1
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Gunasekara H, Perera T, Chao CJ, Bruno J, Saed B, Anderson J, Zhao Z, Hu YS. Phalloidin-PAINT: Enhanced quantitative nanoscale imaging of F-actin. Biophys J 2024:S0006-3495(24)00442-9. [PMID: 38961624 DOI: 10.1016/j.bpj.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
We present phalloidin-based points accumulation for imaging in nanoscale topography (phalloidin-PAINT), enabling quantitative superresolution imaging of filamentous actin (F-actin) in the cell body and delicate membrane protrusions. We demonstrate that the intrinsic phalloidin dissociation enables PAINT superresolution microscopy in an imaging buffer containing low concentrations of dye-conjugated phalloidin. We further show enhanced single-molecule labeling by chemically promoting phalloidin dissociation. Two benefits of phalloidin-PAINT are its ability to consistently quantify F-actin at the nanoscale throughout the entire cell and its enhanced preservation of fragile cellular structures. In a proof-of-concept study, we employed phalloidin-PAINT to superresolve F-actin structures in U2OS and dendritic cells (DCs). We demonstrate more consistent F-actin quantification in the cell body and structurally delicate membrane protrusions of DCs compared with direct stochastic optical reconstruction microscopy (dSTORM). Using DC2.4 mouse DCs as the model system, we show F-actin redistribution from podosomes to actin filaments and altered prevalence of F-actin-associated membrane protrusions on the culture glass surface after lipopolysaccharide exposure. The concept of our work opens new possibilities for quantitative protein-specific PAINT using commercially available reagents.
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Affiliation(s)
- Hirushi Gunasekara
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois
| | - Thilini Perera
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois
| | - Chih-Jia Chao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois
| | - Joshua Bruno
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois
| | - Badeia Saed
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois
| | - Jesse Anderson
- Department of Chemical Engineering, College of Engineering, University of Illinois Chicago, Chicago, Illinois
| | - Zongmin Zhao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois
| | - Ying S Hu
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois.
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2
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Go GE, Jeong U, Park H, Go S, Kim D. Photoswitching Reagent for Super-Resolution Fluorescence Microscopy. Angew Chem Int Ed Engl 2024; 63:e202405246. [PMID: 38622700 DOI: 10.1002/anie.202405246] [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: 03/17/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
Single-molecule localization microscopy (SMLM) has revolutionized optical microscopy by exceeding the diffraction limit and revealing previously unattainable nanoscale details of cellular structures and molecular dynamics. This super-resolution imaging capability relies on fluorophore photoswitching, which is crucial for optimizing the imaging conditions and accurately determining the fluorophore positions. To understand the general on and off photoswitching mechanisms of single dye molecules, various photoswitching reagents were evaluated. Systematic measurement of the single-molecule-level fluorescence on and off rates (kon and koff) in the presence of various photoswitching reagents and theoretical calculation of the structure of the photoswitching reagent-fluorophore pair indicated that the switch-off mechanism is mainly determined by the nucleophilicity of the photoswitching reagent, and the switch-on mechanism is a two-photon-induced dissociation process, which is related to the power of the illuminating laser and bond dissociation energy of this pair. This study contributes to a broader understanding of the molecular photoswitching mechanism in SMLM imaging and provides a basis for designing improved photoswitching reagents with potential applications extending to materials science and chemistry.
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Affiliation(s)
- Ga-Eun Go
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Uidon Jeong
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Hyunbum Park
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Seokran Go
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Doory Kim
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Institute of Nano Science and Technology, and Research Institute for Natural Sciences, Seoul, 04763, Republic of Korea
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3
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Pati AK, Kilic Z, Martin MI, Terry DS, Borgia A, Bar S, Jockusch S, Kiselev R, Altman RB, Blanchard SC. Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation. Nat Methods 2024; 21:1222-1230. [PMID: 38877317 PMCID: PMC11239528 DOI: 10.1038/s41592-024-02293-8] [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] [Received: 03/29/2023] [Accepted: 04/25/2024] [Indexed: 06/16/2024]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) methods employed to quantify time-dependent compositional and conformational changes within biomolecules require elevated illumination intensities to recover robust photon emission streams from individual fluorophores. Here we show that outside the weak-excitation limit, and in regimes where fluorophores must undergo many rapid cycles of excitation and relaxation, non-fluorescing, excitation-induced triplet states with lifetimes orders of magnitude longer lived than photon-emitting singlet states degrade photon emission streams from both donor and acceptor fluorophores resulting in illumination-intensity-dependent changes in FRET efficiency. These changes are not commonly taken into consideration; therefore, robust strategies to suppress excited state accumulations are required to recover accurate and precise FRET efficiency, and thus distance, estimates. We propose both robust triplet state suppression and data correction strategies that enable the recovery of FRET efficiencies more closely approximating true values, thereby extending the spatial and temporal resolution of smFRET.
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Affiliation(s)
- Avik K Pati
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maxwell I Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alessandro Borgia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sukanta Bar
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Steffen Jockusch
- Center for Photochemical Sciences and Department of Chemistry, Bowling Green State University, Bowling Green, OH, USA
| | - Roman Kiselev
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Roger B Altman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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4
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Bharadwaj A, Kumar A, Mitra R, Jaganathan BG, Boruah BR. Enhanced fluorescence blinking of AF647 fluorophores in Mowiol via violet and UV light induced recovery for superior localization microscopy. Methods Appl Fluoresc 2024; 12:035007. [PMID: 38740072 DOI: 10.1088/2050-6120/ad4ae6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/13/2024] [Indexed: 05/16/2024]
Abstract
Blinking of fluorophores is essential in the context of single molecule localization-based optical super-resolution microscopy methods. To make the fluorescence molecule undergo blinking specific complex chemical mounting buffer systems, combined with suitable oxygen scavengers, and reducing agents are required. For instance to realise blinking in widely used fluorescence tags, like Alexa Fluor 647 (AF647), they are to be mounted on anti-fading buffer such as Mowiol and reducing agent such as Beta (β) - ME. However, the quality of the super-resolved images is decided by the total number of blinking events or in other words net duration for which the fluorescence blinking persists. In this paper we investigate how a violet and UV light induced fluorescence recovery mechanism can enhance the duration of fluorescence blinking. Our study uses AF647 dye conjugated with Phalloidin antibody in U87MG cell line mounted on Mowiol andβ- ME. On the basis of the investigation we optimize the intensity, at the sample plane, of fluorescence excitation laser at 638 nm and fluorescence recovery beam at 405 nm or in the UV giving the maximum possible fluorescence blinking duration. We observe that the longer blinking duration, using the optimized illumination scheme, has brought down the resolution in the super-resolved image, as given by Fourier Ring Correlation method, from 168 nm to 112 nm, while the separation between two nearby resolvable filaments has been brought down to ≤ 60 nm.
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Affiliation(s)
- Anupam Bharadwaj
- Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Amalesh Kumar
- Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Rumela Mitra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Bithiah Grace Jaganathan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Bosanta R Boruah
- Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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5
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Shin S, Kwon Y, Hwang C, Jeon W, Yu Y, Paik HJ, Lee W, Kwon MS, Ahn D. Visible-Light-Driven Rapid 3D Printing of Photoresponsive Resins for Optically Clear Multifunctional 3D Objects. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311917. [PMID: 38288894 DOI: 10.1002/adma.202311917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/18/2024] [Indexed: 02/09/2024]
Abstract
Light-driven 3D printing is gaining significant attention for its unparalleled build speed and high-resolution in additive manufacturing. However, extending vat photopolymerization to multifunctional, photoresponsive materials poses challenges, such as light attenuation and interference between the photocatalysts (PCs) and photoactive moieties. This study introduces novel visible-light-driven acrylic resins that enable rapid, high-resolution photoactive 3D printing. The synergistic combination of a cyanine-based PC, borate, and iodonium coinitiators (HNu 254) achieves an excellent printing rate and feature resolution under low-intensity, red light exposure. The incorporation of novel hexaarylbiimidazole (HABI) crosslinkers allows for spatially-resolved photoactivation upon exposure to violet/blue light. Furthermore, a photobleaching mechanism inhibited by HNu 254 during the photopolymerization process results in the production of optically-clear 3D printed objects. Real-time Fourier transform infrared spectroscopy validates the rapid photopolymerization of the HABI-containing acrylic resin, whereas mechanistic evaluations reveal the underlying dynamics that are responsible for the rapid photopolymerization rate, wavelength-orthogonal photoactivation, and observed photobleaching phenomenon. Ultimately, this visible-light-based printing method demonstrates: (i) rapid printing rate of 22.5 mm h-1, (ii) excellent feature resolution (≈20 µm), and (iii) production of optically clear object with self-healing capability and spatially controlled cleavage. This study serves as a roadmap for developing next-generation "smart" 3D printing technologies.
