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Szydlowski NA, Go JS, Hu YS. Chromatin imaging and new technologies for imaging the nucleome. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1442. [PMID: 30456928 DOI: 10.1002/wsbm.1442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/03/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022]
Abstract
Synergistic developments in advanced fluorescent imaging and labeling techniques enable direct visualization of the chromatin structure and dynamics at the nanoscale level and in live cells. Super-resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement and can readily achieve live multicolor imaging using conventional fluorophores. Single-molecule localization microscopy increases the spatial resolution by approximately 10-fold at the expense of slower acquisition speed. Stimulated emission-depletion microscopy generates a roughly fivefold resolution improvement with an imaging speed proportional to the scanning area. In parallel, advanced labeling strategies have been developed to "light up" global and sequence-specific DNA regions. DNA binding dyes have been exploited to achieve high labeling densities in single-molecule localization microscopy and enhance contrast in correlated light and electron microscopy. New-generation Oligopaint utilizes bioinformatics analyses to optimize the design of fluorescence in situ hybridization probes. Through sequential and combinatorial labeling, direct characterization of the DNA domain volume and length as well as the spatial organization of distinct topologically associated domains has been reported. In live cells, locus-specific labeling has been achieved by either inserting artificial loci next to the gene of interest, such as the repressor-operator array systems, or utilizing genome editing tools, including zinc finer proteins, transcription activator-like effectors, and the clustered regularly interspaced short palindromic repeats systems. Combined with single-molecule tracking, these labeling techniques enable direct visualization of intra- and inter-chromatin interactions. This article is categorized under: Laboratory Methods and Technologies > Imaging.
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Affiliation(s)
- Nicole A Szydlowski
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Jane S Go
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Ying S Hu
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
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52
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Haimerl JM, Ghosh I, König B, Lupton JM, Vogelsang J. Chemical Photocatalysis with Rhodamine 6G: Investigation of Photoreduction by Simultaneous Fluorescence Correlation Spectroscopy and Fluorescence Lifetime Measurements. J Phys Chem B 2018; 122:10728-10735. [DOI: 10.1021/acs.jpcb.8b08615] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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53
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Zhang Y, Song KH, Tang S, Ravelo L, Cusido J, Sun C, Zhang HF, Raymo FM. Far-Red Photoactivatable BODIPYs for the Super-Resolution Imaging of Live Cells. J Am Chem Soc 2018; 140:12741-12745. [PMID: 30247890 PMCID: PMC9884153 DOI: 10.1021/jacs.8b09099] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The photoinduced disconnection of an oxazine heterocycle from a borondipyrromethene (BODIPY) chromophore activates bright far-red fluorescence. The high brightness of the product and the lack of autofluorescence in this spectral region allow its detection at the single-molecule level within the organelles of live cells. Indeed, these photoactivatable fluorophores localize in lysosomal compartments and remain covalently immobilized within these organelles. The suppression of diffusion allows the reiterative reconstruction of subdiffraction images and the visualization of the labeled organelles with excellent localization precision. Thus, the combination of photochemical, photophysical and structural properties designed into our fluorophores enable the visualization of live cells with a spatial resolution that is inaccessible to conventional fluorescence imaging.
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Affiliation(s)
- Yang Zhang
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431,,Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60201
| | - Ki-Hee Song
- Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60201
| | - Sicheng Tang
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
| | - Laura Ravelo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431
| | - Janet Cusido
- Department of Natural and Social Sciences, Miami Dade College – InterAmerican Campus, 627 S.W. 27th Avenue, Miami, FL 33135-2937
| | - Cheng Sun
- Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60201
| | - Hao F. Zhang
- Departments of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60201,Corresponding Author,
| | - Françisco M. Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146-0431,,Corresponding Author,
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Golfetto O, Wakefield DL, Cacao EE, Avery KN, Kenyon V, Jorand R, Tobin SJ, Biswas S, Gutierrez J, Clinton R, Ma Y, Horne DA, Williams JC, Jovanović-Talisman T. A Platform To Enhance Quantitative Single Molecule Localization Microscopy. J Am Chem Soc 2018; 140:12785-12797. [PMID: 30256630 PMCID: PMC6187371 DOI: 10.1021/jacs.8b04939] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Quantitative single molecule localization microscopy (qSMLM) is a powerful approach to study in situ protein organization. However, uncertainty regarding the photophysical properties of fluorescent reporters can bias the interpretation of detected localizations and subsequent quantification. Furthermore, strategies to efficiently detect endogenous proteins are often constrained by label heterogeneity and reporter size. Here, a new surface assay for molecular isolation (SAMI) was developed for qSMLM and used to characterize photophysical properties of fluorescent proteins and dyes. SAMI-qSMLM afforded robust quantification. To efficiently detect endogenous proteins, we used fluorescent ligands that bind to a specific site on engineered antibody fragments. Both the density and nano-organization of membrane-bound epidermal growth factor receptors (EGFR, HER2, and HER3) were determined by a combination of SAMI, antibody engineering, and pair-correlation analysis. In breast cancer cell lines, we detected distinct differences in receptor density and nano-organization upon treatment with therapeutic agents. This new platform can improve molecular quantification and can be developed to study the local protein environment of intact cells.
