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Huisjes NM, Retzer TM, Scherr MJ, Agarwal R, Rajappa L, Safaric B, Minnen A, Duderstadt KE. Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages. eLife 2022; 11:75899. [PMID: 36098381 PMCID: PMC9470159 DOI: 10.7554/elife.75899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/26/2021] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The rapid development of new imaging approaches is generating larger and more complex datasets, revealing the time evolution of individual cells and biomolecules. Single-molecule techniques, in particular, provide access to rare intermediates in complex, multistage molecular pathways. However, few standards exist for processing these information-rich datasets, posing challenges for wider dissemination. Here, we present Mars, an open-source platform for storing and processing image-derived properties of biomolecules. Mars provides Fiji/ImageJ2 commands written in Java for common single-molecule analysis tasks using a Molecule Archive architecture that is easily adapted to complex, multistep analysis workflows. Three diverse workflows involving molecule tracking, multichannel fluorescence imaging, and force spectroscopy, demonstrate the range of analysis applications. A comprehensive graphical user interface written in JavaFX enhances biomolecule feature exploration by providing charting, tagging, region highlighting, scriptable dashboards, and interactive image views. The interoperability of ImageJ2 ensures Molecule Archives can easily be opened in multiple environments, including those written in Python using PyImageJ, for interactive scripting and visualization. Mars provides a flexible solution for reproducible analysis of image-derived properties, facilitating the discovery and quantitative classification of new biological phenomena with an open data format accessible to everyone.
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Affiliation(s)
- Nadia M Huisjes
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Thomas M Retzer
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Rohit Agarwal
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Anita Minnen
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.,Physik Department, Technische Universität München, Garching, Germany
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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. Inside Back Cover: Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling (Angew. Chem. Int. Ed. 19/2022). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202205055] [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: 11/11/2022]
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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3
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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] [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: 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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4
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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. Innenrücktitelbild: Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling (Angew. Chem. 19/2022). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205055] [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: 11/11/2022]
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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