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Affiliation(s)
- Sangbin Shin
- Center for Specialty Chemicals, Korea Research Institute of Chemical Technology (KRICT), Ulsan, 44412, Republic of Korea
- Department of Polymer Science and Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Yonghwan Kwon
- Department of Materials Science and Engineering, Seoul National University (SNU), Seoul, 08826, Republic of Korea
| | - Chiwon Hwang
- Center for Specialty Chemicals, Korea Research Institute of Chemical Technology (KRICT), Ulsan, 44412, Republic of Korea
- Department of Polymer Science and Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Woojin Jeon
- Department of Materials Science and Engineering, Seoul National University (SNU), Seoul, 08826, Republic of Korea
| | - Youngchang Yu
- Center for Specialty Chemicals, Korea Research Institute of Chemical Technology (KRICT), Ulsan, 44412, Republic of Korea
| | - Hyun-Jong Paik
- Department of Polymer Science and Engineering, Pusan National University, Busan, 46241, Republic of Korea
| | - Wonjoo Lee
- Center for Specialty Chemicals, Korea Research Institute of Chemical Technology (KRICT), Ulsan, 44412, Republic of Korea
| | - Min Sang Kwon
- Department of Materials Science and Engineering, Seoul National University (SNU), Seoul, 08826, Republic of Korea
| | - Dowon Ahn
- Center for Specialty Chemicals, Korea Research Institute of Chemical Technology (KRICT), Ulsan, 44412, Republic of Korea
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6
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Gunasekara H, Perera T, Chao CJ, Bruno J, Saed B, Anderson J, Zhao Z, Hu YS. Quantitative Superresolution Imaging of F-Actin in the Cell Body and Cytoskeletal Protrusions Using Phalloidin-Based Single-Molecule Labeling and Localization Microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583337. [PMID: 38496456 PMCID: PMC10942307 DOI: 10.1101/2024.03.04.583337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We present single-molecule labeling and localization microscopy (SMLLM) using dye-conjugated phalloidin to achieve enhanced superresolution imaging of filamentous actin (F-actin). We demonstrate that the intrinsic phalloidin dissociation enables SMLLM in an imaging buffer containing low concentrations of dye-conjugated phalloidin. We further show enhanced single-molecule labeling by chemically promoting phalloidin dissociation. Two benefits of phalloidin-based SMLLM are better preservation of cellular structures sensitive to mechanical and shear forces during standard sample preparation and more consistent F-actin quantification at the nanoscale. In a proof-of-concept study, we employed SMLLM to super-resolve F-actin structures in U2OS and dendritic cells (DCs) and demonstrate more consistent F-actin quantification in the cell body and structurally delicate cytoskeletal proportions, which we termed membrane fibers, of DCs compared to direct stochastic optical reconstruction microscopy (dSTORM). Using DC2.4 mouse dendritic cells as the model system, we show F-actin redistribution from podosomes to actin filaments and altered prevalence of F-actin-associated membrane fibers on the culture glass surface after lipopolysaccharide exposure. While our work demonstrates SMLLM for F-actin, the concept opens new possibilities for protein-specific single-molecule labeling and localization in the same step using commercially available reagents.
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Affiliation(s)
- Hirushi Gunasekara
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Thilini Perera
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Chih-Jia Chao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Joshua Bruno
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Badeia Saed
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Jesse Anderson
- Department of Chemical Engineering, College of Engineering, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Zongmin Zhao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Ying S. Hu
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
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7
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Chen Z, Ge C, Zhu X, Sun P, Sun Z, Derkach T, Zhou M, Wang Y, Luan M. A novel nanoprobe for visually investigating the controversial role of miRNA-34a as an oncogene or tumor suppressor in cancer cells. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:667-675. [PMID: 38230518 DOI: 10.1039/d3ay02270f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
MiRNA-targeted therapy has become a hot topic in current cancer research. The key to this treatment strategy is to clarify the specific role of miRNA in cancer. However, the roles of some miRNAs acting as oncogenic or tumor suppressors are still controversial, which are influenced by different tumor types, even in the same cancer type. Hence, we designed a novel fluorescent nanoprobe based on polydopamine nanoparticles (PDA NPs) for simultaneously detecting caspase-3 and miRNA-34a within living cells. The specific role of miRNA-34a in different cancer cells could be further identified by studying the expression alterations of caspase-3 and miRNA-34a. Confocal imaging indicated that miRNA-34a indeed acted as a tumor suppressor in anticancer drug-treated MCF-7 and HeLa cells, where the effect of miRNA-34a remains controversial. The designed nanoprobe can offer a promising approach to ascertain the oncogenic or tumor-suppressing role of miRNA in different cancer cells with a simple visualization method, which has valuable implications for exploring the practicability of precision therapy focused on miRNA and evaluating the efficacy of new miRNA-targeted anticancer medications.
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Affiliation(s)
- Zhe Chen
- Institute for Functional Biomolecules, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Chuandong Ge
- Institute for Functional Biomolecules, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Xiaokai Zhu
- Institute for Functional Biomolecules, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Ping Sun
- Institute for Functional Biomolecules, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Zeyuan Sun
- Kyiv National University of Technologies and Design, 01011, Kyiv, Ukraine
| | - Tetiana Derkach
- Kyiv National University of Technologies and Design, 01011, Kyiv, Ukraine
| | - Mingyang Zhou
- Institute for Functional Biomolecules, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Yaoguang Wang
- Institute for Functional Biomolecules, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Mingming Luan
- Institute for Functional Biomolecules, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
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8
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Jing Y, Huang L, Dong Z, Gong Z, Yu B, Lin D, Qu J. Super-resolution imaging of folate receptor alpha on cell membranes using peptide-based probes. Talanta 2024; 268:125286. [PMID: 37832456 DOI: 10.1016/j.talanta.2023.125286] [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: 06/28/2023] [Revised: 09/13/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023]
Abstract
Folate receptor alpha (FRα) is a vital membrane protein which have great association with cancers and involved in various biological processes including folate transport and cell signaling. However, the distribution and organization pattern of FRα on cell membranes remains unclear. Previous studies relied on antibodies to recognize the proteins. However, multivalent crosslinking and large size of antibodies confuse the direct observation to some extent. Fortunately, the emergence of peptide, which are small-sized and monovalent, has supplied us an unprecedented choice. Here, we applied fluorophore-conjugated peptide probe to recognize the FRα and study the distribution pattern of FRα on cell membrane using dSTORM super-resolution imaging technique. FRα were found to organized as clusters on cell surface with different sizes. And they have a higher expression level and formed larger clusters on various cancer cells than normal cells, which hinted that its specific distribution could be utilized for cancer diagnosis. Furthermore, we revealed that the lipid raft and cortical actin as restrictive factors for the FRα clustering, suggesting a potential assembly mechanism insight into FRα clustering on cell membrane. Collectively, our work clarified the morphology distribution and clustered organization of FRα with peptide probes at the nanometer scale, which paves the way for further revealing the relationship between the spatial organization and functions of membranal proteins.
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Affiliation(s)
- Yingying Jing
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Lilin Huang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Zufu Dong
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Zhenquan Gong
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Bin Yu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Danying Lin
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China.
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China.
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9
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Fan F, Su B, Kolodychak A, Ekwueme E, Alderfer L, Saha S, Webber MJ, Hanjaya-Putra D. Hyaluronic Acid Hydrogels with Phototunable Supramolecular Cross-Linking for Spatially Controlled Lymphatic Tube Formation. ACS APPLIED MATERIALS & INTERFACES 2023; 15:58181-58195. [PMID: 38065571 PMCID: PMC10739586 DOI: 10.1021/acsami.3c12514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/22/2023]
Abstract
The dynamics of the extracellular matrix (ECM) influences stem cell differentiation and morphogenesis into complex lymphatic networks. While dynamic hydrogels with stress relaxation properties have been developed, many require detailed chemical processing to tune viscoelasticity, offering a limited opportunity for in situ and spatiotemporal control. Here, a hyaluronic acid (HA) hydrogel is reported with viscoelasticity that is controlled and spatially tunable using UV light to direct the extent of supramolecular and covalent cross-linking interactions. This is achieved using UV-mediated photodimerization of a supramolecular ternary complex of pendant trans-Brooker's Merocyanine (BM) guests and a cucurbit[8]uril (CB[8]) macrocycle. The UV-mediated conversion of this supramolecular complex to its covalent photodimerized form is catalyzed by CB[8], offering a user-directed route to spatially control hydrogel dynamics in combination with orthogonal photopatterning by UV irradiation through photomasks. This material thus achieves spatial heterogeneity of substrate dynamics, recreating features of native ECM without the need for additional chemical reagents. Moreover, these dynamic hydrogels afford spatial control of substrate mechanics to direct human lymphatic endothelial cells (LECs) to form lymphatic cord-like structures (CLS). Specifically, cells cultured on viscoelastic supramolecular hydrogels have enhanced formation of CLS, arising from increased expression of key lymphatic markers, such as LYVE-1, Podoplanin, and Prox1, compared to static elastic hydrogels prepared from fully covalent cross-linking. Viscoelastic hydrogels promote lymphatic CLS formation through the expression of Nrp2, VEGFR2, and VEGFR3 to enhance the VEGF-C stimulation. Overall, viscoelastic supramolecular hydrogels offer a facile route to spatially control lymphatic CLS formation, providing a tool for future studies of basic lymphatic biology and tissue engineering applications.
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Affiliation(s)
- Fei Fan
- Bioengineering
Graduate Program, Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Bo Su
- Chemical
and Biomolecular Engineering, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Alexander Kolodychak
- Chemical
and Biomolecular Engineering, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ephraim Ekwueme
- Bioengineering
Graduate Program, Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Laura Alderfer
- Bioengineering
Graduate Program, Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Sanjoy Saha
- Bioengineering
Graduate Program, Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Matthew J. Webber
- Chemical
and Biomolecular Engineering, University
of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Donny Hanjaya-Putra
- Bioengineering
Graduate Program, Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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10
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Fazel M, Grussmayer KS, Ferdman B, Radenovic A, Shechtman Y, Enderlein J, Pressé S. Fluorescence Microscopy: a statistics-optics perspective. ARXIV 2023:arXiv:2304.01456v3. [PMID: 37064525 PMCID: PMC10104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Modeling these features is ever more important in quantitatively interpreting microscopy images collected at scales on par or smaller than light's wavelength. Here we review the optics responsible for generating fluorescent images, fluorophore properties, microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement.