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Affiliation(s)
- Ottavia Golfetto
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Devin L Wakefield
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Eliedonna E Cacao
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Kendra N Avery
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Victor Kenyon
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Raphael Jorand
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Steven J Tobin
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Sunetra Biswas
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Jennifer Gutierrez
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Ronald Clinton
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Yuelong Ma
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - David A Horne
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - John C Williams
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
| | - Tijana Jovanović-Talisman
- Department of Molecular Medicine , Beckman Research Institute, City of Hope , 1500 East Duarte Road , Duarte , California 91010 , United States
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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A highly selective fluorescence switch for Cu2+ and Fe3+ based on a new diarylethene with a triazole-linked rhodamine 6G unit. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Fang K, Chen X, Li X, Shen Y, Sun J, Czajkowsky DM, Shao Z. Super-resolution Imaging of Individual Human Subchromosomal Regions in Situ Reveals Nanoscopic Building Blocks of Higher-Order Structure. ACS NANO 2018; 12:4909-4918. [PMID: 29715004 DOI: 10.1021/acsnano.8b01963] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It is widely recognized that the higher-order spatial organization of the genome, beyond the nucleosome, plays an important role in many biological processes. However, to date, direct information on even such fundamental structural details as the typical sizes and DNA content of these higher-order structures in situ is poorly characterized. Here, we examine the nanoscopic DNA organization within human nuclei using super-resolution direct stochastic optical reconstruction microscopy (dSTORM) imaging and 5-ethynyl-2'-deoxyuridine click chemistry, studying single fully labeled chromosomes within an otherwise unlabeled nuclei to improve the attainable resolution. We find that, regardless of nuclear position, individual subchromosomal regions consist of three different levels of DNA compaction: (i) dispersed chromatin; (ii) nanodomains of sizes ranging tens of nanometers containing a few kilobases (kb) of DNA; and (iii) clusters of nanodomains. Interestingly, the sizes and DNA content of the nanodomains are approximately the same at the nuclear periphery, nucleolar proximity, and nuclear interior, suggesting that these nanodomains share a roughly common higher-order architecture. Overall, these results suggest that DNA compaction within the eukaryote nucleus occurs via the condensation of DNA into few-kb nanodomains of approximately similar structure, with further compaction occurring via the clustering of nanodomains.
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Vangindertael J, Camacho R, Sempels W, Mizuno H, Dedecker P, Janssen KPF. An introduction to optical super-resolution microscopy for the adventurous biologist. Methods Appl Fluoresc 2018; 6:022003. [DOI: 10.1088/2050-6120/aaae0c] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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60
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Yuasa J, Nakagawa T, Kita Y, Kaito A, Kawai T. Photoactivatable europium luminescence turn-on by photo-oxygenation of β-diketone having pyrrole rings. Chem Commun (Camb) 2018; 53:6748-6751. [PMID: 28594026 DOI: 10.1039/c7cc03753h] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work demonstrates a novel photoactivatable turn-on-type lanthanide(iii) luminescence. A β-diketone substrate having redox-active pyrrole moieties (LH2) undergoes efficient photo-oxygenation to afford the corresponding α-alkoxy diketone (LHOH) in the presence of lanthanide(iii) ions, which trigger bright europium(iii) red luminescence (PA-EuIII) turn-on, as well as activating the near-infrared luminescence (λem = 976 nm) of ytterbium(iii). A photo-patterning process for security imaging is successfully demonstrated.
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Affiliation(s)
- Junpei Yuasa
- Department of Applied Chemistry, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan.
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63
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Zhang R, Chouket R, Plamont MA, Kelemen Z, Espagne A, Tebo AG, Gautier A, Gissot L, Faure JD, Jullien L, Croquette V, Le Saux T. Macroscale fluorescence imaging against autofluorescence under ambient light. LIGHT, SCIENCE & APPLICATIONS 2018; 7:97. [PMID: 30510693 PMCID: PMC6261969 DOI: 10.1038/s41377-018-0098-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/27/2018] [Accepted: 10/27/2018] [Indexed: 05/07/2023]
Abstract
Macroscale fluorescence imaging is increasingly used to observe biological samples. However, it may suffer from spectral interferences that originate from ambient light or autofluorescence of the sample or its support. In this manuscript, we built a simple and inexpensive fluorescence macroscope, which has been used to evaluate the performance of Speed OPIOM (Out of Phase Imaging after Optical Modulation), which is a reference-free dynamic contrast protocol, to selectively image reversibly photoswitchable fluorophores as labels against detrimental autofluorescence and ambient light. By tuning the intensity and radial frequency of the modulated illumination to the Speed OPIOM resonance and adopting a phase-sensitive detection scheme that ensures noise rejection, we enhanced the sensitivity and the signal-to-noise ratio for fluorescence detection in blot assays by factors of 50 and 10, respectively, over direct fluorescence observation under constant illumination. Then, we overcame the strong autofluorescence of growth media that are currently used in microbiology and realized multiplexed fluorescence observation of colonies of spectrally similar fluorescent bacteria with a unique configuration of excitation and emission wavelengths. Finally, we easily discriminated fluorescent labels from the autofluorescent and reflective background in labeled leaves, even under the interference of incident light at intensities that are comparable to sunlight. The proposed approach is expected to find multiple applications, from biological assays to outdoor observations, in fluorescence macroimaging.
