1
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Engdahl A, Grauberger O, Brockhinke A, Schüttpelz M, Huser TR. Switching of Organic Fluorophores by Glycerol‐Sulfite Interactions for Single‐Molecule Super‐Resolution Microscopy. CHEMPHOTOCHEM 2023. [DOI: 10.1002/cptc.202200305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Anders Engdahl
- Bielefeld University: Universitat Bielefeld Department of Physics GERMANY
| | - Oleg Grauberger
- Bielefeld University: Universitat Bielefeld Department of Physics GERMANY
| | - Andreas Brockhinke
- Bielefeld University: Universitat Bielefeld Department of Chemistry GERMANY
| | - Mark Schüttpelz
- Bielefeld University: Universitat Bielefeld Department of Physics GERMANY
| | - Thomas R. Huser
- Bielefeld University: Universitat Bielefeld Department of Physics Universitaetsstr. 25D3-231 33615 Bielefeld GERMANY
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2
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Ahmadi A, Till K, Backe PH, Blicher P, Diekmann R, Schüttpelz M, Glette K, Tørresen J, Bjørås M, Rowe AD, Dalhus B. Non-flipping DNA glycosylase AlkD scans DNA without formation of a stable interrogation complex. Commun Biol 2021; 4:876. [PMID: 34267321 PMCID: PMC8282808 DOI: 10.1038/s42003-021-02400-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/25/2021] [Indexed: 11/09/2022] Open
Abstract
The multi-step base excision repair (BER) pathway is initiated by a set of enzymes, known as DNA glycosylases, able to scan DNA and detect modified bases among a vast number of normal bases. While DNA glycosylases in the BER pathway generally bend the DNA and flip damaged bases into lesion specific pockets, the HEAT-like repeat DNA glycosylase AlkD detects and excises bases without sequestering the base from the DNA helix. We show by single-molecule tracking experiments that AlkD scans DNA without forming a stable interrogation complex. This contrasts with previously studied repair enzymes that need to flip bases into lesion-recognition pockets and form stable interrogation complexes. Moreover, we show by design of a loss-of-function mutant that the bimodality in scanning observed for the structural homologue AlkF is due to a key structural differentiator between AlkD and AlkF; a positively charged β-hairpin able to protrude into the major groove of DNA.
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Affiliation(s)
- Arash Ahmadi
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Katharina Till
- FOM Institute AMOLF, Science Park 104, Amsterdam, The Netherlands.,Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Paul Hoff Backe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway
| | - Pernille Blicher
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Robin Diekmann
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Kyrre Glette
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Jim Tørresen
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Alexander D Rowe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Newborn Screening, Division of Child and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway. .,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway.
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3
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Kong C, Bobe S, Pilger C, Lachetta M, Øie CI, Kirschnick N, Mönkemöller V, Hübner W, Förster C, Schüttpelz M, Kiefer F, Huser T, Schulte Am Esch J. Multiscale and Multimodal Optical Imaging of the Ultrastructure of Human Liver Biopsies. Front Physiol 2021; 12:637136. [PMID: 33679449 PMCID: PMC7925637 DOI: 10.3389/fphys.2021.637136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/27/2021] [Indexed: 12/30/2022] Open
Abstract
The liver as the largest organ in the human body is composed of a complex macroscopic and microscopic architecture that supports its indispensable function to maintain physiological homeostasis. Optical imaging of the human liver is particularly challenging because of the need to cover length scales across 7 orders of magnitude (from the centimeter scale to the nanometer scale) in order to fully assess the ultrastructure of the entire organ down to the subcellular scale and probe its physiological function. This task becomes even more challenging the deeper within the organ one hopes to image, because of the strong absorption and scattering of visible light by the liver. Here, we demonstrate how optical imaging methods utilizing highly specific fluorescent labels, as well as label-free optical methods can seamlessly cover this entire size range in excised, fixed human liver tissue and we exemplify this by reconstructing the biliary tree in three-dimensional space. Imaging of tissue beyond approximately 0.5 mm length requires optical clearing of the human liver. We present the successful use of optical projection tomography and light-sheet fluorescence microscopy to derive information about the liver architecture on the millimeter scale. The intermediate size range is covered using label-free structural and chemically sensitive methods, such as second harmonic generation and coherent anti-Stokes Raman scattering microscopy. Laser-scanning confocal microscopy extends the resolution to the nanoscale, allowing us to ultimately image individual liver sinusoidal endothelial cells and their fenestrations by super-resolution structured illumination microscopy. This allowed us to visualize the human hepatobiliary system in 3D down to the cellular level, which indicates that reticular biliary networks communicate with portal bile ducts via single or a few ductuli. Non-linear optical microscopy enabled us to identify fibrotic regions extending from the portal field to the parenchyma, along with microvesicular steatosis in liver biopsies from an older patient. Lastly, super-resolution microscopy allowed us to visualize and determine the size distribution of fenestrations in human liver sinusoidal endothelial cells for the first time under aqueous conditions. Thus, this proof-of-concept study allows us to demonstrate, how, in combination, these techniques open up a new chapter in liver biopsy analysis.