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Affiliation(s)
- Mohamadreza Fazel
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Kristin S Grussmayer
- Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Boris Ferdman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Yoav Shechtman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
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11
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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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12
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Gidi Y, Ramos-Sanchez J, Lovell TC, Glembockyte V, Cheah IK, Schnermann MJ, Halliwell B, Cosa G. Superior Photoprotection of Cyanine Dyes with Thio-imidazole Amino Acids. J Am Chem Soc 2023; 145:19571-19577. [PMID: 37658476 DOI: 10.1021/jacs.3c03058] [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] [Indexed: 09/03/2023]
Abstract
Preventing fluorophore photobleaching and unwanted blinking is crucial for single-molecule fluorescence (SMF) studies. Reductants achieve photoprotection via quenching excited triplet states, yet either require counteragents or, for popular alkyl-thiols, are limited to cyanine dye Cy3 protection. Here, we provide mechanistic and imaging results showing that the naturally occurring amino acid ergothioneine and its analogue dramatically enhance photostability for Cy3, Cy5, and their conformationally restrained congeners, providing a biocompatible universal solution for demanding fluorescence imaging.
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Affiliation(s)
- Yasser Gidi
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Jorge Ramos-Sanchez
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Terri C Lovell
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Viktorija Glembockyte
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Irwin K Cheah
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Life Science Institute, Neurobiology Programme, Centre for Life Sciences, National University of Singapore, Singapore 117456, Singapore
| | - Martin J Schnermann
- Laboratory of Chemical Biology, NIH/NCI/CCR, 376 Boyles Street, Frederick, Maryland 21702, United States
| | - Barry Halliwell
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Life Science Institute, Neurobiology Programme, Centre for Life Sciences, National University of Singapore, Singapore 117456, Singapore
| | - Gonzalo Cosa
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM), McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
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13
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Köckenberger J, Klemt I, Sauer C, Arkhypov A, Reshetnikov V, Mokhir A, Heinrich MR. Cyanine- and Rhodamine-Derived Alkynes for the Selective Targeting of Cancerous Mitochondria through Radical Thiol-Yne Coupling in Live Cells. Chemistry 2023; 29:e202301340. [PMID: 37171462 DOI: 10.1002/chem.202301340] [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: 04/28/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/13/2023]
Abstract
Despite their long history and their synthetic potential underlined by various recent advances, radical thiol-yne coupling reactions have so far only rarely been exploited for the functionalization of biomolecules, and no examples yet exist for their application in live cells - although natural thiols show widespread occurrence therein. By taking advantage of the particular cellular conditions of mitochondria in cancer cells, we have demonstrated that radical thiol-yne coupling represents a powerful reaction principle for the selective targeting of these organelles. Within our studies, fluorescently labeled reactive alkyne probes were investigated, for which the fluorescent moiety was chosen to enable both mitochondria accumulation as well as highly sensitive detection. After preliminary studies under cell-free conditions, the most promising alkyne-dye conjugates were evaluated in various cellular experiments comprising analysis by flow cytometry and microscopy. All in all, these results pave the way for improved future therapeutic strategies relying on live-cell compatibility and selectivity among cellular compartments.
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Affiliation(s)
- Johannes Köckenberger
- Department of Chemistry and Pharmacy Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Insa Klemt
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Caroline Sauer
- Department of Chemistry and Pharmacy Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Anton Arkhypov
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Viktor Reshetnikov
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Andriy Mokhir
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
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14
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Han Y, Luo C, Quan Z, Li H, Sun S, Xu Y. New "Destruction Seek to Survive" Strategy Based on a Serum Albumin Assembly with a Squaraine Molecule for the Detection of Peroxynitrite. Anal Chem 2023; 95:7278-7285. [PMID: 37115498 DOI: 10.1021/acs.analchem.3c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Peroxynitrite (ONOO-), a kind of active nitrogen species, plays an important role in biological systems. Overproduction of ONOO- is closely related to the pathogenesis of many diseases. Therefore, it is necessary to quantify intracellular ONOO- for differentiating health and disease states. Fluorescent probes with near-infrared (NIR) fluorescence can detect ONOO- with high sensitivity and selectivity. However, there is an inevitable problem that many NIR fluorophores are easily oxidized by ONOO- to give a false-negative result. To avoid this problem, herein, we ingeniously propose a "destruction to seek to survive" strategy to detect ONOO-. Two NIR squaraine (SQ) dyes were connected together to form a fluorescent probe (SQDC). This method utilizes the destructive effect of peroxynitrite on one of the SQ moieties of SQDC to eliminate the steric hindrance, enabling the other "survived" SQ segment to enter the hydrophobic cavity of bovine serum albumin (BSA) via the well-known host-guest interactions. The encapsulation of albumin protects the "survived" SQ from further attack of ONOO-. As a result, a NIR fluorescence turn-on response coming from the host-guest interaction between BSA and the "survived" SQ escaped from SQDC was found, which can be used for the detection of ONOO-. The assembly of SQDC mixed with BSA can be located in mitochondria to detect endogenous and exogenous ONOO- sensitively in living cells. As a proof-of-concept method, it is envisioned that this novel detection strategy with a simple assembly would become a powerful means for the detection of ONOO- when employing NIR fluorophores.
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Affiliation(s)
- Ying Han
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Canxia Luo
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Zongyan Quan
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Hongjuan Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shiguo Sun
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Yongqian Xu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
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15
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Sun N, Jia Y, Bai S, Li Q, Dai L, Li J. The power of super-resolution microscopy in modern biomedical science. Adv Colloid Interface Sci 2023; 314:102880. [PMID: 36965225 DOI: 10.1016/j.cis.2023.102880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Super-resolution microscopy (SRM) technology that breaks the diffraction limit has revolutionized the field of cell biology since its appearance, which enables researchers to visualize cellular structures with nanometric resolution, multiple colors and single-molecule sensitivity. With the flourishing development of hardware and the availability of novel fluorescent probes, the impact of SRM has already gone beyond cell biology and extended to nanomedicine, material science and nanotechnology, and remarkably boosted important breakthroughs in these fields. In this review, we will mainly highlight the power of SRM in modern biomedical science, discussing how these SRM techniques revolutionize the way we understand cell structures, biomaterials assembly and how assembled biomaterials interact with cellular organelles, and finally their promotion to the clinical pre-diagnosis. Moreover, we also provide an outlook on the current technical challenges and future improvement direction of SRM. We hope this review can provide useful information, inspire new ideas and propel the development both from the perspective of SRM techniques and from the perspective of SRM's applications.
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Affiliation(s)
- Nan Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Shiwei Bai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Qi Li
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences, Beijing 100190, China
| | - Luru Dai
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049.
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16
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Gong J, Jin Z, Chen H, He J, Zhang Y, Yang X. Super-resolution fluorescence microscopic imaging in pathogenesis and drug treatment of neurological disease. Adv Drug Deliv Rev 2023; 196:114791. [PMID: 37004939 DOI: 10.1016/j.addr.2023.114791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 04/03/2023]
Abstract
Since super-resolution fluorescence microscopic technology breaks the diffraction limit that has existed for a long time in optical imaging, it can observe the process of synapses formed between nerve cells and the protein aggregation related to neurological disease. Thus, super-resolution fluorescence microscopic imaging has significantly impacted several industries, including drug development and pathogenesis research, and it is anticipated that it will significantly alter the future of life science research. Here, we focus on several typical super-resolution fluorescence microscopic technologies, introducing their benefits and drawbacks, as well as applications in several common neurological diseases, in the hope that their services will be expanded and improved in the pathogenesis and drug treatment of neurological diseases.
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17
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Remmel M, Scheiderer L, Butkevich AN, Bossi ML, Hell SW. Accelerated MINFLUX Nanoscopy, through Spontaneously Fast-Blinking Fluorophores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206026. [PMID: 36642798 DOI: 10.1002/smll.202206026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/24/2022] [Indexed: 06/17/2023]
Abstract
The introduction of MINFLUX nanoscopy allows single molecules to be localized with one nanometer precision in as little as one millisecond. However, current applications have so far focused on increasing this precision by optimizing photon collection, rather than minimizing the localization time. Concurrently, commonly used fluorescent switches are specifically designed for stochastic methods (e.g., STORM), optimized for a high photon yield and rather long on-times (tens of milliseconds). Here, accelerated MINFLUX nanoscopy with up to a 30-fold gain in localization speed is presented. The improvement is attained by designing spontaneously blinking fluorescent markers with remarkably fast on-times, down to 1-3 ms, matching the iterative localization process used in a MINFLUX microscope. This design utilizes a silicon rhodamine amide core, shifting the spirocyclization equilibrium toward an uncharged closed form at physiological conditions and imparting intact live cell permeability, modified with a fused (benzo)thiophene spirolactam fragment. The best candidate for MINFLUX microscopy (also suitable for STORM imaging) is selected through detailed characterization of the blinking behavior of single fluorophores, bound to different protein tags. Finally, optimization of the localization routines, customized to the fast blinking times, renders a significant speed improvement on a commercial MINFLUX microscope.