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Affiliation(s)
- Ruikang Zhang
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Raja Chouket
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Zsolt Kelemen
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Saclay Plant Science (SPS), Université Paris-Saclay, Versailles, France
| | - Agathe Espagne
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Lionel Gissot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Saclay Plant Science (SPS), Université Paris-Saclay, Versailles, France
| | - Jean-Denis Faure
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Saclay Plant Science (SPS), Université Paris-Saclay, Versailles, France
| | - Ludovic Jullien
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Vincent Croquette
- Laboratoire de Physique Statistique, École Normale Supérieure, PSL Research University, Université Paris Diderot Sorbonne Paris-Cité, Sorbonne Université, CNRS, 75005 Paris, France
- Institut de biologie de l’École normale supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Thomas Le Saux
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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64
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Pellissier-Tanon A, Chouket R, Le Saux T, Jullien L, Lemarchand A. Light-assisted dynamic titration: from theory to an experimental protocol. Phys Chem Chem Phys 2018; 20:23998-24010. [DOI: 10.1039/c8cp03953d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Forced light oscillations are used to titrate any targeted species using its specific kinetics and choosing adapted control parameter values.
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Affiliation(s)
| | - Raja Chouket
- PASTEUR
- Département de Chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Thomas Le Saux
- PASTEUR
- Département de Chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Ludovic Jullien
- PASTEUR
- Département de Chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Annie Lemarchand
- Sorbonne Université
- Centre National de la Recherche Scientifique (CNRS) Laboratoire de Physique Théorique de la Matière Condensée (LPTMC)
- 75252 Paris Cedex 05
- France
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65
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Chen TH, Chang HT. Stable and Photoswitchable Carbon-Dot Liposome. ACS APPLIED MATERIALS & INTERFACES 2017; 9:44259-44263. [PMID: 29218985 DOI: 10.1021/acsami.7b14969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Carbon-dot (C-dot) liposome consisting of several thousands of C-dots shows interesting photoswitching properties. The water-dispersible C-dot liposome possesses intrinsic photoluminescence (PL) and is stable against salt and photoirradiation. The PL of C-dot liposome can be turned off and then on under photoirradiation over the wavelength regions of 510-540 nm and 365-420 nm, respectively. Like reported C-dots, the C-dot liposome emits various colors when excited at different wavelengths. Having great stability and high contrast, images of individual C-dot liposome have been recorded, showing negligible photoblinking. Through a simple photolithographic approach, micropatterns of C-dot liposomes emitting different colors have been fabricated.
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Affiliation(s)
- Tzu-Heng Chen
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
- Department of Chemistry, Chung Yuan Christian University , Taoyuan City, Taiwan
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66
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Reisch A, Trofymchuk K, Runser A, Fleith G, Rawiso M, Klymchenko AS. Tailoring Fluorescence Brightness and Switching of Nanoparticles through Dye Organization in the Polymer Matrix. ACS APPLIED MATERIALS & INTERFACES 2017; 9:43030-43042. [PMID: 29185702 DOI: 10.1021/acsami.7b12292] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fluorescent nanoparticles (NPs) help to increase spatial and temporal resolution in bioimaging. Advanced microscopy techniques require very bright NPs that exhibit either stable emission for single-particle tracking or complete on/off switching (blinking) for super-resolution imaging. Here, ultrabright dye-loaded polymer NPs with controlled switching properties are developed. To this aim, the salt of a dye (rhodamine B octadecyl ester) with a hydrophobic counterion (fluorinated tetraphenylborate) is encapsulated at very high concentrations up to 30 wt % in NPs made of poly(lactic-co-glycolic acid) (PLGA), poly(methyl methacrylate) (PMMA), and polycaprolactone (PCL) through nanoprecipitation. The obtained 35 nm NPs are nearly 100 times brighter than quantum dots. The nature of the polymer is found to define the collective behavior of the encapsulated dyes so that NPs containing thousands of dyes exhibit either whole particle blinking, for PLGA, or stable emission, for PMMA and PCL. Fluorescence anisotropy measurements together with small-angle X-ray scattering experiments suggest that in less hydrophobic PLGA, dyes tend to cluster, whereas in more hydrophobic PMMA and PCL, dyes are dispersed within the matrix, thus altering the switching behavior of NPs. Experiments using a perylene diimide derivative show a similar effect of the polymer nature. The resulting fluorescent NPs are suitable for a wide range of imaging applications from tracking to super-resolution imaging. The findings on the organization of the load innside NPs will have impact on the development of materials for applications ranging from photovoltaics to drug delivery.
