1
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Xu N, Ge H, Zheng J, Sun W, Du J, Fan J, Peng X. Wavelength-Tuneable Fluorescent Carbon Dots for Nucleic Acid Imaging. Anal Chem 2024. [PMID: 38327078 DOI: 10.1021/acs.analchem.3c05670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Nucleic acid is one of the most important substances in organisms, and its dynamic changes are closely related to physiological processes. Nucleic acid labeling is conducive to providing important information for the early diagnosis and treatment of pathophysiological processes. Here, we utilized the transfer mechanism between carbon sources and CDs to synthesize wavelength-adjustable N-CDs for the nucleic acid image. Along with the increased graphite nitrogen (from 10.6 to 30.1%) gradually by the precise design of the nitrogen structure in carbon sources (e.g., primary amines, secondary amines, tertiary amines, and liking graphite-nitrogen), the energy gap of CDs reduced, resulting in adjustable wavelength from visible to near-infrared range (from 461 nm/527 nm to 650 nm/676 nm). Furthermore, N-CDs exhibited a selective affinity for nucleic acids, especially RNA. Therefore, N-CDs support an efficient platform for real-time tracking of RNA dynamic changes in cells.
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Affiliation(s)
- Ning Xu
- Ningbo Institute of Dalian University of Technology, 26 Yucai Road, Jiangbei District, Ningbo 315016, China
| | - Haoying Ge
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| | - Jiazhu Zheng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| | - Wen Sun
- Ningbo Institute of Dalian University of Technology, 26 Yucai Road, Jiangbei District, Ningbo 315016, China
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| | - Jianjun Du
- Ningbo Institute of Dalian University of Technology, 26 Yucai Road, Jiangbei District, Ningbo 315016, China
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| | - Jiangli Fan
- Ningbo Institute of Dalian University of Technology, 26 Yucai Road, Jiangbei District, Ningbo 315016, China
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
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2
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Breindl M, Spitzer D, Gerasimaitė R, Kairys V, Schubert T, Henfling R, Schwartz U, Lukinavičius G, Manelytė L. Biochemical and cellular insights into the Baz2B protein, a non-catalytic subunit of the chromatin remodeling complex. Nucleic Acids Res 2024; 52:337-354. [PMID: 38000389 PMCID: PMC10783490 DOI: 10.1093/nar/gkad1096] [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: 02/20/2023] [Revised: 09/21/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Baz2B is a regulatory subunit of the ATP-dependent chromatin remodeling complexes BRF1 and BRF5, which control access to DNA during DNA-templated processes. Baz2B has been implicated in several diseases and also in unhealthy ageing, however limited information is available on the domains and cellular roles of Baz2B. To gain more insight into the Baz2B function, we biochemically characterized the TAM (Tip5/ARBP/MBD) domain with the auxiliary AT-hook motifs and the bromodomain (BRD). We observed alterations in histone code recognition in bromodomains carrying cancer-associated point mutations, suggesting their potential involvement in disease. Furthermore, the depletion of Baz2B in the Hap1 cell line resulted in altered cell morphology, reduced colony formation and perturbed transcriptional profiles. Despite that, super-resolution microscopy images revealed no changes in the overall chromatin structure in the absence of Baz2B. These findings provide insights into the biological function of Baz2B.
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Affiliation(s)
- Matthias Breindl
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Dominika Spitzer
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Visvaldas Kairys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | | | - Ramona Henfling
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Uwe Schwartz
- NGS Analysis Center, University of Regensburg, Regensburg DE-93053, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Laura Manelytė
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
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3
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Samanta S, Lai K, Wu F, Liu Y, Cai S, Yang X, Qu J, Yang Z. Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging. Chem Soc Rev 2023; 52:7197-7261. [PMID: 37743716 DOI: 10.1039/d2cs00905f] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.