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Affiliation(s)
- Michael Remmel
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Lukas Scheiderer
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Alexey N Butkevich
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Mariano L Bossi
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
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18
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Maity S, Bingham C, Sheng W, Ehyaei N, Chakraborty D, Tahmasebi-Nick S, Kimmel TE, Vasileiou C, Geiger JH, Borhan B. Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins. Analyst 2023; 148:1085-1092. [PMID: 36722993 PMCID: PMC9992065 DOI: 10.1039/d2an01395a] [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] [Indexed: 01/26/2023]
Abstract
Cysteine-based Michael addition is a widely employed strategy for covalent conjugation of proteins, peptides, and drugs. The covalent reaction is irreversible in most cases, leading to a lack of control over the process. Utilizing spectroscopic analyses along with X-ray crystallographic studies, we demonstrate Michael addition of an engineered cysteine residue in human Cellular Retinol Binding Protein II (hCRBPII) with a coumarin analog that creates a non-fluorescent complex. UV-illumination reverses the conjugation, yielding a fluorescent species, presumably through a retro-Michael process. This series of events can be repeated between a bound and non-bound form of the cysteine reversibly, resulting in the ON-OFF control of fluorescence. The details of the mechanism of photoswitching was illuminated by recapitulation of the process in light irradiated single crystals, confirming the mechanism at atomic resolution.
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Affiliation(s)
- Soham Maity
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Courtney Bingham
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Wei Sheng
- Roche Tissue Diagnostics, 1910 E Innovation Park Dr, Oro Valley, AZ, 85755, USA
| | - Nona Ehyaei
- Lycia Therapeutics, 400 East Jamie Court, S San Francisco, CA 94080, USA
| | - Debarshi Chakraborty
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | | | - Thomas E Kimmel
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - James H Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
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19
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Ganguly S, Margel S. Bioimaging Probes Based on Magneto-Fluorescent Nanoparticles. Pharmaceutics 2023; 15:pharmaceutics15020686. [PMID: 36840008 PMCID: PMC9967590 DOI: 10.3390/pharmaceutics15020686] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023] Open
Abstract
Novel nanomaterials are of interest in biology, medicine, and imaging applications. Multimodal fluorescent-magnetic nanoparticles demand special attention because they have the potential to be employed as diagnostic and medication-delivery tools, which, in turn, might make it easier to diagnose and treat cancer, as well as a wide variety of other disorders. The most recent advancements in the development of magneto-fluorescent nanocomposites and their applications in the biomedical field are the primary focus of this review. We describe the most current developments in synthetic methodologies and methods for the fabrication of magneto-fluorescent nanocomposites. The primary applications of multimodal magneto-fluorescent nanoparticles in biomedicine, including biological imaging, cancer treatment, and drug administration, are covered in this article, and an overview of the future possibilities for these technologies is provided.
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20
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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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21
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Boukhatem H, Durel B, Raimbault M, Laurent A, Olivier N. Evaluation of Slowfade Diamond as a buffer for STORM microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:550-558. [PMID: 36874488 PMCID: PMC9979685 DOI: 10.1364/boe.473463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
We study the potential of the commercial mounting medium Slowfade diamond as a buffer for STORM microscopy. We show that although it does not work with the popular far-red dyes typically used for STORM imaging, such as Alexa Fluor 647, it performs really well with a wide variety of green-excited dyes such as Alexa Fluor 532, Alexa Fluor 555 or CF 568. Moreover, imaging can be performed several months after the samples are mounted in this environment and kept in the fridge, providing a convenient way to preserve samples for STORM imaging, as well as to keep calibration samples, for example for metrology or teaching in particular in imaging facilities.
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Affiliation(s)
- Hadjer Boukhatem
- Laboratory for Optics and Biosciences (LOB), CNRS, INSERM, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Beatrice Durel
- Cell Imaging Platform, Structure Fédérative de Recherche Necker, INSERM US24, CNRS UMS3633, Paris, F-75015, France
| | - Manon Raimbault
- Cell Imaging Platform, Structure Fédérative de Recherche Necker, INSERM US24, CNRS UMS3633, Paris, F-75015, France
| | - Audrey Laurent
- Université de Paris, Institut-Necker-Enfants-Malades, Inserm, CNRS, Paris, France
- École Doctorale BioSPC 562, Université de Paris, Paris, France
| | - Nicolas Olivier
- Laboratory for Optics and Biosciences (LOB), CNRS, INSERM, École polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
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22
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Laitenberger O, Aspelmeier T, Staudt T, Geisler C, Munk A, Egner A. Towards Unbiased Fluorophore Counting in Superresolution Fluorescence Microscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:459. [PMID: 36770420 PMCID: PMC9921631 DOI: 10.3390/nano13030459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
With the advent of fluorescence superresolution microscopy, nano-sized structures can be imaged with a previously unprecedented accuracy. Therefore, it is rapidly gaining importance as an analytical tool in the life sciences and beyond. However, the images obtained so far lack an absolute scale in terms of fluorophore numbers. Here, we use, for the first time, a detailed statistical model of the temporal imaging process which relies on a hidden Markov model operating on two timescales. This allows us to extract this information from the raw data without additional calibration measurements. We show this on the basis of added data from experiments on single Alexa 647 molecules as well as GSDIM/dSTORM measurements on DNA origami structures with a known number of labeling positions.
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Affiliation(s)
- Oskar Laitenberger
- Department of Optical Nanoscopy, Institut für Nanophotonik e.V., 37077 Göttingen, Germany
| | - Timo Aspelmeier
- Institute for Mathematical Stochastics, Georg-August-University of Göttingen, 37073 Göttingen, Germany
| | - Thomas Staudt
- Institute for Mathematical Stochastics, Georg-August-University of Göttingen, 37073 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Claudia Geisler
- Department of Optical Nanoscopy, Institut für Nanophotonik e.V., 37077 Göttingen, Germany
| | - Axel Munk
- Institute for Mathematical Stochastics, Georg-August-University of Göttingen, 37073 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Alexander Egner
- Department of Optical Nanoscopy, Institut für Nanophotonik e.V., 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
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23
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Herdly L, Tinning PW, Geiser A, Taylor H, Gould GW, van de Linde S. Benchmarking Thiolate-Driven Photoswitching of Cyanine Dyes. J Phys Chem B 2023; 127:732-741. [PMID: 36638265 PMCID: PMC9884076 DOI: 10.1021/acs.jpcb.2c06872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Carbocyanines are among the best performing dyes in single-molecule localization microscopy (SMLM), but their performance critically relies on optimized photoswitching buffers. Here, we study the versatile role of thiols in cyanine photoswitching at varying intensities generated in a single acquisition by a microelectromechanical systems (MEMS) mirror placed in the excitation path. The key metrics we have analyzed as a function of the thiolate concentration are photon budget, on-state and off-state lifetimes and the corresponding impact on image resolution. We show that thiolate acts as a concentration bandpass filter for the maximum achievable resolution and determine a minimum of ∼1 mM is necessary to facilitate SMLM measurements. We also identify a concentration bandwidth of 1-16 mM in which the photoswitching performance can be balanced between high molecular brightness and high off-time to on-time ratios. Furthermore, we monitor the performance of the popular oxygen scavenger system based on glucose and glucose oxidase over time and show simple measures to avoid acidification during prolonged measurements. Finally, the impact of buffer settings is quantitatively tested on the distribution of the glucose transporter protein 4 within the plasma membrane of adipocytes. Our work provides a general strategy for achieving optimal resolution in SMLM with relevance for the development of novel buffers and dyes.
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Affiliation(s)
- Lucas Herdly
- Department
of Physics, SUPA, University of Strathclyde, GlasgowG4 0NG, Scotland, United Kingdom
| | - Peter W. Tinning
- Department
of Physics, SUPA, University of Strathclyde, GlasgowG4 0NG, Scotland, United Kingdom
| | - Angéline Geiser
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, GlasgowG4 0RE, Scotland, United Kingdom
| | - Holly Taylor
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, GlasgowG4 0RE, Scotland, United Kingdom
| | - Gwyn W. Gould
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, GlasgowG4 0RE, Scotland, United Kingdom
| | - Sebastian van de Linde
- Department
of Physics, SUPA, University of Strathclyde, GlasgowG4 0NG, Scotland, United Kingdom,
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24
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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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25
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Multi-color live-cell STED nanoscopy of mitochondria with a gentle inner membrane stain. Proc Natl Acad Sci U S A 2022; 119:e2215799119. [PMID: 36534799 PMCID: PMC9907107 DOI: 10.1073/pnas.2215799119] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Capturing mitochondria's intricate and dynamic structure poses a daunting challenge for optical nanoscopy. Different labeling strategies have been demonstrated for live-cell stimulated emission depletion (STED) microscopy of mitochondria, but orthogonal strategies are yet to be established, and image acquisition has suffered either from photodamage to the organelles or from rapid photobleaching. Therefore, live-cell nanoscopy of mitochondria has been largely restricted to two-dimensional (2D) single-color recordings of cancer cells. Here, by conjugation of cyclooctatetraene (COT) to a benzo-fused cyanine dye, we report a mitochondrial inner membrane (IM) fluorescent marker, PK Mito Orange (PKMO), featuring efficient STED at 775 nm, strong photostability, and markedly reduced phototoxicity. PKMO enables super-resolution (SR) recordings of IM dynamics for extended periods in immortalized mammalian cell lines, primary cells, and organoids. Photostability and reduced phototoxicity of PKMO open the door to live-cell three-dimensional (3D) STED nanoscopy of mitochondria for 3D analysis of the convoluted IM. PKMO is optically orthogonal with green and far-red markers, allowing multiplexed recordings of mitochondria using commercial STED microscopes. Using multi-color STED microscopy, we demonstrate that imaging with PKMO can capture interactions of mitochondria with different cellular components such as the endoplasmic reticulum (ER) or the cytoskeleton, Bcl-2-associated X protein (BAX)-induced apoptotic process, or crista phenotypes in genetically modified cells, all at sub-100 nm resolution. Thereby, this work offers a versatile tool for studying mitochondrial IM architecture and dynamics in a multiplexed manner.