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Affiliation(s)
- Andreas Reisch
- Laboratoire de Biophotonique et Pharmacologie, UMR CNRS 7213, Université de Strasbourg , 74 route du Rhin, 67401 Illkirch Cedex, France
| | - Kateryna Trofymchuk
- Laboratoire de Biophotonique et Pharmacologie, UMR CNRS 7213, Université de Strasbourg , 74 route du Rhin, 67401 Illkirch Cedex, France
| | - Anne Runser
- Laboratoire de Biophotonique et Pharmacologie, UMR CNRS 7213, Université de Strasbourg , 74 route du Rhin, 67401 Illkirch Cedex, France
| | - Guillaume Fleith
- Institut Charles Sadron (CNRS-UdS) , 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2, France
| | - Michel Rawiso
- Institut Charles Sadron (CNRS-UdS) , 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2, France
| | - Andrey S Klymchenko
- Laboratoire de Biophotonique et Pharmacologie, UMR CNRS 7213, Université de Strasbourg , 74 route du Rhin, 67401 Illkirch Cedex, France
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67
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Pyle JR, Chen J. Photobleaching of YOYO-1 in super-resolution single DNA fluorescence imaging. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:2296-2306. [PMID: 29181286 PMCID: PMC5687005 DOI: 10.3762/bjnano.8.229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/05/2017] [Indexed: 06/07/2023]
Abstract
Super-resolution imaging of single DNA molecules via point accumulation for imaging in nanoscale topography (PAINT) has great potential to visualize fine DNA structures with nanometer resolution. In a typical PAINT video acquisition, dye molecules (YOYO-1) in solution sparsely bind to the target surfaces (DNA) whose locations can be mathematically determined by fitting their fluorescent point spread function. Many YOYO-1 molecules intercalate into DNA and remain there during imaging, and most of them have to be temporarily or permanently fluorescently bleached, often stochastically, to allow for the visualization of a few fluorescent events per DNA per frame of the video. Thus, controlling the fluorescence on-off rate is important in PAINT. In this paper, we study the photobleaching of YOYO-1 and its correlation with the quality of the PAINT images. At a low excitation laser power density, the photobleaching of YOYO-1 is too slow and a minimum required power density was identified, which can be theoretically predicted with the proposed method in this report.
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Affiliation(s)
- Joseph R Pyle
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701, USA
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701, USA
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68
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Gutiérrez-Arzaluz L, López-Arteaga R, Cortés-Guzmán F, Peon J. Nitrated Fluorophore Formation upon Two-Photon Excitation of an Azide with Extended Conjugation. J Phys Chem B 2017; 121:9910-9919. [PMID: 28981286 DOI: 10.1021/acs.jpcb.7b09446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The transformation of an aromatic azide into a highly fluorescent species through a nonlinear optical process was studied. The azide system was designed to undergo N2 release and nitrene to nitro conversion upon two-photon electronic excitation. The formation of the nitro form of the compound through reactions with O2 and its high radiative quantum yield implies that the azide can be used as a biphotonic activatable fluorogen. The electronic state in which the azide to nitrene transformation takes place can be accessed nonlinearly with near-infrared light which allows for photoactivation with commonly available lasers. Furthermore, the system was built with a sulfonate functionality which allows for the molecule to be adsorbed at surfaces like that of cadmium sulfide nanocrystals which further improves the nonlinear optical absorption properties in the composite, through an energy transfer mechanism. The yield of the process as a function of the excitation photon energy together with computational studies indicate that the N2 release in this azide is due to a reactive channel in the second singlet excited state of the molecule. This feature implies that the system is intrinsically photostable for excitation below and above a certain wavelength and that the system can be phototriggered selectively by the nonlinear optical process.
