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Moya Muñoz GG, Brix O, Klocke P, Harris PD, Luna Piedra JR, Wendler ND, Lerner E, Zijlstra N, Cordes T. Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.29.573596. [PMID: 38234760 PMCID: PMC10793419 DOI: 10.1101/2023.12.29.573596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Over the past decades, single-molecule and super-resolution microscopy have advanced and represent essential tools for life science research. There is,however, a growing gap between the state-of-the-art and what is accessible to biologists, biochemists, medical researchers or labs with financial constraints. To bridge this gap, we introduce Brick-MIC, a versatile and affordable open-source 3D-printed micro-spectroscopy and imaging platform. Brick-MIC enables the integration of various fluorescence imaging techniques with single-molecule resolution within a single platform and exchange between different modalities within minutes. We here present variants of Brick-MIC that facilitate single-molecule fluorescence detection, fluorescence correlation spectroscopy and super-resolution imaging (STORM and PAINT). Detailed descriptions of the hardware and software components, as well as data analysis routines are provided, to allow non-optics specialist to operate their own Brick-MIC with minimal effort and investments. We foresee that our affordable, flexible, and opensource Brick-MIC platform will be a valuable tool for many laboratories worldwide.
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Affiliation(s)
- Gabriel G. Moya Muñoz
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Oliver Brix
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Philipp Klocke
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Paul D. Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Jorge R. Luna Piedra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Nicolas D. Wendler
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Niels Zijlstra
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
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2
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Zhang Y, Yang C, Peng S, Ling J, Chen P, Ma Y, Wang W, Chen Z, Chen C. General Strategy To Improve the Photon Budget of Thiol-Conjugated Cyanine Dyes. J Am Chem Soc 2023; 145:4187-4198. [PMID: 36756850 DOI: 10.1021/jacs.2c12635] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Maleimide-cysteine chemistry has been a routine practice for the site-specific labeling of fluorophores to proteins since the 1950s. This approach, however, cannot bring out the best photon budget of fluorophores. Here, we systematically measured the Cyanine3/5 dye conjugates via maleimide-thiol and amide linkages by counting the total emitted photons at the single-molecule level. While brightness and signal-to-noise ratios do not change significantly, dyes with thioether linkages exhibit more severe photobleaching than amide linkers. We then screened modern arylation-type bioconjugation strategies to alleviate this damage. Labeling thiols with phenyloxadiazole (POD) methyl sulfone, p-chloronitrobenzene, and fluorobenzene probes gave rise to electron-deficient aryl thioethers, effectively increasing the total emitted photons by 1.5-3 fold. Among the linkers, POD maintains labeling efficiency and specificity that are comparable to maleimide. Such an increase has proved to be universal among bulk and single-molecule assays, with or without triplet-state quenchers and oxygen scavengers, and on conformationally unrestricted or restricted cyanines. We demonstrated that cyanine-POD conjugates are general and superior fluorophores for thiol labeling in single-molecule FRET measurements of biomolecular conformational dynamics and in two-color STED nanoscopy using site-selectively labeled nanobodies. This work sheds light on the photobleaching mechanism of cyanines under single-molecule imaging while highlighting the interplay between the protein microenvironment, bioconjugation chemistry, and fluorophore photochemistry.
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Affiliation(s)
- Yuan Zhang
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Chen Yang
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Sijia Peng
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Jing Ling
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peng Chen
- PKU-Nanjing Institute of Translational Medicine, Nanjing 211800, China
| | - Yumiao Ma
- BSJ Institute, Beijing 100084, China
- Hangzhou Yanqu Information Technology Co., Ltd., Xihu District, Hangzhou City, Zhejiang Province 310003, China
| | - Wenjuan Wang
- School of Life Sciences, Technology Center for Protein Sciences, Tsinghua University, Beijing 100084, China
| | - Zhixing Chen
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- PKU-Nanjing Institute of Translational Medicine, Nanjing 211800, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
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Fan S, Takada T, Maruyama A, Fujitsuka M, Kawai K. Programmed Control of Fluorescence Blinking Patterns based on Electron Transfer in DNA. Chemistry 2023; 29:e202203552. [PMID: 36601797 DOI: 10.1002/chem.202203552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/01/2023] [Accepted: 01/02/2023] [Indexed: 01/06/2023]
Abstract
Fluorescence imaging uses changes in the fluorescence intensity and emission wavelength to analyze multiple targets simultaneously. To increase the number of targets that can be identified simultaneously, fluorescence blinking can be used as an additional parameter. To understand and eventually control blinking, we used DNA as a platform to elucidate the processes of electron transfer (ET) leading to blinking, down to the rate constants. With a fixed ET distance, various blinking patterns were observed depending on the DNA sequence between the donor and acceptor units of the DNA platform. The blinking pattern was successfully described with a combination of ET rate constants. Therefore, molecules with various blinking patterns can be developed by tuning ET. It is expected that the number of targets that can be analyzed simultaneously will increase by the power of the number of blinking patterns.
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Affiliation(s)
- Shuya Fan
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Tadao Takada
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Mamoru Fujitsuka
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kiyohiko Kawai
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
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4
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Kikuchi K, Adair LD, Lin J, New EJ, Kaur A. Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy. Angew Chem Int Ed Engl 2023; 62:e202204745. [PMID: 36177530 PMCID: PMC10100239 DOI: 10.1002/anie.202204745] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 02/02/2023]
Abstract
Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.
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Affiliation(s)
- Kai Kikuchi
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liam D Adair
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jiarun Lin
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth J New
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Amandeep Kaur
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
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5
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Dömling A. Innovations and Inventions: Why Was the Ugi Reaction Discovered Only 37 Years after the Passerini Reaction? J Org Chem 2022; 88:5242-5247. [PMID: 35881912 PMCID: PMC10167652 DOI: 10.1021/acs.joc.2c00792] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This year represents the 100th anniversary of the discovery of the Passerini three-component reaction. The related Ugi four-compound reaction was discovered 37 years after the Passerini reaction. Undoubtedly, both reactions are very important multicomponent reactions but the Ugi reactions outperform the Passerini reactions in terms of combinatorial space according to the equation xy [x is the number of building blocks per component, and y is the order of the multicomponent reaction (for Passerini, y = 3; for Ugi, y = 4)]. In this work, a historical but contemporary perspective of the discoveries and innovations of the two reactions is given. From a bird's eye view and in a more general sense, the discovery of novel reactions is discussed and how it relates to inventions and innovations.
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Affiliation(s)
- Alexander Dömling
- Department of Drug Design, University of Groningen, Groningen 9700 AD, The Netherlands
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6
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao-Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling. Angew Chem Int Ed Engl 2022; 61:e202112959. [PMID: 35146855 PMCID: PMC9305292 DOI: 10.1002/anie.202112959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.
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Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nadia M Huisjes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Miguel Guirao-Ortiz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hartmann Harz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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