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26
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Gong Q, Zhang X, Li W, Guo X, Wu Q, Yu C, Jiao L, Xiao Y, Hao E. Long-Wavelength Photoconvertible Dimeric BODIPYs for Super-Resolution Single-Molecule Localization Imaging in Near-Infrared Emission. J Am Chem Soc 2022; 144:21992-21999. [PMID: 36414278 DOI: 10.1021/jacs.2c08947] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Sulfoxide-bridged dimeric BODIPYs were developed as a new class of long-wavelength photoconvertible fluorophores. Upon visible-light irradiation, a sulfoxide moiety was released to generate the corresponding α,α-directly linked dimeric BODIPYs. The extrusion of SO from sulfoxides was mainly through an intramolecular fashion involving reactive triplet states. By this photoconversion, not only were more than 100 nm red shifts of absorption and emission maxima (up to 648/714 nm) achieved but also stable products with bright fluorescence were produced with high efficiency. The combination of photoactivation and red-shifted excitation/emission offered optimal contrast and eliminated the interference from biological autofluorescence. More importantly, the in situ products of these visible-light-induced reactions demonstrated ideal single-molecule fluorescence properties in the near-infrared region. Therefore, this new photoconversion could be a powerful photoactivation method achieving super-resolution single-molecule localization imaging in a living cell without using UV illumination and cell-toxic additives.
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Affiliation(s)
- Qingbao Gong
- The Key Laboratory of Functional Molecular Solids, Ministry of Education, School of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, China
| | - Xinfu Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Wanwan Li
- The Key Laboratory of Functional Molecular Solids, Ministry of Education, School of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, China
| | - Xing Guo
- The Key Laboratory of Functional Molecular Solids, Ministry of Education, School of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, China
| | - Qinghua Wu
- The Key Laboratory of Functional Molecular Solids, Ministry of Education, School of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, China
| | - Changjiang Yu
- The Key Laboratory of Functional Molecular Solids, Ministry of Education, School of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, China
| | - Lijuan Jiao
- The Key Laboratory of Functional Molecular Solids, Ministry of Education, School of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, China
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Erhong Hao
- The Key Laboratory of Functional Molecular Solids, Ministry of Education, School of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, China
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27
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Huang L, Zhang J, Wu Z, Zhou L, Yu B, Jing Y, Lin D, Qu J. Revealing the structure and organization of intercellular tunneling nanotubes (TNTs) by STORM imaging. NANOSCALE ADVANCES 2022; 4:4258-4262. [PMID: 36321151 PMCID: PMC9552758 DOI: 10.1039/d2na00415a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Tunneling nanotubes (TNTs) are nanoscale, actin-rich, transient intercellular tubes for cell-to-cell communication, which transport various cargoes between distant cells. The structural complexity and spatial organization of the involved components of TNTs remain unknown. In this work, the STORM super-resolution imaging technique was applied to elucidate the structural organization of microfilaments and microtubules in intercellular TNTs at the nanometer scale. Our results reveal different distributions of microfilaments and intertwined structures of microtubules in TNTs, which promote the knowledge of TNT communications.
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Affiliation(s)
- Lilin Huang
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University Shenzhen 518060 P. R. China
| | - Jiao Zhang
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University Shenzhen 518060 P. R. China
| | - Zekai Wu
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University Shenzhen 518060 P. R. China
| | - Liangliang Zhou
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University Shenzhen 518060 P. R. China
| | - Bin Yu
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University Shenzhen 518060 P. R. China
| | - Yingying Jing
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University Shenzhen 518060 P. R. China
| | - Danying Lin
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University Shenzhen 518060 P. R. China
| | - Junle Qu
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University Shenzhen 518060 P. R. China
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28
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Aparin IO, Yan R, Pelletier R, Choi AA, Danylchuk DI, Xu K, Klymchenko AS. Fluorogenic Dimers as Bright Switchable Probes for Enhanced Super-Resolution Imaging of Cell Membranes. J Am Chem Soc 2022; 144:18043-18053. [PMID: 36153973 DOI: 10.1021/jacs.2c07542] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Super-resolution fluorescence imaging based on single-molecule localization microscopy (SMLM) enables visualizing cellular structures with nanometric precision. However, its spatial and temporal resolution largely relies on the brightness of ON/OFF switchable fluorescent dyes. Moreover, in cell plasma membranes, the single-molecule localization is hampered by the fast lateral diffusion of membrane probes. Here, to address these two fundamental problems, we propose a concept of ON/OFF switchable probes for SMLM (points accumulation for imaging in nanoscale topography, PAINT) based on fluorogenic dimers of bright cyanine dyes. In these probes, the two cyanine units connected with a linker were modified at their extremities with low-affinity membrane anchors. Being self-quenched in water due to intramolecular dye H-aggregation, they displayed light up on reversible binding to lipid membranes. The charged group in the linker further decreased the probe affinity to the lipid membranes, thus accelerating its dynamic reversible ON/OFF switching. The concept was validated on cyanines 3 and 5. SMLM of live cells revealed that the new probes provided higher brightness and ∼10-fold slower diffusion at the cell surface, compared to reference probes Nile Red and DiD, which boosted axial localization precision >3-fold down to 31 nm. The new probe allowed unprecedented observation of nanoscale fibrous protrusions on plasma membranes of live cells with 40 s time resolution, revealing their fast dynamics. Thus, going beyond the brightness limit of single switchable dyes by cooperative dequenching in fluorogenic dimers and slowing down probe diffusion in biomembranes open the route to significant enhancement of super-resolution fluorescence microscopy of live cells.
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Affiliation(s)
- Ilya O Aparin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Alexander A Choi
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
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29
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Tapia Hernandez R, Lee MC, Yadav AK, Chan J. Repurposing Cyanine Photoinstability To Develop Near-Infrared Light-Activatable Nanogels for In Vivo Cargo Delivery. J Am Chem Soc 2022; 144:18101-18108. [PMID: 36153991 PMCID: PMC10088867 DOI: 10.1021/jacs.2c08187] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The favorable properties of cyanines (e.g., near-infrared (NIR) absorbance and emission) have made this class of dyes popular for a wide variety of biomedical applications. However, many cyanines are prone to rapid photobleaching when irradiated with light. In this study, we have exploited this undesirable trait to develop NIR-nanogels for NIR light-mediated cargo delivery. NIR-nanogels feature a photolabile cyanine cross-linker (Cy780-Acryl) that can cleave via dioxetane chemistry when irradiated. This photochemical process results in the formation of two carbonyl fragments and concomitant NIR-nanogel degradation to facilitate cargo release. In contrast to studies where cyanines are utilized as photocages, our approach does not require direct chemical attachment to the cargo, thus expanding our ability to deliver molecules that cannot be covalently modified. We showcase this feature by encapsulating a palette of small-molecule chemotherapeutics that feature a structurally diverse chemical architecture. To demonstrate site-selective release in vivo, we generated a murine model of breast cancer. Relative to nonlight irradiated and drug-free controls, treatment with NIR-nanogels loaded with paclitaxel (a potent cytotoxic agent) and NIR light resulted in significant attenuation of tumor growth. Moreover, we show via histological staining of the vital organs that minimal off-target effects are observed.
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Affiliation(s)
- Rodrigo Tapia Hernandez
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, and Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Michael C Lee
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, and Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Anuj K Yadav
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, and Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jefferson Chan
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, and Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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30
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Graham TGW, Ferrie JJ, Dailey GM, Tjian R, Darzacq X. Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA). eLife 2022; 11:e76870. [PMID: 35976226 PMCID: PMC9531946 DOI: 10.7554/elife.76870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Single-molecule imaging provides a powerful way to study biochemical processes in live cells, yet it remains challenging to track single molecules while simultaneously detecting their interactions. Here, we describe a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), in which one fluorophore (the 'sender') can reactivate a second fluorophore (the 'receiver') from a dark state. PAPA requires proximity between the two fluorophores, yet it operates at a longer average intermolecular distance than Förster resonance energy transfer (FRET). We show that PAPA can be used in live cells both to detect protein-protein interactions and to highlight a subpopulation of labeled protein complexes in which two different labels are in proximity. In proof-of-concept experiments, PAPA detected the expected correlation between androgen receptor self-association and chromatin binding at the single-cell level. These results establish a new way in which a photophysical property of fluorophores can be harnessed to study molecular interactions in single-molecule imaging of live cells.
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Affiliation(s)
- Thomas GW Graham
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - John Joseph Ferrie
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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31
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Helmerich DA, Beliu G, Taban D, Meub M, Streit M, Kuhlemann A, Doose S, Sauer M. Photoswitching fingerprint analysis bypasses the 10-nm resolution barrier. Nat Methods 2022; 19:986-994. [PMID: 35915194 PMCID: PMC9349044 DOI: 10.1038/s41592-022-01548-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/13/2022] [Indexed: 12/20/2022]
Abstract
Advances in super-resolution microscopy have demonstrated single-molecule localization precisions of a few nanometers. However, translation of such high localization precisions into sub-10-nm spatial resolution in biological samples remains challenging. Here we show that resonance energy transfer between fluorophores separated by less than 10 nm results in accelerated fluorescence blinking and consequently lower localization probabilities impeding sub-10-nm fluorescence imaging. We demonstrate that time-resolved fluorescence detection in combination with photoswitching fingerprint analysis can be used to determine the number and distance even of spatially unresolvable fluorophores in the sub-10-nm range. In combination with genetic code expansion with unnatural amino acids and bioorthogonal click labeling with small fluorophores, photoswitching fingerprint analysis can be used advantageously to reveal information about the number of fluorophores present and their distances in the sub-10-nm range in cells. Energy transfer between fluorophores is shown to impede SMLM at sub-10-nm spatial resolution. Time-resolved detection and photoswitching fingerprinting analysis are used to determine the number and separation of closely spaced fluorophores.