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Affiliation(s)
- Luis Gutiérrez-Arzaluz
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Rafael López-Arteaga
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Fernando Cortés-Guzmán
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
| | - Jorge Peon
- Instituto de Química, Universidad Nacional Autónoma de México , Circuito Exterior, Ciudad Universitaria, México, 04510, México
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69
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Kawai K, Miyata T, Shimada N, Ito S, Miyasaka H, Maruyama A. Single-Molecule Monitoring of the Structural Switching Dynamics of Nucleic Acids through Controlling Fluorescence Blinking. Angew Chem Int Ed Engl 2017; 56:15329-15333. [PMID: 28990725 PMCID: PMC5725658 DOI: 10.1002/anie.201708705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Indexed: 01/20/2023]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful tool to investigate the dynamics of biomolecular events in real time. However, it requires two fluorophores and can be applied only to dynamics that accompany large changes in distance between the molecules. Herein, we introduce a method for kinetic analysis based on control of fluorescence blinking (KACB), a general approach to investigate the dynamics of biomolecules by using a single fluorophore. By controlling the kinetics of the redox reaction the blinking kinetics or pattern can be controlled to be affected by microenvironmental changes around a fluorophore (rKACB), thereby enabling real-time single-molecule measurement of the structure-changing dynamics of nucleic acids.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Takafumi Miyata
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Syoji Ito
- Division of Frontier Materials Science and Center for Promotion of Advanced Interdisciplinary Research, Graduate School of Engineering Science, Osaka University, Toyonaka, 567-8531, 226-8501, Japan
| | - Hiroshi Miyasaka
- Division of Frontier Materials Science and Center for Promotion of Advanced Interdisciplinary Research, Graduate School of Engineering Science, Osaka University, Toyonaka, 567-8531, 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
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70
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Kawai K, Miyata T, Shimada N, Ito S, Miyasaka H, Maruyama A. Single-Molecule Monitoring of the Structural Switching Dynamics of Nucleic Acids through Controlling Fluorescence Blinking. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708705] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN); Osaka University; Mihogaoka 8-1 Ibaraki Osaka 567-0047 Japan
| | - Takafumi Miyata
- Department of Life Science and Technology; Tokyo Institute of Technology; 4259 B-57 Nagatsuta Midori-ku, Yokohama Kanagawa 226-8501 Japan
| | - Naohiko Shimada
- Department of Life Science and Technology; Tokyo Institute of Technology; 4259 B-57 Nagatsuta Midori-ku, Yokohama Kanagawa 226-8501 Japan
| | - Syoji Ito
- Division of Frontier Materials Science and Center for Promotion of Advanced Interdisciplinary Research; Graduate School of Engineering Science; Osaka University; Toyonaka, 567-8531 226-8501 Japan
| | - Hiroshi Miyasaka
- Division of Frontier Materials Science and Center for Promotion of Advanced Interdisciplinary Research; Graduate School of Engineering Science; Osaka University; Toyonaka, 567-8531 226-8501 Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology; Tokyo Institute of Technology; 4259 B-57 Nagatsuta Midori-ku, Yokohama Kanagawa 226-8501 Japan
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71
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Resonant out-of-phase fluorescence microscopy and remote imaging overcome spectral limitations. Nat Commun 2017; 8:969. [PMID: 29042541 PMCID: PMC5645393 DOI: 10.1038/s41467-017-00847-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/01/2017] [Indexed: 01/10/2023] Open
Abstract
We present speed out-of-phase imaging after optical modulation (OPIOM), which exploits reversible photoswitchable fluorophores as fluorescent labels and combines optimized periodic illumination with phase-sensitive detection to specifically retrieve the label signal. Speed OPIOM can extract the fluorescence emission from a targeted label in the presence of spectrally interfering fluorophores and autofluorescence. Up to four fluorescent proteins exhibiting a similar green fluorescence have been distinguished in cells either sequentially or in parallel. Speed OPIOM is compatible with imaging biological processes in real time in live cells. Finally speed OPIOM is not limited to microscopy but is relevant for remote imaging as well, in particular, under ambient light. Thus, speed OPIOM has proved to enable fast and quantitative live microscopic and remote-multiplexed fluorescence imaging of biological samples while filtering out noise, interfering fluorophores, as well as ambient light. Generally, fluorescence imaging needs to be done in a dark environment using molecules with spectrally separated emissions. Here, Quérard et al. develop a protocol for high-speed imaging and remote sensing of spectrally overlapping reversible photoswitchable fluorophores in ambient light.
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72
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Measuring Nanometer Distances Between Fluorescent Labels Step-by-Step. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1663:189-203. [PMID: 28924669 DOI: 10.1007/978-1-4939-7265-4_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Super-resolution fluorescence microscopy methods are increasingly applied to study the structure of biological molecules within their natural context or at biomaterial interfaces. We here provide a protocol for Single-molecule High-Resolution Imaging with Photobleaching (SHRImP) that can be used to obtain information about the conformation of large proteins or other macromolecules at the single-molecule level. This procedure requires site-specific protein labeling with fluorescent dyes, immobilization and sample preparation, optimization of imaging buffer composition and microscope settings, and acquisition of short time-lapse movies that capture the stepwise bleaching behavior of individual molecules. We then describe a method for reliably determining the relative positions of labels from bleaching movies using the free image processing package Fiji (ImageJ) with the help of auxiliary macros that are provided as Supplementary Material. The presented approach allows for measuring intramolecular distance distributions in the range of a few to hundreds of nanometers and can be applied to a wide variety of biological systems.
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73
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Molecular Counting with Localization Microscopy: A Bayesian Estimate Based on Fluorophore Statistics. Biophys J 2017; 112:1777-1785. [PMID: 28494949 DOI: 10.1016/j.bpj.2017.03.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 03/16/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022] Open
Abstract
Superresolved localization microscopy has the potential to serve as an accurate, single-cell technique for counting the abundance of intracellular molecules. However, the stochastic blinking of single fluorophores can introduce large uncertainties into the final count. Here we provide a theoretical foundation for applying superresolved localization microscopy to the problem of molecular counting based on the distribution of blinking events from a single fluorophore. We also show that by redundantly tagging single molecules with multiple, blinking fluorophores, the accuracy of the technique can be enhanced by harnessing the central limit theorem. The coefficient of variation then, for the number of molecules M estimated from a given number of blinks B, scales like ∼1/Nl, where Nl is the mean number of labels on a target. As an example, we apply our theory to the challenging problem of quantifying the cell-to-cell variability of plasmid copy number in bacteria.
