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Rahman F, Augoustides V, Tyler E, Daugird TA, Arthur C, Legant WR. Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.27.605159. [PMID: 39211261 PMCID: PMC11360932 DOI: 10.1101/2024.07.27.605159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The nucleus coordinates many different processes. Visualizing how these are spatially organized requires imaging protein complexes, epigenetic marks, and DNA across scales from single molecules to the whole nucleus. To accomplish this, we developed a multiplexed imaging protocol to localize 13 different nuclear targets with nanometer precision in single cells. We show that nuclear specification into active and repressive states exists along a spectrum of length scales, emerging below one micron and becoming strengthened at the nanoscale with unique organizational principles in both heterochromatin and euchromatin. HP1-α was positively correlated with DNA at the microscale but uncorrelated at the nanoscale. RNA Polymerase II, p300, and CDK9 were positively correlated at the microscale but became partitioned below 300 nm. Perturbing histone acetylation or transcription disrupted nanoscale organization but had less effect at the microscale. We envision that our imaging and analysis pipeline will be useful to reveal the organizational principles not only of the cell nucleus but also other cellular compartments.
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Ye C, Guo H, Wei Y, Zhou S, Zhang S, Li J, Cui J, Wu D. K 2Cr 2O 7-induced DNA damage in HT1080 cells: Electrochemical signal response mechanism. Int J Biol Macromol 2024; 261:129629. [PMID: 38266843 DOI: 10.1016/j.ijbiomac.2024.129629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The existing DNA damage detection technology cannot meet the current detection requirements. It is critical to build new methods and discover novel biomarkers. In this study, alkaline comet and 8-OHDG ELISA assays were used to identify DNA damage in HT-1080 cells exposed to K2Cr2O7, and electrochemical behaviors of HT-1080 cells with DNA damage was studied. With an increase in K2Cr2O7 exposure time, two electrochemical signals from HT-1080 cells at 0.69 and 1.01 V steadily grew before decreasing after reaching their highest values. The electrochemical signal's initial response time and peak time decreased as the concentration of K2Cr2O7 increased. The duration of the high dose group was 0.5 and 1 h, while the low dose group was 1.5 and 6 h. Western blotting analysis revealed that DNA damage increased the expression of proteins involved in catabolism and de novo purine synthesis, particularly de novo purine synthesis. Expressions of PRPP amidotransferase, IMPDH, and ADA were all higher than those of ADSS, XOD, and GDA, which resulted in larger concentrations of hypoxanthine, guanine, and xanthine, and in turn improved electrochemical signaling. These findings suggest that intracellular purine identified by linear scan voltammetry is predicted to evolve as a marker of early DNA damage.
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Affiliation(s)
- Cai Ye
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China
| | - Haohuan Guo
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China
| | - Ying Wei
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China
| | - Shi Zhou
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China
| | - Simiao Zhang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China
| | - Jinlian Li
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China.
| | - Jiwen Cui
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China.
| | - Dongmei Wu
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi, Heilongjiang 154007, PR China.
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Morgan STB, Whelan DR, Rozario AM. Visualizing DNA damage and repair using single molecule super resolution microscopy. Methods Cell Biol 2023; 182:237-245. [PMID: 38359980 DOI: 10.1016/bs.mcb.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Single molecule super resolution microscopy overcomes the diffraction limit by separating individual fluorophore emissions over time, resulting in spatial resolutions that are far superior to epifluorescence microscopy. This allows for DNA damage response (DDR) events to be investigated in greater detail. A variety of DNA damaging drugs can be used on S-phase synchronized immortalized cell lines alongside 5-ethynyl-2'-deoxyuridine (EdU) pulse labelling to ultimately visualize DNA repair pathways at distinct time points and quantify colocalizations between nascent DNA and immunolabeled DDR proteins. This chapter will outline super resolution microscopy assays to interrogate the spatiotemporal organization of DNA repair proteins at damaged foci during DDR events within immortalized cell lines.
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Affiliation(s)
- Sophie T B Morgan
- La Trobe Institute for Molecular Science, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
| | - Donna R Whelan
- La Trobe Institute for Molecular Science, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
| | - Ashley M Rozario
- La Trobe Institute for Molecular Science, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia.
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Rozario AM, Morey A, Elliott C, Russ B, Whelan DR, Turner SJ, Bell TDM. 3D Single Molecule Super-Resolution Microscopy of Whole Nuclear Lamina. Front Chem 2022; 10:863610. [PMID: 35572104 PMCID: PMC9096160 DOI: 10.3389/fchem.2022.863610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
Single molecule (SM) super-resolution microscopies bypass the diffraction limit of conventional optical techniques and provide excellent spatial resolutions in the tens of nanometers without overly complex microscope hardware. SM imaging using optical astigmatism is an efficient strategy for visualizing subcellular features in 3D with a z-range of up to ∼1 µm per acquisition. This approach however, places high demands on fluorophore brightness and photoswitching resilience meaning that imaging entire cell volumes in 3D using SM super-resolution remains challenging. Here we employ SM astigmatism together with multiplane acquisition to visualize the whole nuclear lamina of COS-7 and T cells in 3D. Nuclear lamina provides structural support to the nuclear envelope and participates in vital nuclear functions including internuclear transport, chromatin organization and gene regulation. Its position at the periphery of the nucleus provides a visible reference of the nuclear boundary and can be used to quantify the spatial distribution of intranuclear components such as histone modifications and transcription factors. We found Alexa Fluor 647, a popular photoswitchable fluorophore, remained viable for over an hour of continuous high laser power exposure, and provided sufficient brightness detectable up to 8 µm deep into a cell, allowing us to capture the entire nuclear lamina in 3D. Our approach provides sufficient super-resolution detail of nuclear lamina morphology to enable quantification of overall nuclear dimensions and local membrane features.