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Affiliation(s)
- Dominic A Helmerich
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany.,Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Danush Taban
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Marcel Streit
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Alexander Kuhlemann
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany. .,Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany.
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32
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Xiao M, Zhang YK, Li R, Li S, Wang D, An P. Photoactivatable Fluorogenic Azide-Alkyne Click Reaction: A Dual-Activation Fluorescent Probe. Chem Asian J 2022; 17:e202200634. [PMID: 35819362 DOI: 10.1002/asia.202200634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/01/2022] [Indexed: 11/12/2022]
Abstract
Aryl azide and diaryl tetrazole are both photoactive molecules, which can form nitrene and nitrile imine intermediates respectively by photolysis. Depending on the new finding that the azide can suppress the photolysis of tetrazole in the azide-tetrazole conjugated system, we developed aryl azide-tetrazole probes for the photoactivatable fluorogenic azide alkyne click (PFAAC) reaction, in which the aryl azide-tetrazole probes were not phoroactivatable fluorogenic itself, but the triazole products after click reaction were prefluorophore that can be activated by light. Therefore, in PFAAC chemistry, the fluorescent probes can be activated by two orthogonal events: azide-alkyne click reaction and light, which leads to spatiotemporal resolution and high signal-to-noise ratio. This PFAAC process was proved in vitro by copper catalyzed or strain-promoted azide-alkyne reactions and in live cells by spatiotemporally controlled organelle imaging. By incorporation a linker to the azide-tetrazole conjugate, this PFAAC chemistry could covalently label extra probes to the biomolecules and spatiotemporally detecting this process by photoinduced fluorescence.
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Affiliation(s)
| | | | | | | | - Di Wang
- Yunnan University, chemistry, CHINA
| | - Peng An
- Yunnan University, school of chemical science and technology, South Outer Ring Road, 650500, Kunming, CHINA
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33
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Chinnaraj M, Flaumenhaft R, Pozzi N. Reduction of protein disulfide isomerase results in open conformations and stimulates dynamic exchange between structural ensembles. J Biol Chem 2022; 298:102217. [PMID: 35780832 PMCID: PMC9352907 DOI: 10.1016/j.jbc.2022.102217] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022] Open
Abstract
Human protein disulfide isomerase (PDI) is an essential redox-regulated enzyme required for oxidative protein folding. It comprises four thioredoxin domains, two catalytically active (a, a’) and two inactive (b, b’), organized to form a flexible abb’a’ U-shape. Snapshots of unbound oxidized and reduced PDI have been obtained by X-ray crystallography. Yet, how PDI’s structure changes in response to the redox environment and inhibitor binding remains controversial. Here, we used multiparameter confocal single-molecule FRET to track the movements of the two catalytic domains with high temporal resolution. We found that at equilibrium, PDI visits three structurally distinct conformational ensembles, two “open” (O1 and O2) and one “closed” (C). We show that the redox environment dictates the time spent in each ensemble and the rate at which they exchange. While oxidized PDI samples O1, O2, and C more evenly and in a slower fashion, reduced PDI predominantly populates O1 and O2 and exchanges between them more rapidly, on the submillisecond timescale. These findings were not expected based on crystallographic data. Using mutational analyses, we further demonstrate that the R300-W396 cation-π interaction and active site cysteines dictate, in unexpected ways, how the catalytic domains relocate. Finally, we show that irreversible inhibitors targeting the active sites of reduced PDI did not abolish these protein dynamics but rather shifted the equilibrium toward the closed ensemble. This work introduces a new structural framework that challenges current views of PDI dynamics, helps rationalize its multifaceted role in biology, and should be considered when designing PDI-targeted therapeutics.
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Affiliation(s)
- Mathivanan Chinnaraj
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
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Zingale E, Romeo A, Rizzo S, Cimino C, Bonaccorso A, Carbone C, Musumeci T, Pignatello R. Fluorescent Nanosystems for Drug Tracking and Theranostics: Recent Applications in the Ocular Field. Pharmaceutics 2022; 14:pharmaceutics14050955. [PMID: 35631540 PMCID: PMC9147643 DOI: 10.3390/pharmaceutics14050955] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 12/14/2022] Open
Abstract
The greatest challenge associated with topical drug delivery for the treatment of diseases affecting the posterior segment of the eye is to overcome the poor bioavailability of the carried molecules. Nanomedicine offers the possibility to overcome obstacles related to physiological mechanisms and ocular barriers by exploiting different ocular routes. Functionalization of nanosystems by fluorescent probes could be a useful strategy to understand the pathway taken by nanocarriers into the ocular globe and to improve the desired targeting accuracy. The application of fluorescence to decorate nanocarrier surfaces or the encapsulation of fluorophore molecules makes the nanosystems a light probe useful in the landscape of diagnostics and theranostics. In this review, a state of the art on ocular routes of administration is reported, with a focus on pathways undertaken after topical application. Numerous studies are reported in the first section, confirming that the use of fluorescent within nanoparticles is already spread for tracking and biodistribution studies. The first section presents fluorescent molecules used for tracking nanosystems’ cellular internalization and permeation of ocular tissues; discussions on the classification of nanosystems according to their nature (lipid-based, polymer-based, metallic-based and protein-based) follows. The following sections are dedicated to diagnostic and theranostic uses, respectively, which represent an innovation in the ocular field obtained by combining dual goals in a single administration system. For its great potential, this application of fluorescent nanoparticles would experience a great development in the near future. Finally, a brief overview is dedicated to the use of fluorescent markers in clinical trials and the market in the ocular field.
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Affiliation(s)
- Elide Zingale
- Department of Pharmaceutical and Health Sciences, University of Catania, 95124 Catania, Italy; (E.Z.); (A.R.); (S.R.); (C.C.); (A.B.); (C.C.); (T.M.)
| | - Alessia Romeo
- Department of Pharmaceutical and Health Sciences, University of Catania, 95124 Catania, Italy; (E.Z.); (A.R.); (S.R.); (C.C.); (A.B.); (C.C.); (T.M.)
| | - Salvatore Rizzo
- Department of Pharmaceutical and Health Sciences, University of Catania, 95124 Catania, Italy; (E.Z.); (A.R.); (S.R.); (C.C.); (A.B.); (C.C.); (T.M.)
| | - Cinzia Cimino
- Department of Pharmaceutical and Health Sciences, University of Catania, 95124 Catania, Italy; (E.Z.); (A.R.); (S.R.); (C.C.); (A.B.); (C.C.); (T.M.)
| | - Angela Bonaccorso
- Department of Pharmaceutical and Health Sciences, University of Catania, 95124 Catania, Italy; (E.Z.); (A.R.); (S.R.); (C.C.); (A.B.); (C.C.); (T.M.)
- NANO-i—Research Center for Ocular Nanotechnology, University of Catania, 95124 Catania, Italy
| | - Claudia Carbone
- Department of Pharmaceutical and Health Sciences, University of Catania, 95124 Catania, Italy; (E.Z.); (A.R.); (S.R.); (C.C.); (A.B.); (C.C.); (T.M.)
- NANO-i—Research Center for Ocular Nanotechnology, University of Catania, 95124 Catania, Italy
| | - Teresa Musumeci
- Department of Pharmaceutical and Health Sciences, University of Catania, 95124 Catania, Italy; (E.Z.); (A.R.); (S.R.); (C.C.); (A.B.); (C.C.); (T.M.)
- NANO-i—Research Center for Ocular Nanotechnology, University of Catania, 95124 Catania, Italy
| | - Rosario Pignatello
- Department of Pharmaceutical and Health Sciences, University of Catania, 95124 Catania, Italy; (E.Z.); (A.R.); (S.R.); (C.C.); (A.B.); (C.C.); (T.M.)
- NANO-i—Research Center for Ocular Nanotechnology, University of Catania, 95124 Catania, Italy
- Correspondence:
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35
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Kwon J, Elgawish MS, Shim S. Bleaching-Resistant Super-Resolution Fluorescence Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2101817. [PMID: 35088584 PMCID: PMC8948665 DOI: 10.1002/advs.202101817] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 01/07/2022] [Indexed: 05/08/2023]
Abstract
Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.
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Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD21205USA
| | - Mohamed Saleh Elgawish
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
- Medicinal Chemistry DepartmentFaculty of PharmacySuez Canal UniversityIsmailia41522Egypt
| | - Sang‐Hee Shim
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
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36
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Vatan T, Minehart JA, Zhang C, Agarwal V, Yang J, Speer CM. Volumetric super-resolution imaging by serial ultrasectioning and stochastic optical reconstruction microscopy in mouse neural tissue. STAR Protoc 2021; 2:100971. [PMID: 34901889 PMCID: PMC8637648 DOI: 10.1016/j.xpro.2021.100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here, we present a protocol for collecting large-volume, four-color, single-molecule localization imaging data from neural tissue. We have applied this technique to map the location and identities of chemical synapses across whole cells in mouse retinae. Our sample preparation approach improves 3D STORM image quality by reducing tissue scattering, photobleaching, and optical distortions associated with deep imaging. This approach can be extended for use on other tissue types enabling life scientists to perform volumetric super-resolution imaging in diverse biological models. For complete details on the use and execution of this protocol, please refer to Sigal et al. (2015).