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Affiliation(s)
- Soham Samanta
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Kaitao Lai
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Feihu Wu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Yingchao Liu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Songtao Cai
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Xusan Yang
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Junle Qu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Zhigang Yang
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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4
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Orsi GA, Tortora MMC, Horard B, Baas D, Kleman JP, Bucevičius J, Lukinavičius G, Jost D, Loppin B. Biophysical ordering transitions underlie genome 3D re-organization during cricket spermiogenesis. Nat Commun 2023; 14:4187. [PMID: 37443316 PMCID: PMC10345107 DOI: 10.1038/s41467-023-39908-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Spermiogenesis is a radical process of differentiation whereby sperm cells acquire a compact and specialized morphology to cope with the constraints of sexual reproduction while preserving their main cargo, an intact copy of the paternal genome. In animals, this often involves the replacement of most histones by sperm-specific nuclear basic proteins (SNBPs). Yet, how the SNBP-structured genome achieves compaction and accommodates shaping remain largely unknown. Here, we exploit confocal, electron and super-resolution microscopy, coupled with polymer modeling to identify the higher-order architecture of sperm chromatin in the needle-shaped nucleus of the emerging model cricket Gryllus bimaculatus. Accompanying spermatid differentiation, the SNBP-based genome is strikingly reorganized as ~25nm-thick fibers orderly coiled along the elongated nucleus axis. This chromatin spool is further found to achieve large-scale helical twisting in the final stages of spermiogenesis, favoring its ultracompaction. We reveal that these dramatic transitions may be recapitulated by a surprisingly simple biophysical principle based on a nucleated rigidification of chromatin linked to the histone-to-SNBP transition within a confined nuclear space. Our work highlights a unique, liquid crystal-like mode of higher-order genome organization in ultracompact cricket sperm, and establishes a multidisciplinary methodological framework to explore the diversity of non-canonical modes of DNA organization.
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Affiliation(s)
- Guillermo A Orsi
- Institute for Advanced Biosciences, University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, 38000, Grenoble, France.
| | - Maxime M C Tortora
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Béatrice Horard
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France
| | - Dominique Baas
- Laboratoire MeLiS, CNRS UMR 52684, Inserm U 1314, Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Lyon, France
| | - Jean-Philippe Kleman
- Institut de Biologie Structurale, UMR5075, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Jonas Bucevičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France.
| | - Benjamin Loppin
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France.
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5
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Weiss LE, Love JF, Yoon J, Comerci CJ, Milenkovic L, Kanie T, Jackson PK, Stearns T, Gustavsson AK. Single-molecule imaging in the primary cilium. Methods Cell Biol 2023; 176:59-83. [PMID: 37164543 PMCID: PMC10509820 DOI: 10.1016/bs.mcb.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The primary cilium is an important signaling organelle critical for normal development and tissue homeostasis. Its small dimensions and complexity necessitate advanced imaging approaches to uncover the molecular mechanisms behind its function. Here, we outline how single-molecule fluorescence microscopy can be used for tracking molecular dynamics and interactions and for super-resolution imaging of nanoscale structures in the primary cilium. Specifically, we describe in detail how to capture and quantify the 2D dynamics of individual transmembrane proteins PTCH1 and SMO and how to map the 3D nanoscale distributions of the inversin compartment proteins INVS, ANKS6, and NPHP3. This protocol can, with minor modifications, be adapted for studies of other proteins and cell lines to further elucidate the structure and function of the primary cilium at the molecular level.
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Affiliation(s)
- Lucien E Weiss
- Department of Engineering Physics, Polytechnique Montréal, Montreal, QC, Canada.
| | - Julia F Love
- Department of Chemistry, Rice University, Houston, TX, United States
| | | | - Colin J Comerci
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States
| | | | - Tomoharu Kanie
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, United States; Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA, United States; Rockefeller University, New York City, NY, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States; Department of BioSciences, Rice University, Houston, TX, United States; Institute of Biosciences and Bioengineering, Rice University, Houston, TX, United States; Smalley-Curl Institute, Rice University, Houston, TX, United States.