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74
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Wang C, Taki M, Sato Y, Fukazawa A, Higashiyama T, Yamaguchi S. Super-Photostable Phosphole-Based Dye for Multiple-Acquisition Stimulated Emission Depletion Imaging. J Am Chem Soc 2017; 139:10374-10381. [PMID: 28741935 DOI: 10.1021/jacs.7b04418] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As stimulated emission depletion (STED) microscopy can provide structural details of cells with an optical resolution beyond the diffraction limit, it has become an indispensable tool in cell biology. However, the intense STED laser beam usually causes rapid photobleaching of the employed fluorescent dyes, which significantly limits the utility of STED microscopy from a practical perspective. Herein we report a new design of super-photostable dye, PhoxBright 430 (PB430), comprising a fully ring-fused π-conjugated skeleton with an electron-accepting phosphole P-oxide unit. We previously developed a super-photostable dye C-Naphox by combining the phosphole unit with an electron-donating triphenylamine moiety. In PB430, removal of the amino group alters the transition type from intramolecular charge transfer character to π-π* transition character, which gives rise to intense fluorescence insensitive to molecular environment in terms of fluorescence colors and intensity, and bright fluorescence even in aqueous media. PB430 also furnishes high solubility in water, and is capable of labeling proteins with maintaining high fluorescence quantum yields. This dye exhibits outstanding resistance to photoirradiation even under the STED conditions and allows continuous acquisition of STED images. Indeed, using a PB430-conjugated antibody, we succeed in attaining a 3-D reconstruction of super-resolution STED images as well as photostability-based multicolor STED imaging of fluorescently labeled cytoskeletal structures.
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Affiliation(s)
- Chenguang Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan
| | - Masayasu Taki
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan
| | - Aiko Fukazawa
- Department of Chemistry, Graduate School of Science, Nagoya University , Furo, Chikusa, Nagoya 464-8602, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University , Furo, Chikusa, Nagoya 464-8602, Japan
| | - Shigehiro Yamaguchi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University , Furo, Chikusa, Nagoya 464-8602, Japan
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75
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Patel SK, Cao J, Lippert AR. A volumetric three-dimensional digital light photoactivatable dye display. Nat Commun 2017; 8:15239. [PMID: 28695887 PMCID: PMC5508202 DOI: 10.1038/ncomms15239] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/13/2017] [Indexed: 12/14/2022] Open
Abstract
Volumetric three-dimensional displays offer spatially accurate representations of images with a 360° view, but have been difficult to implement due to complex fabrication requirements. Herein, a chemically enabled volumetric 3D digital light photoactivatable dye display (3D Light PAD) is reported. The operating principle relies on photoactivatable dyes that become reversibly fluorescent upon illumination with ultraviolet light. Proper tuning of kinetics and emission wavelengths enables the generation of a spatial pattern of fluorescent emission at the intersection of two structured light beams. A first-generation 3D Light PAD was fabricated using the photoactivatable dye N-phenyl spirolactam rhodamine B, a commercial picoprojector, an ultraviolet projector and a custom quartz imaging chamber. The system displays a minimum voxel size of 0.68 mm3, 200 μm resolution and good stability over repeated ‘on-off’ cycles. A range of high-resolution 3D images and animations can be projected, setting the foundation for widely accessible volumetric 3D displays. Despite living in a three-dimensional world, almost all information in our society is conveyed in a two-dimensional format. Here, the authors provide a technique for the generation of spatially accurate and high-resolution three-dimensional images using fluorescent photoswitch chemistry.
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Affiliation(s)
- Shreya K Patel
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
| | - Jian Cao
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA.,Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
| | - Alexander R Lippert
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA.,Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA.,Center for Global Health Impact (CGHI), Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
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76
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Cloin BMC, De Zitter E, Salas D, Gielen V, Folkers GE, Mikhaylova M, Bergeler M, Krajnik B, Harvey J, Hoogenraad CC, Van Meervelt L, Dedecker P, Kapitein LC. Efficient switching of mCherry fluorescence using chemical caging. Proc Natl Acad Sci U S A 2017; 114:7013-7018. [PMID: 28630286 PMCID: PMC5502588 DOI: 10.1073/pnas.1617280114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME). The molecules can be recovered to the red fluorescent state by washing out the βME or through irradiation with violet light, with up to 80% total recovery. We show that this can be used to perform single-molecule localization microscopy (SMLM) on cells expressing mCherry, which renders this approach applicable to a very wide range of existing constructs. We performed a detailed investigation of the mechanism underlying these dynamics, using X-ray crystallography, NMR spectroscopy, and ab initio quantum-mechanical calculations. We find that the βME-induced fluorescence quenching of mCherry occurs both via the direct addition of βME to the chromophore and through βME-mediated reduction of the chromophore. These results not only offer a strategy to expand SMLM imaging to a broad range of available biological models, but also present unique insights into the chemistry and functioning of a highly important class of fluorophores.