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Affiliation(s)
- Tarlan Vatan
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Neuroscience and Cognitive Science Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Jacqueline A. Minehart
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Neuroscience and Cognitive Science Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Chenghang Zhang
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Vatsal Agarwal
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Jerry Yang
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Brain and Behavior Institute, University of Maryland, College Park, MD 20742, USA
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37
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Volarić J, Szymanski W, Simeth NA, Feringa BL. Molecular photoswitches in aqueous environments. Chem Soc Rev 2021; 50:12377-12449. [PMID: 34590636 PMCID: PMC8591629 DOI: 10.1039/d0cs00547a] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 12/17/2022]
Abstract
Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.
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Affiliation(s)
- Jana Volarić
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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38
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Chung J, Jeong U, Jeong D, Go S, Kim D. Development of a New Approach for Low-Laser-Power Super-Resolution Fluorescence Imaging. Anal Chem 2021; 94:618-627. [PMID: 34752081 DOI: 10.1021/acs.analchem.1c01047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The development of super-resolution fluorescence microscopy over the past decade has drastically improved the resolution of light microscopy to ∼10 nm. Stochastic optical reconstruction microscopy (STORM) can be used to achieve subdiffraction-limit resolution by sequentially imaging and localizing individual fluorophores. In principle, the super-resolution of STORM can be obtained by high-accuracy localization of photoswitchable fluorophores, which require fast photoswitching and bright fluorescence intensity from a single emitter. It is known that the switching rate of photoswitchable fluorophores depends on the laser power─a high laser power being required for the enhancement of imaging resolution. However, high laser power is usually harmful to biological specimens and limits the imaging time because of its photobleaching effects and high phototoxicity. In this study, we attempted to overcome this problem by improving the STORM resolution at a lower laser power. Through the quantitative analysis of the photoswitching behavior of single fluorophores under different laser power conditions, we developed a new approach to achieve super-resolution fluorescence images at a laser power 10 times lower than had previously been reported. This approach is expected to play an increasingly significant role in super-resolution imaging of power-sensitive samples.
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Affiliation(s)
- Jinkyoung Chung
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Uidon Jeong
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Dokyung Jeong
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Seokran Go
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Doory Kim
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea.,Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea.,Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Republic of Korea.,Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
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39
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Patel VR, Salinas AM, Qi D, Gupta S, Sidote DJ, Goldschen-Ohm MP. Single-molecule imaging with cell-derived nanovesicles reveals early binding dynamics at a cyclic nucleotide-gated ion channel. Nat Commun 2021; 12:6459. [PMID: 34753946 PMCID: PMC8578382 DOI: 10.1038/s41467-021-26816-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/21/2021] [Indexed: 12/05/2022] Open
Abstract
Ligand binding to membrane proteins is critical for many biological signaling processes. However, individual binding events are rarely directly observed, and their asynchronous dynamics are occluded in ensemble-averaged measures. For membrane proteins, single-molecule approaches that resolve these dynamics are challenged by dysfunction in non-native lipid environments, lack of access to intracellular sites, and costly sample preparation. Here, we introduce an approach combining cell-derived nanovesicles, microfluidics, and single-molecule fluorescence colocalization microscopy to track individual binding events at a cyclic nucleotide-gated TAX-4 ion channel critical for sensory transduction. Our observations reveal dynamics of both nucleotide binding and a subsequent conformational change likely preceding pore opening. Kinetic modeling suggests that binding of the second ligand is either independent of the first ligand or exhibits up to ~10-fold positive binding cooperativity. This approach is broadly applicable to studies of binding dynamics for proteins with extracellular or intracellular domains in native cell membrane.
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Affiliation(s)
- Vishal R Patel
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
- Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Arturo M Salinas
- Department of Physics, The University of Texas at Austin, Austin, TX, USA
| | - Darong Qi
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - Shipra Gupta
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - David J Sidote
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
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40
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Lee WTC, Gupta D, Rothenberg E. Single-molecule imaging of replication fork conflicts at genomic DNA G4 structures in human cells. Methods Enzymol 2021; 661:77-94. [PMID: 34776224 DOI: 10.1016/bs.mie.2021.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA G-quadruplexes (G4s) are stable, non-canonical DNA secondary structures formed within guanine(G)-rich sequences. While extensively studied in vitro, evidence of the occurrence of G4s in vivo has only recently emerged. The formation of G4 structures may pose an obstacle for diverse DNA transactions including replication, which is linked to mutagenesis and genomic instability. A fundamental question in the field has been whether and how the formation of G4s is coupled to the progression of replication forks. This process has remained undefined largely due to the lack of experimental approaches capable of monitoring the presence of G4s and their association with the replication machinery in cells. Here, we describe a detailed multicolor single-molecule localization microscopy (SMLM) protocol for detecting nanoscale spatial-association of DNA G4s with the cellular replisome complex. This method offers a unique platform for visualizing the mechanisms of G4 formation at the molecular level, as well as addressing key biological questions as to the functional roles of these structures in the maintenance of genome integrity.
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Affiliation(s)
- Wei Ting C Lee
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States.
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States.
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States.
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41
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Unsupervised selection of optimal single-molecule time series idealization criterion. Biophys J 2021; 120:4472-4483. [PMID: 34487708 PMCID: PMC8553667 DOI: 10.1016/j.bpj.2021.08.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/22/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022] Open
Abstract
Single-molecule (SM) approaches have provided valuable mechanistic information on many biophysical systems. As technological advances lead to ever-larger data sets, tools for rapid analysis and identification of molecules exhibiting the behavior of interest are increasingly important. In many cases the underlying mechanism is unknown, making unsupervised techniques desirable. The divisive segmentation and clustering (DISC) algorithm is one such unsupervised method that idealizes noisy SM time series much faster than computationally intensive approaches without sacrificing accuracy. However, DISC relies on a user-selected objective criterion (OC) to guide its estimation of the ideal time series. Here, we explore how different OCs affect DISC’s performance for data typical of SM fluorescence imaging experiments. We find that OCs differing in their penalty for model complexity each optimize DISC’s performance for time series with different properties such as signal/noise and number of sample points. Using a machine learning approach, we generate a decision boundary that allows unsupervised selection of OCs based on the input time series to maximize performance for different types of data. This is particularly relevant for SM fluorescence data sets, which often have signal/noise near the derived decision boundary and include time series of nonuniform length because of stochastic bleaching. Our approach, AutoDISC, allows unsupervised per-molecule optimization of DISC, which will substantially assist in the rapid analysis of high-throughput SM data sets with noisy samples and nonuniform time windows.
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42
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Ghosh S, Feigelson SW, Montresor A, Shimoni E, Roncato F, Legler DF, Laudanna C, Haran G, Alon R. CCR7 signalosomes are preassembled on tips of lymphocyte microvilli in proximity to LFA-1. Biophys J 2021; 120:4002-4012. [PMID: 34411577 DOI: 10.1016/j.bpj.2021.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/27/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022] Open
Abstract
Leukocyte microvilli are elastic actin-rich projections implicated in rapid sensing and penetration across glycocalyx barriers. Microvilli are critical for the capture and arrest of flowing lymphocytes by high endothelial venules, the main lymph node portal vessels. T lymphocyte arrest involves subsecond activation of the integrin LFA-1 by the G-protein-coupled receptor CCR7 and its endothelial-displayed ligands, the chemokines CCL21 and CCL19. The topographical distribution of CCR7 and of LFA-1 in relation to lymphocyte microvilli has never been elucidated. We applied the recently developed microvillar cartography imaging technique to determine the topographical distribution of CCR7 and LFA-1 with respect to microvilli on peripheral blood T lymphocytes. We found that CCR7 is clustered on the tips of T cell microvilli. The vast majority of LFA-1 molecules were found on the cell body, likely assembled in macroclusters, but a subset of LFA-1, 5% of the total, were found scattered within 20 nm from the CCR7 clusters, implicating these LFA-1 molecules as targets for inside-out activation signals transmitted within a fraction of a second by chemokine-bound CCR7. Indeed, RhoA, the key GTPase involved in rapid LFA-1 affinity triggering by CCR7, was also found to be clustered near CCR7. In addition, we observed that the tyrosine kinase JAK2 controls CCR7-mediated LFA-1 affinity triggering and is also highly enriched on tips of microvilli. We propose that tips of lymphocyte microvilli are novel signalosomes for subsecond CCR7-mediated inside-out signaling to neighboring LFA-1 molecules, a critical checkpoint in LFA-1-mediated lymphocyte arrest on high endothelial venules.
