also provide quantitative access to more challenging biological targets featuring heterogeneous cluster sizes in the future.
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Affiliation(s)
- Johannes Stein
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Florian Stehr
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Patrick Schueler
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Florian Schueder
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Faculty
of Physics, Ludwig Maximilian University, 80539 Munich, Germany
| | - Jonas Mücksch
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ralf Jungmann
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Faculty
of Physics, Ludwig Maximilian University, 80539 Munich, Germany
| | - Petra Schwille
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
- E-mail:
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43
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Schueder F, Stein J, Stehr F, Auer A, Sperl B, Strauss MT, Schwille P, Jungmann R. An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions. Nat Methods 2019; 16:1101-1104. [DOI: 10.1038/s41592-019-0584-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/26/2019] [Indexed: 11/09/2022]
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44
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Mahecic D, Testa I, Griffié J, Manley S. Strategies for increasing the throughput of super-resolution microscopies. Curr Opin Chem Biol 2019; 51:84-91. [DOI: 10.1016/j.cbpa.2019.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/30/2019] [Accepted: 05/13/2019] [Indexed: 11/29/2022]
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