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6
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Sanders EW, Carr AR, Bruggeman E, Körbel M, Benaissa SI, Donat RF, Santos AM, McColl J, O'Holleran K, Klenerman D, Davis SJ, Lee SF, Ponjavic A. resPAINT: Accelerating Volumetric Super-Resolution Localisation Microscopy by Active Control of Probe Emission. Angew Chem Int Ed Engl 2022; 61:e202206919. [PMID: 35876263 DOI: 10.1002/anie.202206919] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 01/07/2023]
Abstract
Points for accumulation in nanoscale topography (PAINT) allows practically unlimited measurements in localisation microscopy but is limited by background fluorescence at high probe concentrations, especially in volumetric imaging. We present reservoir-PAINT (resPAINT), which combines PAINT and active control of probe photophysics. In resPAINT, an activatable probe "reservoir" accumulates on target, enabling a 50-fold increase in localisation rate versus conventional PAINT, without compromising contrast. By combining resPAINT with large depth-of-field microscopy, we demonstrate super-resolution imaging of entire cell surfaces. We generalise the approach by implementing various switching strategies and 3D imaging techniques. Finally, we use resPAINT with a Fab to image membrane proteins, extending the operating regime of PAINT to include a wider range of biological interactions.
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Affiliation(s)
- Edward W Sanders
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alexander R Carr
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Ezra Bruggeman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Markus Körbel
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Sarah I Benaissa
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Robert F Donat
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana M Santos
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - James McColl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Kevin O'Holleran
- Cambridge Advanced Imaging Centre, University of Cambridge, Cambridge, CB2 3DY, UK
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Simon J Davis
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Steven F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Aleks Ponjavic
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.,School of Food Science and Nutrition, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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7
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Sanders EW, Carr AR, Bruggeman E, Körbel M, Benaissa SI, Donat RF, Santos AM, McColl J, O'Holleran K, Klenerman D, Davis SJ, Lee SF, Ponjavic A. resPAINT: Accelerating Volumetric Super-Resolution Localisation Microscopy by Active Control of Probe Emission. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202206919. [PMID: 38505515 PMCID: PMC10946633 DOI: 10.1002/ange.202206919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 03/21/2024]
Abstract
Points for accumulation in nanoscale topography (PAINT) allows practically unlimited measurements in localisation microscopy but is limited by background fluorescence at high probe concentrations, especially in volumetric imaging. We present reservoir-PAINT (resPAINT), which combines PAINT and active control of probe photophysics. In resPAINT, an activatable probe "reservoir" accumulates on target, enabling a 50-fold increase in localisation rate versus conventional PAINT, without compromising contrast. By combining resPAINT with large depth-of-field microscopy, we demonstrate super-resolution imaging of entire cell surfaces. We generalise the approach by implementing various switching strategies and 3D imaging techniques. Finally, we use resPAINT with a Fab to image membrane proteins, extending the operating regime of PAINT to include a wider range of biological interactions.