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Affiliation(s)
- Bas M C Cloin
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Elke De Zitter
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
| | - Desiree Salas
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Vincent Gielen
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
| | - Gert E Folkers
- NMR Spectroscopy, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Marina Mikhaylova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Maike Bergeler
- Quantum Chemistry and Physical Chemistry, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
| | - Bartosz Krajnik
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Jeremy Harvey
- Quantum Chemistry and Physical Chemistry, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Luc Van Meervelt
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium;
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands;
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77
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Rodríguez-Romero J, Guarin CA, Arroyo-Pieck A, Gutiérrez-Arzaluz L, López-Arteaga R, Cortés-Guzmán F, Navarro P, Peon J. Fluorophore Release from a Polymethinic Photoremovable Protecting Group Through a Nonlinear Optical Process. CHEMPHOTOCHEM 2017. [DOI: 10.1002/cptc.201700076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jesús Rodríguez-Romero
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Cesar A. Guarin
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Andres Arroyo-Pieck
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Luis Gutiérrez-Arzaluz
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Rafael López-Arteaga
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Fernando Cortés-Guzmán
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Pedro Navarro
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
| | - Jorge Peon
- Instituto de Química; Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; Ciudad de México 04510 México
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78
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Agarwal K, Prasad DK. Eigen-analysis reveals components supporting super-resolution imaging of blinking fluorophores. Sci Rep 2017; 7:4445. [PMID: 28667336 PMCID: PMC5493635 DOI: 10.1038/s41598-017-04544-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022] Open
Abstract
This paper presents eigen-analysis of image stack of blinking fluorophores to identify the components that enable super-resolved imaging of blinking fluorophores. Eigen-analysis reveals that the contributions of spatial distribution of fluorophores and their temporal photon emission characteristics can be completely separated. While cross-emitter cross-pixel information of spatial distribution that permits super-resolution is encoded in two matrices, temporal statistics weigh the contribution of these matrices to the measured data. The properties and conditions of exploitation of these matrices are investigated. Con-temporary super-resolution imaging methods that use blinking for super-resolution are studied in the context of the presented analysis. Besides providing insight into the capabilities and limitations of existing super-resolution methods, the analysis shall help in designing better super-resolution techniques that directly exploit these matrices.
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Affiliation(s)
- Krishna Agarwal
- BioSystems and Micromechanics Inter-Disciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore. .,Department of Physics and Technology, UiT-The Arctic University of Norway, 9037, Tromsø, Norway.
| | - Dilip K Prasad
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
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79
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Klementieva NV, Bozhanova NG, Zagaynova EV, Lukyanov KA, Mishin AS. Fluorophores for single-molecule localization microscopy. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017030074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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80
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Chan KM, Kölmel DK, Wang S, Kool ET. Color-Change Photoswitching of an Alkynylpyrene Excimer Dye. Angew Chem Int Ed Engl 2017; 56:6497-6501. [PMID: 28474388 PMCID: PMC5665017 DOI: 10.1002/anie.201701235] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/20/2017] [Indexed: 01/06/2023]
Abstract
We describe a photoswitchable DNA-based dimeric dye that visibly changes fluorescence from green to blue upon UV irradiation. A novel bis-alkyne-dependent [2+2+2] cycloaddition is proposed as a mechanism for the color change in air. The photoinduced structural switching results in spatial separation of stacked pyrene units, thereby causing selective loss of the excimer emission. We demonstrate and suggest several applications for this novel photoswitch.
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Affiliation(s)
- Ke Min Chan
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Dominik K Kölmel
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Shenliang Wang
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
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81
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Chan KM, Kölmel DK, Wang S, Kool ET. Color‐Change Photoswitching of an Alkynylpyrene Excimer Dye. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ke Min Chan
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | | | - Shenliang Wang
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Eric T. Kool
- Department of Chemistry Stanford University Stanford CA 94305 USA
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82
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Abstract
Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology & Biophysics, Julius-Maximilian-University of Würzburg , 97074 Würzburg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt , 60438 Frankfurt, Germany
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83
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Maier J, Pärs M, Weller T, Thelakkat M, Köhler J. Deliberate Switching of Single Photochromic Triads. Sci Rep 2017; 7:41739. [PMID: 28139764 PMCID: PMC5282491 DOI: 10.1038/srep41739] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/03/2017] [Indexed: 11/24/2022] Open
Abstract
Photochromic molecules can be reversibly converted between two bistable conformations by light, and are considered as promising building blocks in novel macromolecular structures for sensing and imaging techniques. We have studied individual molecular triads consisting of two strong fluorophores (perylene bisimide) that are covalently linked via a photochromic unit (dithienylcyclopentene) and distinguished between deliberate switching and spontaneous blinking. It was verified that the probability for observing deliberate light-induced switching of a single triad (rather than stochastic blinking) amounts to 0.8 ± 0.1. In a few exceptional cases this probability can exceed 0.95. These numbers are sufficiently large for application in sensitive biosensing, and super-resolution imaging. This opens the possibility to develop devices that can be controlled by an external optical stimulus on a truly molecular length scale.
