1
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Kessler L, Balakrishnan A, Menche T, Wang D, Li Y, Mantel M, Glogger M, Dietz MS, Heilemann M. Self-Quenched Fluorophore-DNA Labels for Super-Resolution Fluorescence Microscopy. J Phys Chem B 2024; 128:6751-6759. [PMID: 38955346 PMCID: PMC11264260 DOI: 10.1021/acs.jpcb.4c02065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 07/04/2024]
Abstract
Protein labeling through transient and repetitive hybridization of short, fluorophore-labeled DNA oligonucleotides has become widely applied in various optical super-resolution microscopy methods. The main advantages are multitarget imaging and molecular quantification. A challenge is the high background signal originating from the presence of unbound fluorophore-DNA labels in solution. Here, we report the self-quenching of fluorophore dimers conjugated to DNA oligonucleotides as a general concept to reduce the fluorescence background. Upon hybridization, the fluorescence signals of both fluorophores are restored. We expand the toolbox of fluorophores suitable for self-quenching and report their spectra and hybridization equilibria. We apply self-quenched fluorophore-DNA labels to stimulated emission depletion microscopy and single-molecule localization microscopy and report improved imaging performances.
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Affiliation(s)
- Laurell
F. Kessler
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue-Str. 7, Frankfurt 60438, Germany
| | - Ashwin Balakrishnan
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue-Str. 7, Frankfurt 60438, Germany
| | - Tanja Menche
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue-Str. 7, Frankfurt 60438, Germany
| | - Dongni Wang
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue-Str. 7, Frankfurt 60438, Germany
| | - Yunqing Li
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue-Str. 7, Frankfurt 60438, Germany
| | - Maximilian Mantel
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue-Str. 7, Frankfurt 60438, Germany
| | - Marius Glogger
- Optical
Imaging Competence Centre, Universität
Erlangen-Nürnberg, Cauerstraße 3, Erlangen 91058, Germany
| | - Marina S. Dietz
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue-Str. 7, Frankfurt 60438, Germany
| | - Mike Heilemann
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue-Str. 7, Frankfurt 60438, Germany
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2
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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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3
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Saliba N, Gagliano G, Gustavsson AK. Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559876. [PMID: 37808751 PMCID: PMC10557638 DOI: 10.1101/2023.09.27.559876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Multi-target single-molecule super-resolution fluorescence microscopy offers a powerful means of understanding the distributions and interplay between multiple subcellular structures at the nanoscale. However, single-molecule super-resolution imaging of whole mammalian cells is often hampered by high fluorescence background and slow acquisition speeds, especially when imaging multiple targets in 3D. In this work, we have mitigated these issues by developing a steerable, dithered, single-objective tilted light sheet for optical sectioning to reduce fluorescence background and a pipeline for 3D nanoprinting microfluidic systems for reflection of the light sheet into the sample and for efficient and automated solution exchange. By combining these innovations with PSF engineering for nanoscale localization of individual molecules in 3D, deep learning for analysis of overlapping emitters, active 3D stabilization for drift correction and long-term imaging, and Exchange-PAINT for sequential multi-target imaging without chromatic offsets, we demonstrate whole-cell multi-target 3D single-molecule super-resolution imaging with improved precision and imaging speed.
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Affiliation(s)
- Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, 77005
| | - Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, 77005
- Smalley-Curl Institute, Rice University, Houston, TX, 77005
- Applied Physics Program, Rice University, Houston, TX, 77005
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, 77005
- Smalley-Curl Institute, Rice University, Houston, TX, 77005
- Department of BioSciences, Rice University, Houston, TX, 77005
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77005
- Institute of Biosciences and Bioengineering, Rice University, Houston, TX, 77005
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030
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4
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Jang S, Narayanasamy KK, Rahm JV, Saguy A, Kompa J, Dietz MS, Johnsson K, Shechtman Y, Heilemann M. Neural network-assisted single-molecule localization microscopy with a weak-affinity protein tag. BIOPHYSICAL REPORTS 2023; 3:100123. [PMID: 37680382 PMCID: PMC10480660 DOI: 10.1016/j.bpr.2023.100123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023]
Abstract
Single-molecule localization microscopy achieves nanometer spatial resolution by localizing single fluorophores separated in space and time. A major challenge of single-molecule localization microscopy is the long acquisition time, leading to low throughput, as well as to a poor temporal resolution that limits its use to visualize the dynamics of cellular structures in live cells. Another challenge is photobleaching, which reduces information density over time and limits throughput and the available observation time in live-cell applications. To address both challenges, we combine two concepts: first, we integrate the neural network DeepSTORM to predict super-resolution images from high-density imaging data, which increases acquisition speed. Second, we employ a direct protein label, HaloTag7, in combination with exchangeable ligands (xHTLs), for fluorescence labeling. This labeling method bypasses photobleaching by providing a constant signal over time and is compatible with live-cell imaging. The combination of both a neural network and a weak-affinity protein label reduced the acquisition time up to ∼25-fold. Furthermore, we demonstrate live-cell imaging with increased temporal resolution, and capture the dynamics of the endoplasmic reticulum over extended time without signal loss.