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Affiliation(s)
- Edward W. Sanders
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Alexander R. Carr
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Ezra Bruggeman
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Markus Körbel
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Sarah I. Benaissa
- Cambridge Advanced Imaging CentreUniversity of CambridgeCambridgeCB2 3DYUK
| | - Robert F. Donat
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology UnitJohn Radcliffe HospitalUniversity of OxfordOxfordOX3 9DSUK
| | - Ana M. Santos
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology UnitJohn Radcliffe HospitalUniversity of OxfordOxfordOX3 9DSUK
| | - James McColl
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Kevin O'Holleran
- Cambridge Advanced Imaging CentreUniversity of CambridgeCambridgeCB2 3DYUK
| | - David Klenerman
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Simon J. Davis
- Radcliffe Department of Medicine and United Kingdom Medical Research Council Human Immunology UnitJohn Radcliffe HospitalUniversity of OxfordOxfordOX3 9DSUK
| | - Steven F. Lee
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Aleks Ponjavic
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
- School of Physics and AstronomyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of Food Science and NutritionUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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8
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Peng HY, Zhang G, Xu YJ, Sun R, Ge JF. Near-infrared fluorescent probes based on a quinoxaline skeleton for imaging nucleic acids in mitochondria. Org Biomol Chem 2022; 20:5558-5565. [PMID: 35791887 DOI: 10.1039/d2ob01095j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, two cationic probes 1a and 1b and a neutral dye 1c were successfully designed and synthesized according to the Knoevenagel condensation reaction, which combines the good optical properties of hemocyanine and the biocompatibility of nitrogen-containing heterocyclic rings based on a quinoxaline skeleton. Probes 1a and 1b showed an OFF-ON fluorescence response to nucleic acids with excellent selectivity. Specifically, the fluorescence intensity of probe 1a was enhanced by 18 and 133 times, respectively, along with the increase of DNA or RNA concentrations (0-600 μg mL-1). Furthermore, a good linear correlation between the fluorescence intensity of probes 1a and 1b and the concentrations of DNA or RNA (0-350 μg mL-1) was obtained. In particular, the maximum emission wavelengths of probes 1a and 1b reached the near-infrared region (660-664 nm) when DNA or RNA was detected, which might reduce the light damage to cells and facilitate cell experiments. Fluorescence imaging revealed that all three dyes could be localized in the mitochondria of HeLa cells. The difference was that probes 1a and 1b could stain the nucleic acid in the mitochondria, while dye 1c was only a neutral mitochondrial biomarker. The results indicated that probes 1a and 1b are promising in the development of low toxicity mitochondrial nucleic acid probes and are expected to be used in monitoring the normal state of mitochondrial nucleic acids for living cells, which will help improve the situation in that currently reported studies of fluorescent probes are mainly focused on the nucleic acids in the nucleus, but less so on DNA in the mitochondria.
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Affiliation(s)
- Hai-Yan Peng
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
| | - Gang Zhang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Yu-Jie Xu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Ru Sun
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
| | - Jian-Feng Ge
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
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9
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Jei BB, Yang L, Ackermann L. Selective Labeling of Peptides with o-Carboranes via Manganese(I)-Catalyzed C-H Activation. Chemistry 2022; 28:e202200811. [PMID: 35420234 PMCID: PMC9320968 DOI: 10.1002/chem.202200811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Indexed: 12/15/2022]
Abstract
A robust method for the selective labeling of peptides via manganese(I) catalysis was devised to achieve the C-2 alkenylation of tryptophan containing peptides with 1-ethynyl-o-carboranes. The manganese-catalyzed C-H activation was accomplished with high catalytic efficiency, and featured low toxicity, high functional group tolerance and excellent E-stereoselectivity. This approach unravels a promising tool for the assembly of o-carborane with structurally complex peptides of relevance to applications in boron neutron capture therapy.
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Affiliation(s)
- Becky Bongsuiru Jei
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTamannstraße 237077GöttingenGermany
- Woehler Research Institute for Sustainable Chemistry (WISCh)Georg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
| | - Long Yang
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTamannstraße 237077GöttingenGermany
- Woehler Research Institute for Sustainable Chemistry (WISCh)Georg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität GöttingenTamannstraße 237077GöttingenGermany
- Woehler Research Institute for Sustainable Chemistry (WISCh)Georg-August-Universität GöttingenTammannstraße 237077GöttingenGermany
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10
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Cortesi M, Giordano E. Non-destructive monitoring of 3D cell cultures: new technologies and applications. PeerJ 2022; 10:e13338. [PMID: 35582620 PMCID: PMC9107788 DOI: 10.7717/peerj.13338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/05/2022] [Indexed: 01/13/2023] Open
Abstract
3D cell cultures are becoming the new standard for cell-based in vitro research, due to their higher transferrability toward in vivo biology. The lack of established techniques for the non-destructive quantification of relevant variables, however, constitutes a major barrier to the adoption of these technologies, as it increases the resources needed for the experimentation and reduces its accuracy. In this review, we aim at addressing this limitation by providing an overview of different non-destructive approaches for the evaluation of biological features commonly quantified in a number of studies and applications. In this regard, we will cover cell viability, gene expression, population distribution, cell morphology and interactions between the cells and the environment. This analysis is expected to promote the use of the showcased technologies, together with the further development of these and other monitoring methods for 3D cell cultures. Overall, an extensive technology shift is required, in order for monolayer cultures to be superseded, but the potential benefit derived from an increased accuracy of in vitro studies, justifies the effort and the investment.