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Affiliation(s)
- Ashley M. Rozario
- School of Chemistry, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Alison Morey
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Cade Elliott
- School of Chemistry, Monash University, Clayton, VIC, Australia
| | - Brendan Russ
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Donna R. Whelan
- La Trobe Institute for Molecular Science, Bendigo, VIC, Australia
| | - Stephen J. Turner
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
- *Correspondence: Stephen J. Turner, ; Toby D. M. Bell,
| | - Toby D. M. Bell
- School of Chemistry, Monash University, Clayton, VIC, Australia
- *Correspondence: Stephen J. Turner, ; Toby D. M. Bell,
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Birch DJS, Levitus M, Mély Y. MAFmoves higher and faster. Methods Appl Fluoresc 2021; 10. [PMID: 34904961 DOI: 10.1088/2050-6120/ac3ec0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 11/12/2022]
Affiliation(s)
- David J S Birch
- The Photophysics Research Group, University of Strathclyde, Department of Physics, SUPA, John Anderson Building, 107 Rottenrow, Glasgow, G4 0NG, United Kingdom
| | - Marcia Levitus
- School of Molecular Sciences and The Biodesign Institute, Arizona State University, PO Box 875601, Tempe AZ, 85287-5601, United States of America
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Cedex, 67401 Illkirch, France
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Chernov NM, Shutov RV, Sipkina NY, Krivchun MN, Yakovlev IP. A Flexible Synthetic Approach to Fluorescent Chromeno[4,3-b]pyridines and Pyrano[3,2-c]chromenes from Electron-Deficient 3-Vinylchromones. Chempluschem 2021; 86:1256-1266. [PMID: 34472730 DOI: 10.1002/cplu.202100296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/18/2021] [Indexed: 11/09/2022]
Abstract
We report a flexible approach to the synthesis of phenanthrene-like heterocycles through organocatalytic ANRORC (Addition of the Nucleophile, Ring Opening, and Ring Closure) reaction of electron-deficient 3-vinylchromones with cyanoacetamide. Addition of highly basic DBU (1,8-diazabicyclo[5.4.0]undec-7-ene) or tetramethylguanidine (TMG) at 80 °C leads to chromeno[4,3-b]pyridines in good yields, whereas Et3 N at 20 °C made it possible to obtain the less accessible pyrano[3,2-c]chromenes and their 2-imines. The synthesis proceeds in mild conditions (EtOH, 20-80 °C), is versatile and applicable for a wide scope of reactants. The obtained compounds show bright fluorescence in the range 460-595 nm with high quantum yields (up to 0.84) in various solvents (MeCN, DMSO, EtOH, H2 O).
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Affiliation(s)
- Nikita M Chernov
- Organic Chemistry Department, Saint-Petersburg State Chemical Pharmaceutical University, Prof. Popov st., 14, Saint-Petersburg, 197376, Russia
| | - Roman V Shutov
- Organic Chemistry Department, Saint-Petersburg State Chemical Pharmaceutical University, Prof. Popov st., 14, Saint-Petersburg, 197376, Russia
| | - Nadezhda Yu Sipkina
- Analytical Center, Saint-Petersburg State Chemical Pharmaceutical University, Prof. Popov st., 14, Saint-Petersburg, 197376, Russia
| | - Maxim N Krivchun
- Organic Chemistry Department, Saint-Petersburg State Institute of Technology, Moskovsky av., 26, Saint-Petersburg, 190013, Russia
| | - Igor P Yakovlev
- Organic Chemistry Department, Saint-Petersburg State Chemical Pharmaceutical University, Prof. Popov st., 14, Saint-Petersburg, 197376, Russia
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Wolfbeis OS. Fluorescent chameleon labels for bioconjugation and imaging of proteins, nucleic acids, biogenic amines and surface amino groups. a review. Methods Appl Fluoresc 2021; 9. [PMID: 34340216 DOI: 10.1088/2050-6120/ac1a0a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/02/2021] [Indexed: 12/14/2022]
Abstract
Chameleon labels (ChLs) possess the unique property of changing (visible) color and fluorescence on binding to amino groups of biomolecules. MostChLs react with primary aliphatic amino groups such as those in lysine or with amino groups artificially introduced into polynucleic acids or saccharides, but someothers also react with secondary amino groups. Under controlled circumstances, the reactions are fairly specific. The review is subdivided into the following sections: (1) An introduction and classification of fluorescent labels; (2) pyrylium labels that undergo shortwave color changes upon labelling, typically from blue to red; (3) polymethine type of labels (that also undergo shortwave color changes, typically from green to blue; (4) various other (less common) chromogenic and fluorogenic systems; (5) hemicyanine labels that undergolongwavecolor changes, typically from yellow to purple; (6) the application of ChLs to labeling of proteins and oligonucleotides; (7) applications to fluorometric assays and sensing; (8) applications to fluorescence imaging of biomolecules; (9) applications in studies on affinity interactions (receptor-ligand binding); (10) applications in surface and interface chemistry; and (11) applications in chromatography, electrophoresis and isotachophoresis of biomolecules.
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Affiliation(s)
- Otto S Wolfbeis
- University of Regensburg, Institute of Analytical Chemistry, Chemo- and Biosensors, 94040 Regensburg, Germany
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