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Affiliation(s)
- Cihang Kong
- Department of Physics, Bielefeld University, Bielefeld, Germany
| | - Stefanie Bobe
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
| | | | - Mario Lachetta
- Department of Physics, Bielefeld University, Bielefeld, Germany
| | - Cristina Ionica Øie
- Vascular Biology Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Nils Kirschnick
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
| | | | - Wolfgang Hübner
- Department of Physics, Bielefeld University, Bielefeld, Germany.,Forschungsverbund BioMedizin Bielefeld (FBMB), Bielefeld, Germany
| | | | - Mark Schüttpelz
- Department of Physics, Bielefeld University, Bielefeld, Germany
| | - Friedemann Kiefer
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
| | - Thomas Huser
- Department of Physics, Bielefeld University, Bielefeld, Germany.,Forschungsverbund BioMedizin Bielefeld (FBMB), Bielefeld, Germany
| | - Jan Schulte Am Esch
- Forschungsverbund BioMedizin Bielefeld (FBMB), Bielefeld, Germany.,Department of General and Visceral Surgery, Evangelisches Klinikum Bethel gGmbH, University Hospital OWL of the University of Bielefeld, Bielefeld, Germany
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4
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Ahmadi A, Rosnes I, Blicher P, Diekmann R, Schüttpelz M, Glette K, Tørresen J, Bjørås M, Dalhus B, Rowe AD. Publisher Correction: Breaking the speed limit with multimode fast scanning of DNA by Endonuclease V. Nat Commun 2019; 10:1991. [PMID: 31024006 PMCID: PMC6484037 DOI: 10.1038/s41467-019-10070-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article was updated shortly after publication to add a link to the Peer Review file, which was inadvertently omitted. The Peer Review file is available to download as a Supplementary File from the HTML version of the Article.
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Affiliation(s)
- Arash Ahmadi
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway
| | - Ida Rosnes
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway.,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, PO Box 4950 Nydalen, NO-0424, Oslo, Norway
| | - Pernille Blicher
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway
| | - Robin Diekmann
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstraße 25, DE-33615, Bielefeld, Germany.,European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße 1, DE-69117, Heidelberg, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstraße 25, DE-33615, Bielefeld, Germany
| | - Kyrre Glette
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | - Jim Tørresen
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, PO Box 4950 Nydalen, NO-0424, Oslo, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), PO Box 8905, NO-7491, Trondheim, Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway. .,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, PO Box 4950 Nydalen, NO-0424, Oslo, Norway.
| | - Alexander D Rowe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway. .,Department of Newborn Screening, Division of Child and Adolescent Medicine, Oslo University Hospital, PO Box 4950 Nydalen, NO-0424, Oslo, Norway.
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5
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Diekmann R, Wolfson DL, Spahn C, Heilemann M, Schüttpelz M, Huser T. Nanoscopy of bacterial cells immobilized by holographic optical tweezers. Nat Commun 2016; 7:13711. [PMID: 27958271 PMCID: PMC5159804 DOI: 10.1038/ncomms13711] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/26/2016] [Indexed: 01/19/2023] Open
Abstract
Imaging non-adherent cells by super-resolution far-field fluorescence microscopy is currently not possible because of their rapid movement while in suspension. Holographic optical tweezers (HOTs) enable the ability to freely control the number and position of optical traps, thus facilitating the unrestricted manipulation of cells in a volume around the focal plane. Here we show that immobilizing non-adherent cells by optical tweezers is sufficient to achieve optical resolution well below the diffraction limit using localization microscopy. Individual cells can be oriented arbitrarily but preferably either horizontally or vertically relative to the microscope's image plane, enabling access to sample sections that are impossible to achieve with conventional sample preparation and immobilization. This opens up new opportunities to super-resolve the nanoscale organization of chromosomal DNA in individual bacterial cells.