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Affiliation(s)
- Marilisa Cortesi
- Department of Electrical, Electronic and Information Engineering ”G.Marconi”, University of Bologna, Bologna, Italy
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Kensington, Australia
| | - Emanuele Giordano
- Department of Electrical, Electronic and Information Engineering ”G.Marconi”, University of Bologna, Bologna, Italy
- BioEngLab, Health Science and Technology, Interdepartmental Center for Industrial Research (HST-CIRI), University of Bologna, Ozzano Emilia, Italy
- Advanced Research Center on Electronic Systems (ARCES), University of Bologna, Bologna, Italy
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11
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Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
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Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
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12
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Gerasimaitė R, Bucevičius J, Kiszka KA, Schnorrenberg S, Kostiuk G, Koenen T, Lukinavičius G. Blinking Fluorescent Probes for Tubulin Nanoscopy in Living and Fixed Cells. ACS Chem Biol 2021; 16:2130-2136. [PMID: 34734690 PMCID: PMC8609524 DOI: 10.1021/acschembio.1c00538] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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Here we report a
small molecule tubulin probe for single-molecule
localization microscopy (SMLM), stimulated emission depletion (STED)
microscopy and MINFLUX nanoscopy, which can be used in living and
fixed cells. We explored a series of taxane derivatives containing
spontaneously blinking far-red dye hydroxymethyl silicon–rhodamine
(HMSiR) and found that the linker length profoundly affects the probe
permeability and off-targeting in living cells. The best performing
probe, HMSiR-tubulin, is composed of cabazitaxel and the 6′-regioisomer
of HMSiR bridged by a C6 linker. Microtubule diameter of ≤50
nm was routinely measured in SMLM experiments on living and fixed
cells. HMSiR-tubulin allows a complementary use of different nanoscopy
techniques for investigating microtubule functions and developing
imaging methods. For the first time, we resolved the inner microtubule
diameter of 16 ± 5 nm by optical nanoscopy and thereby demonstrated
the utility of a self-blinking dye for MINFLUX imaging.