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Affiliation(s)
- Shirsendu Ghosh
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Sara W Feigelson
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Eyal Shimoni
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Roncato
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel F Legler
- Biotechnology Institute Thurgau, University of Konstanz, Kreuzlingen, Switzerland
| | - Carlo Laudanna
- Department of Medicine, University of Verona, Verona, Italy
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Ronen Alon
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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43
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Wang H, Xiao H, Zhu X, Liu Y, Fu Z, Li C, Lu C, Yang H. A Cyanine‐Mediated Self‐Assembly System for the Construction of a Two‐in‐One Nanodrug. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Haihui Wang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety College of Chemistry Fuzhou University Fuzhou Fujian 350116 P. R. China
| | - Han Xiao
- State Key Laboratory of Structure of Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiaohui Zhu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety College of Chemistry Fuzhou University Fuzhou Fujian 350116 P. R. China
| | - Yongfei Liu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety College of Chemistry Fuzhou University Fuzhou Fujian 350116 P. R. China
| | - Zhangcheng Fu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety College of Chemistry Fuzhou University Fuzhou Fujian 350116 P. R. China
| | - Chunsen Li
- State Key Laboratory of Structure of Chemistry Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Fuzhou Fujian 350002 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety College of Chemistry Fuzhou University Fuzhou Fujian 350116 P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety College of Chemistry Fuzhou University Fuzhou Fujian 350116 P. R. China
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44
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Cho Y, An HJ, Kim T, Lee C, Lee NK. Mechanism of Cyanine5 to Cyanine3 Photoconversion and Its Application for High-Density Single-Particle Tracking in a Living Cell. J Am Chem Soc 2021; 143:14125-14135. [PMID: 34432445 DOI: 10.1021/jacs.1c04178] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanine (Cy) dyes are among the most useful organic fluorophores that have found a wide range of applications in single-molecule and super-resolution imaging as well as in other biophysical studies. However, recent observations that blueshifted derivatives of Cy dyes are formed via photoconversion have raised concerns as to the potential artifacts in multicolor imaging. Here, we report the mechanism for the photoconversion of Cy5 to Cy3 that occurs upon photoexcitation during fluorescent imaging. Our studies show that the formal C2H2 excision from Cy5 occurs mainly through an intermolecular pathway involving a combination of bond cleavage and reconstitution while unambiguously confirming the identity of the fluorescent photoproduct of Cy5 to be Cy3 using various spectroscopic tools. The carbonyl products generated from singlet oxygen-mediated photooxidation of Cy5 undergo a sequence of carbon-carbon bond-breaking and -forming events to bring about the novel dye-to-dye transformation. We also show that the deletion of a two-methine unit from the polymethine chain, which results in the formation of blueshifted products, commonly occurs in other cyanine dyes, such as Alexa Fluor 647 (AF647) and Cyanine5.5. The formation of a blueshifted congener dye can obscure the multicolor fluorescence imaging, leading to misinterpretation of the data. We demonstrate that the potentially deleterious photoconversion, however, can be exploited to develop a new photoactivation method for high-density single-particle tracking in a living cell without using UV illumination and cell-toxic additives.
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Affiliation(s)
- Yoonjung Cho
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyeong Jeon An
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Taehoon Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chulbom Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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45
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Out-of-Phase Imaging after Optical Modulation (OPIOM) for Multiplexed Fluorescence Imaging Under Adverse Optical Conditions. Methods Mol Biol 2021; 2350:191-227. [PMID: 34331287 DOI: 10.1007/978-1-0716-1593-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence imaging has become a powerful tool for observations in biology. Yet it has also encountered limitations to overcome optical interferences of ambient light, autofluorescence, and spectrally interfering fluorophores. In this account, we first examine the current approaches which address these limitations. Then we more specifically report on Out-of-Phase Imaging after Optical Modulation (OPIOM), which has proved attractive for highly selective multiplexed fluorescence imaging even under adverse optical conditions. After exposing the OPIOM principle, we detail the protocols for successful OPIOM implementation.
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Gebhardt C, Lehmann M, Reif MM, Zacharias M, Gemmecker G, Cordes T. Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series*. Chemphyschem 2021; 22:1566-1583. [PMID: 34185946 PMCID: PMC8457111 DOI: 10.1002/cphc.202000935] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 06/01/2021] [Indexed: 12/23/2022]
Abstract
The use of fluorescence techniques has an enormous impact on various research fields including imaging, biochemical assays, DNA-sequencing and medical technologies. This has been facilitated by the development of numerous commercial dyes with optimized photophysical and chemical properties. Often, however, information about the chemical structures of dyes and the attached linkers used for bioconjugation remain a well-kept secret. This can lead to problems for research applications where knowledge of the dye structure is necessary to predict or understand (unwanted) dye-target interactions, or to establish structural models of the dye-target complex. Using a combination of optical spectroscopy, mass spectrometry, NMR spectroscopy and molecular dynamics simulations, we here investigate the molecular structures and spectroscopic properties of dyes from the Alexa Fluor (Alexa Fluor 555 and 647) and AF series (AF555, AF647, AFD647). Based on available data and published structures of the AF and Cy dyes, we propose a structure for Alexa Fluor 555 and refine that of AF555. We also resolve conflicting reports on the linker composition of Alexa Fluor 647 maleimide. We also conducted a comprehensive comparison between Alexa Fluor and AF dyes by continuous-wave absorption and emission spectroscopy, quantum yield determination, fluorescence lifetime and anisotropy spectroscopy of free and protein-attached dyes. All these data support the idea that Alexa Fluor and AF dyes have a cyanine core and are a derivative of Cy3 and Cy5. In addition, we compared Alexa Fluor 555 and Alexa Fluor 647 to their structural homologs AF555 and AF(D)647 in single-molecule FRET applications. Both pairs showed excellent performance in solution-based smFRET experiments using alternating laser excitation. Minor differences in apparent dye-protein interactions were investigated by molecular dynamics simulations. Our findings clearly demonstrate that the AF-fluorophores are an attractive alternative to Alexa- and Cy-dyes in smFRET studies or other fluorescence applications.
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Affiliation(s)
- Christian Gebhardt
- Physical and Synthetic Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
| | - Martin Lehmann
- Plant Molecular Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
| | - Maria M. Reif
- Theoretical Biophysics (T38), Physics DepartmentTechnical University of MunichCenter for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 885748GarchingGermany
| | - Martin Zacharias
- Theoretical Biophysics (T38), Physics DepartmentTechnical University of MunichCenter for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 885748GarchingGermany
| | - Gerd Gemmecker
- Bavarian NMR Center (B NMRZ), Department of ChemistryTechnical University of MunichLichtenbergstr. 485748GarchingGermany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
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Kaur A, New EJ. Mechanistic Insights on How to Avoid and Harness Cyanine Photoconversion. ACS CENTRAL SCIENCE 2021; 7:1095-1098. [PMID: 34345660 PMCID: PMC8323108 DOI: 10.1021/acscentsci.1c00662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Amandeep Kaur
- School
of Medical Sciences, Faculty of Medicine and Health and The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth J. New
- School of Chemistry, Faculty of Science, The University of Sydney Nano Institute (Sydney Nano) and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
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Wang H, Xiao H, Zhu X, Liu Y, Fu Z, Li C, Lu C, Yang H. A Cyanine-Mediated Self-Assembly System for the Construction of a Two-in-One Nanodrug. Angew Chem Int Ed Engl 2021; 60:21226-21230. [PMID: 34296814 DOI: 10.1002/anie.202108393] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 01/06/2023]
Abstract
The combination of gene therapy and chemotherapy provides a We developed a simple and versatile approach to prepare a series of two-in-one nanodrugs through direct self-assembly of cyanine-labeled single-stranded DNA (Cys-DNA) and different types of drug molecules. Molecular dynamics simulation showed that the Cys introduced into the DNA could enhance the noncovalent interaction between Cys-DNA and drug molecules. More drug molecules were incorporated into Cys-DNA, tending to spontaneously form hybrid Cys-DNA/drug nanosphere. Such nanospheres serve as both carriers and cargoes, excluding the extra use of nontherapeutic excipients and showing ultrahigh drug loading capacity. Following this approach, an antisense oligonucleotides/doxorubicin nanodrug model was constructed, demonstrating the significant synergistic anti-tumor therapeutic effect. As a proof of the concept, our study establishes a simple and reproducible two-in-one nucleic acid-based drug formulation.
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Affiliation(s)
- Haihui Wang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Han Xiao
- State Key Laboratory of Structure of Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaohui Zhu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Yongfei Liu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Zhangcheng Fu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Chunsen Li
- State Key Laboratory of Structure of Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
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Abstract
By synchronizing electrochemical potential scanning with a single-molecule localization super-resolution fluorescence microscope, kinetic fluorescence changes of hundreds of single molecular redox events were tracked simultaneously with high throughput, and subsequent cross-correlation function analysis mapped single molecules' redox potentials (times) out on the imaging area from site to site in unprecedented detail by extracting electrochemically induced fluorescence change from apparently random fluorescence on/off blinking. This work paves the way toward mapping redox states at single-molecule levels in high throughput in chemical and biological systems.
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Affiliation(s)
- Chenghong Lei
- Guilin University of Technology, College of Chemistry and Bioengineering, Guilin, Guangxi 541006, China
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Lisovskaya A, Carmichael I, Harriman A. Pulse Radiolysis Investigation of Radicals Derived from Water-Soluble Cyanine Dyes: Implications for Super-resolution Microscopy. J Phys Chem A 2021; 125:5779-5793. [PMID: 34165985 DOI: 10.1021/acs.jpca.1c03776] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Light-induced blinking, an inherent feature of many forms of super-resolution microscopy, has been linked to transient reduction of the fluorescent cyanine dye used as an imaging agent. There is, however, only scant literature information related to one-electron reduced cyanine dyes, especially in an aqueous environment. Here, we examine a small series of cyanine dyes, possessing disparate π-conjugation lengths, under selective reducing or oxidizing conditions. The experiment allows recording of both differential absorption spectra and decay kinetics of the resultant one-electron reduced or oxidized transient species in water. Relative to the ground state, absorption transitions for the various radicals are weak and somewhat broadened but do allow correlation with the π-conjugation length. In all cases, absorption maxima lie to the blue of the main ground-state transition. Under anaerobic conditions, the transient species decay on the microsecond to millisecond time scale, with the mean lifetime depending on molecular structure, radiation dose, and dye concentration. The experimental absorption spectra recorded for the one-electron reduced radicals and the presumed dimer cation radical compare well to spectra obtained from time-dependent density functional theory calculations. The results allow conclusions to be drawn regarding the plausibility of the reduced species being responsible for light-induced blinking in direct stochastic optical reconstruction microscopy.
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Affiliation(s)
- Alexandra Lisovskaya
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Anthony Harriman
- Molecular Photonics Laboratory, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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