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Affiliation(s)
- Robin Diekmann
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Deanna L. Wolfson
- NSF Center for Biophotonics, University of California, 2700 Stockton Boulevard, Suite 1400, Davis, Sacramento, California 95817, USA
- Department of Physics and Technology, UiT The Arctic University of Norway, Klokkargårdsbakken 35, 9019 Tromsø, Norway
| | - Christoph Spahn
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
- NSF Center for Biophotonics, University of California, 2700 Stockton Boulevard, Suite 1400, Davis, Sacramento, California 95817, USA
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6
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Leder V, Lummer M, Tegeler K, Humpert F, Lewinski M, Schüttpelz M, Staiger D. Mutational definition of binding requirements of an hnRNP-like protein in Arabidopsis using fluorescence correlation spectroscopy. Biochem Biophys Res Commun 2014; 453:69-74. [PMID: 25251471 DOI: 10.1016/j.bbrc.2014.09.056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 09/15/2014] [Indexed: 12/23/2022]
Abstract
Arabidopsis thaliana glycine-rich RNA binding protein 7 (AtGRP7) is part of a negative feedback loop through which it regulates alternative splicing and steady-state abundance of its pre-mRNA. Here we use fluorescence correlation spectroscopy to investigate the requirements for AtGRP7 binding to its intron using fluorescently-labelled synthetic oligonucleotides. By systematically introducing point mutations we identify three nucleotides that lead to an increased Kd value when mutated and thus are critical for AtGRP7 binding. Simultaneous mutation of all three residues abrogates binding. The paralogue AtGRP8 binds to an overlapping motif but with a different sequence preference, in line with overlapping but not identical functions of this protein pair. Truncation of the glycine-rich domain reduces the binding affinity of AtGRP7, showing for the first time that the glycine-rich stretch of a plant hnRNP-like protein contributes to binding. Mutation of the conserved R(49) that is crucial for AtGRP7 function in pathogen defence and splicing abolishes binding.
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Affiliation(s)
- Verena Leder
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Germany; Biomolecular Photonics, Faculty of Physics, Bielefeld University, Germany
| | - Martina Lummer
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Germany
| | - Kathrin Tegeler
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Germany; Biomolecular Photonics, Faculty of Physics, Bielefeld University, Germany
| | - Fabian Humpert
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, Germany
| | - Martin Lewinski
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, Germany
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Germany.
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7
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Mönkemöller V, Schüttpelz M, McCourt P, Sørensen K, Smedsrød B, Huser T. Imaging fenestrations in liver sinusoidal endothelial cells by optical localization microscopy. Phys Chem Chem Phys 2014; 16:12576-81. [DOI: 10.1039/c4cp01574f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We demonstrate the use of single molecule localization microscopy for resolving structural details of fenestrations in liver sinusoidal endothelial cells.
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Affiliation(s)
- Viola Mönkemöller
- Biomolecular Photonics
- Department of Physics
- University of Bielefeld
- 33615 Bielefeld, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics
- Department of Physics
- University of Bielefeld
- 33615 Bielefeld, Germany
| | | | | | | | - Thomas Huser
- Biomolecular Photonics
- Department of Physics
- University of Bielefeld
- 33615 Bielefeld, Germany
- Dep. of Internal Medicine
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8
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Lummer M, Humpert F, Wiedenlübbert M, Sauer M, Schüttpelz M, Staiger D. A new set of reversibly photoswitchable fluorescent proteins for use in transgenic plants. Mol Plant 2013; 6:1518-30. [PMID: 23434876 DOI: 10.1093/mp/sst040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Fluorescent reporter proteins that allow repeated switching between a fluorescent and a non-fluorescent state in response to specific wavelengths of light are novel tools for monitoring of protein trafficking and super-resolution fluorescence microscopy in living organisms. Here, we describe variants of the reversibly photoswitchable fluorescent proteins rsFastLime, bsDronpa, and Padron that have been codon-optimized for the use in transgenic Arabidopsis plants. The synthetic proteins, designated rsFastLIME-s, bsDRONPA-s, and PADRON C-s, showed photophysical properties and switching behavior comparable to those reported for the original proteins. By combining the 'positively switchable' PADRON C-s with the 'negatively switchable' rsFastLIME-s or bsDRONPA-s, two different fluorescent reporter proteins could be imaged at the same wavelength upon transient expression in Nicotiana benthamiana cells. Thus, co-localization analysis can be performed using only a single detection channel. Furthermore, the proteins were used to tag the RNA-binding protein AtGRP7 (Arabidopsis thaliana glycine-rich RNA-binding protein 7) in transgenic Arabidopsis plants. Because the new reversibly photoswitchable fluorescent proteins show an increase in signal strength during each photoactivation cycle, we were able to generate a large number of scans of the same region and reconstruct 3-D images of AtGRP7 expression in the root tip. Upon photoactivation of the AtGRP7:rsFastLIME-s fusion protein in a defined region of a transgenic Arabidopsis root, spreading of the fluorescence signal into adjacent regions was observed, indicating that movement from cell to cell can be monitored. Our results demonstrate that rsFastLIME-s, bsDRONPA-s, and PADRON C-s are versatile fluorescent markers in plants. Furthermore, the proteins also show strong fluorescence in mammalian cells including COS-7 and HeLa cells.