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Affiliation(s)
- Ru̅ta Gerasimaitė
- Chromatin Labeling and Imaging group, Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jonas Bucevičius
- Chromatin Labeling and Imaging group, Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kamila A. Kiszka
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Georgij Kostiuk
- Chromatin Labeling and Imaging group, Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Tanja Koenen
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging group, Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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13
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Optimization of Advanced Live-Cell Imaging through Red/Near-Infrared Dye Labeling and Fluorescence Lifetime-Based Strategies. Int J Mol Sci 2021; 22:ijms222011092. [PMID: 34681761 PMCID: PMC8537913 DOI: 10.3390/ijms222011092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/30/2022] Open
Abstract
Fluorescence microscopy is essential for a detailed understanding of cellular processes; however, live-cell preservation during imaging is a matter of debate. In this study, we proposed a guide to optimize advanced light microscopy approaches by reducing light exposure through fluorescence lifetime (τ) exploitation of red/near-infrared dyes. Firstly, we characterized key instrumental elements which revealed that red/near-infrared laser lines with an 86x (Numerical Aperture (NA) = 1.2, water immersion) objective allowed high transmission of fluorescence signals, low irradiance and super-resolution. As a combination of two technologies, i.e., vacuum tubes (e.g., photomultiplier) and semiconductor microelectronics (e.g., avalanche photodiode), type S, X and R of hybrid detectors (HyD-S, HyD-X and HyD-R) were particularly adapted for red/near-infrared photon counting and τ separation. Secondly, we tested and compared lifetime-based imaging including coarse τ separation for confocal microscopy, fitting and phasor plot analysis for fluorescence lifetime microscopy (FLIM), and lifetimes weighting for enhanced stimulated emission depletion (STED) nanoscopy, in light of red/near-infrared multiplexing. Mainly, we showed that the choice of appropriate imaging approach may depend on fluorochrome number, together with their spectral/lifetime characteristics and STED compatibility. Photon-counting mode and sensitivity of HyDs together with phasor plot analysis of fluorescence lifetimes enabled the flexible and fast imaging of multi-labeled living H28 cells. Therefore, a combination of red/near-infrared dyes labeling with lifetime-based strategies offers new perspectives for live-cell imaging by enhancing sample preservation through acquisition time and light exposure reduction.
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14
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Hara D, Uno SN, Motoki T, Kazuta Y, Norimine Y, Suganuma M, Fujiyama S, Shimaoka Y, Yamashita K, Okada M, Nishikawa Y, Amino H, Iwanaga S. Silinanyl Rhodamines and Silinanyl Fluoresceins for Super-Resolution Microscopy. J Phys Chem B 2021; 125:8703-8711. [PMID: 34328341 DOI: 10.1021/acs.jpcb.1c03193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-molecule localization microscopy (SMLM) enables the visualization of biomolecules at unprecedented resolution and requires control of the fluorescent blinking (ON/OFF) states of fluorophores to detect single-molecule fluorescence without overlapping of the signals. Although SMLM probes based on the intramolecular spirocyclization of Si-xanthene fluorophores have been developed, fluorophores with lower ON/OFF ratios are required for SMLM visualization of high-density structures. Here, we describe a silinane structure that lowers the ON/OFF ratio of Si-xanthene fluorophores. On the basis of Mulliken population analysis, we replaced the dimethylsilane moiety in Si-rhodamine with a silinane moiety to increase the partial charge at the 9-position of the carbon atom in the Si-xanthene ring and to promote the ring-closure reaction. Evaluation of fluorescence properties in a solution and in single-molecule imaging indicated that introducing the silinane sufficiently stabilized the nonfluorescent spirocyclic forms, thus decreasing the fluorescence ON/OFF ratio. This novel substitution was applied to Si-rhodamines with various amine structures and to an Si-fluorescein to expand the color palette. We demonstrated SMLM observation of microtubules in fixed HeLa cells using the developed fluorophores in two color channels. The results demonstrated the feasibility of extending the design strategies of SMLM probes based on Si-xanthenes through modification of the substituents on the Si atom.
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Affiliation(s)
- Daiki Hara
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Shin-Nosuke Uno
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Takafumi Motoki
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba, Ibaraki 300-2635, Japan
| | - Yuji Kazuta
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba, Ibaraki 300-2635, Japan
| | - Yoshihiko Norimine
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba, Ibaraki 300-2635, Japan
| | - Masatoshi Suganuma
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Shingo Fujiyama
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Yuki Shimaoka
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Kazuto Yamashita
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Masaya Okada
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Youichi Nishikawa
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
| | - Hiroyuki Amino
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tokodai 5-1-3, Tsukuba, Ibaraki 300-2635, Japan
| | - Shigeki Iwanaga
- Central Research Laboratories, Sysmex Corporation, Takatsukadai 4-4-4, Nishi-ku, Kobe, Hyogo 651-2271, Japan
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