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Affiliation(s)
- Soohyen Jang
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Institute of Physical and Theoretical Chemistry, IMPRS on Cellular Biophysics, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Kaarjel K. Narayanasamy
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Johanna V. Rahm
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Alon Saguy
- Department of Biomedical Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Julian Kompa
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Marina S. Dietz
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Yoav Shechtman
- Department of Biomedical Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Institute of Physical and Theoretical Chemistry, IMPRS on Cellular Biophysics, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
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5
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Albertazzi L, Heilemann M. When Weak Is Strong: A Plea for Low-Affinity Binders for Optical Microscopy. Angew Chem Int Ed Engl 2023; 62:e202303390. [PMID: 37158582 DOI: 10.1002/anie.202303390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/10/2023]
Abstract
The exploitation of low-affinity molecular interactions in protein labeling is an emerging topic in optical microscopy. Such non-covalent and low-affinity interactions can be realized with various concepts from chemistry and for different molecule classes, and lead to a constant renewal of fluorescence signals at target sites. Further benefits are a versatile use across microscopy methods, in 3D, live and many-target applications. In recent years, several classes of low-affinity labels were developed and a variety of powerful applications demonstrated. Still, this research field is underdeveloped, while the potential is huge.
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6
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Burgers TCQ, Vlijm R. Fluorescence-based super-resolution-microscopy strategies for chromatin studies. Chromosoma 2023:10.1007/s00412-023-00792-9. [PMID: 37000292 PMCID: PMC10356683 DOI: 10.1007/s00412-023-00792-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023]
Abstract
Super-resolution microscopy (SRM) is a prime tool to study chromatin organisation at near biomolecular resolution in the native cellular environment. With fluorescent labels DNA, chromatin-associated proteins and specific epigenetic states can be identified with high molecular specificity. The aim of this review is to introduce the field of diffraction-unlimited SRM to enable an informed selection of the most suitable SRM method for a specific chromatin-related research question. We will explain both diffraction-unlimited approaches (coordinate-targeted and stochastic-localisation-based) and list their characteristic spatio-temporal resolutions, live-cell compatibility, image-processing, and ability for multi-colour imaging. As the increase in resolution, compared to, e.g. confocal microscopy, leads to a central role of the sample quality, important considerations for sample preparation and concrete examples of labelling strategies applicable to chromatin research are discussed. To illustrate how SRM-based methods can significantly improve our understanding of chromatin functioning, and to serve as an inspiring starting point for future work, we conclude with examples of recent applications of SRM in chromatin research.
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Affiliation(s)
- Thomas C Q Burgers
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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7
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Ghanam J, Chetty VK, Zhu X, Liu X, Gelléri M, Barthel L, Reinhardt D, Cremer C, Thakur BK. Single Molecule Localization Microscopy for Studying Small Extracellular Vesicles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205030. [PMID: 36635058 DOI: 10.1002/smll.202205030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Small extracellular vesicles (sEVs) are 30-200 nm nanovesicles enriched with unique cargoes of nucleic acids, lipids, and proteins. sEVs are released by all cell types and have emerged as a critical mediator of cell-to-cell communication. Although many studies have dealt with the role of sEVs in health and disease, the exact mechanism of sEVs biogenesis and uptake remain unexplored due to the lack of suitable imaging technologies. For sEVs functional studies, imaging has long relied on conventional fluorescence microscopy that has only 200-300 nm resolution, thereby generating blurred images. To break this resolution limit, recent developments in super-resolution microscopy techniques, specifically single-molecule localization microscopy (SMLM), expanded the understanding of subcellular details at the few nanometer level. SMLM success relies on the use of appropriate fluorophores with excellent blinking properties. In this review, the basic principle of SMLM is highlighted and the state of the art of SMLM use in sEV biology is summarized. Next, how SMLM techniques implemented for cell imaging can be translated to sEV imaging is discussed by applying different labeling strategies to study sEV biogenesis and their biomolecular interaction with the distant recipient cells.
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Affiliation(s)
- Jamal Ghanam
- Department of Pediatrics III, University Hospital Essen, 45147, Essen, Germany
| | | | - Xingfu Zhu
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Xiaomin Liu
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Lennart Barthel
- Department of Neurosurgery and Spine Surgery, Center for Translational Neuro and Behavioral Sciences, University Hospital Essen, 45147, Essen, Germany
- Institute of Medical Psychology and Behavioral Immunobiology, Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, 45147, Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatrics III, University Hospital Essen, 45147, Essen, Germany
| | - Christoph Cremer
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Basant Kumar Thakur
- Department of Pediatrics III, University Hospital Essen, 45147, Essen, Germany
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8
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Kim SH, Li ITS. Super-Resolution Tension PAINT Imaging with a Molecular Beacon. Angew Chem Int Ed Engl 2023; 62:e202217028. [PMID: 36534951 DOI: 10.1002/anie.202217028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
DNA-PAINT enabled super-resolution imaging through the transient binding of fluorescently-labelled single-stranded DNA (ssDNA) imagers to target ssDNA. However, its performance is constrained by imager background fluorescence, resulting in relatively long image acquisition and potential artifacts. We designed a molecular beacon (MB) as the PAINT imager. Unbound MB in solution reduces the background fluorescence due to its natively quenched state. They are fluorogenic upon binding to target DNA to create individual fluorescence events. We demonstrate that MB-PAINT provides localization precision similar to traditional linear imager DNA-PAINT. We also show that MB-PAINT is ideally suited for fast super-resolution imaging of molecular tension probes in living cells, eliminating the potential of artifacts from free-diffusing imagers in traditional DNA-PAINT at the cell-substrate interface.
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Affiliation(s)
- Seong Ho Kim
- Department of Chemistry, The University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - Isaac T S Li
- Department of Chemistry, The University of British Columbia, Kelowna, BC V1V 1V7, Canada
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