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Affiliation(s)
- Martina Lummer
- Molecular Cell Physiology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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9
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Lummer M, Humpert F, Steuwe C, Caesar K, Schüttpelz M, Sauer M, Staiger D. Reversible Photoswitchable DRONPA-s Monitors Nucleocytoplasmic Transport of an RNA-Binding Protein in Transgenic Plants. Traffic 2011; 12:693-702. [DOI: 10.1111/j.1600-0854.2011.01180.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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Abstract
In the recent past, single-molecule based localization or photoswitching microscopy methods such as stochastic optical reconstruction microscopy (STORM) or photoactivated localization microscopy (PALM) have been successfully implemented for subdiffraction-resolution fluorescence imaging. However, the computational effort needed to localize numerous fluorophores is tremendous, causing long data processing times and thereby limiting the applicability of the technique. Here we present a new computational scheme for data processing consisting of noise reduction, detection of likely fluorophore positions, high-precision fluorophore localization and subsequent visualization of found fluorophore positions in a super-resolution image. We present and benchmark different algorithms for noise reduction and demonstrate the use of non-maximum suppression to quickly find likely fluorophore positions in high depth and very noisy images. The algorithm is evaluated and compared in terms of speed, accuracy and robustness by means of simulated data. On real biological samples, we find that real-time data processing is possible and that super-resolution imaging with organic fluorophores of cellular structures with approximately 20 nm optical resolution can be completed in less than 10 s.
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Affiliation(s)
- S Wolter
- Applied Laser Physics & Laser Spectroscopy, Department of Physics, Bielefeld University, Universitätsstrasse 25, D-33615 Bielefeld, Germany
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11
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van de Linde S, Endesfelder U, Mukherjee A, Schüttpelz M, Wiebusch G, Wolter S, Heilemann M, Sauer M. Multicolor photoswitching microscopy for subdiffraction-resolution fluorescence imaging. Photochem Photobiol Sci 2009; 8:465-9. [PMID: 19337659 DOI: 10.1039/b822533h] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We introduce a general approach for multicolor subdiffraction-resolution fluorescence imaging based on photoswitching of standard organic fluorophores. Photoswitching of ordinary fluorophores such as ATTO520, ATTO565, ATTO655, ATTO680, or ATTO700, i.e. the reversible transition from a fluorescent to a nonfluorescent state in aqueous buffers exploits the formation of long-lived triplet radical anions through reaction with reducing agents such as beta-mercaptoethylamine and repopulation of the singlet ground state by interaction with molecular oxygen. Thus, the time the different fluorophores reside in the fluorescent state can be easily adjusted by the excitation intensity and the concentration of the reducing agent. We demonstrate the potential of multicolor photoswitching microscopy with subdiffraction-resolution on cytoskeletal networks and molecular quantification of proteins in the inner mitochondrial membrane with approximately 20 nm optical resolution.
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Affiliation(s)
- Sebastian van de Linde
- Bielefeld Institute for Biophysics and Nanoscience, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
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12
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Heilemann M, van de Linde S, Schüttpelz M, Kasper R, Seefeldt B, Mukherjee A, Tinnefeld P, Sauer M. Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew Chem Int Ed Engl 2008; 47:6172-6. [PMID: 18646237 DOI: 10.1002/anie.200802376] [Citation(s) in RCA: 1224] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mike Heilemann
- Angewandte Laserphysik & Laserspektroskopie, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany.
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13
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Heilemann M, van de Linde S, Schüttpelz M, Kasper R, Seefeldt B, Mukherjee A, Tinnefeld P, Sauer M. Fluoreszenzmikroskopie unterhalb der optischen Auflösungsgrenze mit konventionellen Fluoreszenzsonden. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802376] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Schüttpelz M, Schöning JC, Doose S, Neuweiler H, Peters E, Staiger D, Sauer M. Changes in conformational dynamics of mRNA upon AtGRP7 binding studied by fluorescence correlation spectroscopy. J Am Chem Soc 2008; 130:9507-13. [PMID: 18576621 DOI: 10.1021/ja801994z] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The clock-regulated RNA recognition motif (RRM)-containing protein AtGRP7 (Arabidopsis thaliana glycine-rich RNA-binding protein) influences the amplitude of its transcript oscillation at the post-transcriptional level. This autoregulation relies on AtGRP7 binding to its own pre-mRNA. The sequence and structural requirements for this interaction are unknown at present. In this work, we used photoinduced electron transfer fluorescence correlation spectroscopy (PET-FCS) as a novel technique to study the role of target RNA secondary structure and conformational dynamics during the recognition and binding process. Conformational dynamics of single-stranded (ss) oligonucleotides were studied in aqueous solution with single-molecule sensitivity and high temporal resolution by monitoring fluorescence quenching of the oxazine fluorophore MR121 by guanosine residues. Comparative analysis of translational diffusion constants revealed that both ssRNA and ssDNA bind to AtGRP7 with similar dissociation constants on the order of 10(-7) M and that a minimal binding sequence 5'-UUC UGG-3' is needed for recognition by AtGRP7. PET-FCS experiments demonstrated that conformational flexibility of short, single-stranded, MR121-labeled oligonucleotides is reduced upon AtGRP7 binding. In contrast to many other RRM proteins, AtGRP7 binds to ssRNA preferentially if the RNA is fully stretched and not embedded within a stable secondary structure. The results suggest that AtGRP7 binding leads to a conformational rearrangement in the mRNA, arresting the flexible target sequence in an extended structure of reduced flexibility that may have consequences for further post-transcriptional processing of the mRNA.
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Affiliation(s)
- Mark Schüttpelz
- Applied Laser Physics and Laser Spectroscopy, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany.
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15
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Schulze P, Schüttpelz M, Sauer M, Belder D. Two-photon excited fluorescence detection at 420 nm for label-free detection of small aromatics and proteins in microchip electrophoresis. Lab Chip 2007; 7:1841-1844. [PMID: 18030410 DOI: 10.1039/b710762e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Two photon excited (TPE) fluorescence detection was applied to native fluorescence detection of aromatics in microchip electrophoresis (MCE). This technique was evaluated as an alternative to common one photon excitation in the deep UV spectral range. TPE enables fluorescence detection of unlabeled aromatic compounds, even in non-deep UV-transparent microfluidic chips. In this study, we demonstrate the proof of concept of native TPE fluorescence detection of small aromatics in commercial microfluidic glass chips. Label-free TPE fluorescence detection of native proteins and small aromatics in MCE was achieved within the micromolar concentration range, utilising 420 nm excitation light.
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Affiliation(s)
- Philipp Schulze
- Institute of Analytical Chemistry, University of Leipzig, Linnéstr. 3, 04103, Leipzig, Germany
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16
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Schüttpelz M, Müller C, Neuweiler H, Sauer M. UV Fluorescence Lifetime Imaging Microscopy: A Label-Free Method for Detection and Quantification of Protein Interactions. Anal Chem 2005; 78:663-9. [PMID: 16448037 DOI: 10.1021/ac051938j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to the ability to detect multiple parameters simultaneously, protein microarrays have found widespread applications from basic biological research to diagnosis of diseases. Generally, readout of protein microarrays is performed by fluorescence detection using either dye-labeled detector antibodies or direct labeling of the target proteins. We developed a method for the label-free detection and quantification of proteins based on time-gated, wide-field, camera-based UV fluorescence lifetime imaging microscopy to gain lifetime information from each pixel of a sensitive CCD camera. The method relies on differences in the native fluorescence lifetime of proteins and takes advantage of binding-induced lifetime changes for the unequivocal detection and quantification of target proteins. Since fitting of the fluorescence decay for every pixel in an image using a classical exponential decay model is time-consuming and unstable at very low fluorescence intensities, we used a new, very robust and fast alternative method to generate UV fluorescence lifetime images by calculating the average lifetime of the decay for each pixel in the image stack using a model-free average decay time algorithm.To validate the method, we demonstrate the detection and quantification of p53 antibodies, a tumor marker in cancer diagnosis. Using tryptophan-containing capture peptides, we achieved a detection sensitivity for monoclonal antibodies down to the picomolar concentration range. The obtained affinity constant, Ka, of (1.4 +/- 0.6) x 10(9) M(-1), represents a typical value for antigen/antibody binding and is in agreement with values determined by traditional binding assays.
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Affiliation(s)
- Mark Schüttpelz
- Applied Laser Physics and Laser Spectroscopy, University of Bielefeld, Germany
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