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Affiliation(s)
- Johannes Maier
- Experimental Physics IV, University of Bayreuth, 95440 Bayreuth, Germany
| | - Martti Pärs
- Experimental Physics IV, University of Bayreuth, 95440 Bayreuth, Germany
| | - Tina Weller
- Applied Functional Polymers, University of Bayreuth, 95440 Bayreuth, Germany
| | - Mukundan Thelakkat
- Applied Functional Polymers, University of Bayreuth, 95440 Bayreuth, Germany
| | - Jürgen Köhler
- Experimental Physics IV, University of Bayreuth, 95440 Bayreuth, Germany
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84
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85
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Wang Y, Zhang G, Zhang W, Wang X, Wu Y, Liang T, Hao X, Fu H, Zhao Y, Zhang D. Tuning the Solid State Emission of the Carbazole and Cyano-Substituted Tetraphenylethylene by Co-Crystallization with Solvents. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:6554-6561. [PMID: 27436216 DOI: 10.1002/smll.201601516] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/19/2016] [Indexed: 06/06/2023]
Abstract
Solid state emissive materials with high quantum yields and tunable emissions are desirable for various applications. A new TPE derivative (1) with two carbazole moieties and two cyano groups is reported, which shows typical aggregation induced emission behavior. Four crystals 1a, 1b, 1c, and 1d are obtained after crystallization from N,N-dimethylformamid (DMF), trichloromethane (CHCl3 ), tetrahydrofuran (THF), and dichloromethane (CH2 Cl2 ), respectively. Crystal structural analyses reveal that (i) molecules of 1 co-crystallize with DMF, CHCl3 , THF, and CH2 Cl2 in 1a, 1b, 1c, and 1d, respectively, and (ii) conformations of 1 are different within 1a, 1b, 1c, and 1d, and compound 1 within crystal 1a adopts the most twisting conformation. Crystalline solids 1a, 1b, 1c, and 1d exhibit high emission quantum yields up to 0.65, but their emission colors are varied from blue to green. In comparison, the amorphous solid of 1 is yellow-emissive with emission maximum at 542 nm. Moreover, the blue- or green-emissive crystalline solids and the yellow-emissive amorphous solid can be inter-converted by the grinding of crystalline solids and exposure of the amorphous solid to vapors of appropriate solvents. It is also demonstrated that microrods of 1a, 1b, and 1d show typical optical waveguiding behavior.
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Affiliation(s)
- Yuancheng Wang
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Guanxin Zhang
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Wei Zhang
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xuedong Wang
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yishi Wu
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Tongling Liang
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Xiang Hao
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongbing Fu
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yongsheng Zhao
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Deqing Zhang
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
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86
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Specht EA, Braselmann E, Palmer AE. A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging. Annu Rev Physiol 2016; 79:93-117. [PMID: 27860833 DOI: 10.1146/annurev-physiol-022516-034055] [Citation(s) in RCA: 259] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescent tools have revolutionized our ability to probe biological dynamics, particularly at the cellular level. Fluorescent sensors have been developed on several platforms, utilizing either small-molecule dyes or fluorescent proteins, to monitor proteins, RNA, DNA, small molecules, and even cellular properties, such as pH and membrane potential. We briefly summarize the impressive history of tool development for these various applications and then discuss the most recent noteworthy developments in more detail. Particular emphasis is placed on tools suitable for single-cell analysis and especially live-cell imaging applications. Finally, we discuss prominent areas of need in future fluorescent tool development-specifically, advancing our capability to analyze and integrate the plethora of high-content data generated by fluorescence imaging.
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Affiliation(s)
- Elizabeth A Specht
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303; .,BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303
| | - Esther Braselmann
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303; .,BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303
| | - Amy E Palmer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303; .,BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303
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87
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Hummer G, Fricke F, Heilemann M. Model-independent counting of molecules in single-molecule localization microscopy. Mol Biol Cell 2016; 27:3637-3644. [PMID: 27466316 PMCID: PMC5221595 DOI: 10.1091/mbc.e16-07-0525] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/26/2022] Open
Abstract
Most biomolecular processes rely on tightly controlled stoichiometries, from the formation of molecular assemblies to cellular signaling. Single-molecule localization micro-scopy studies of fluorophore blinking offer a promising route to probe oligomeric states. Here we show that the distribution of the number of blinking events assumes a universal functional form, independent of photophysics, under relatively mild assumptions. The number of photophysical states, the kinetics of interconversion, and the fraction of active fluorophores enter as two or three constants. This essentially model-independent formulation allows us to determine molecule counts from fluorophore blinking statistics. The formulas hold even if the fluorophores have many different yet unresolved dark states, as long as there is only a single fluorescent state, or if there are different yet unresolvable fluorescent states, as long as there is only a single dark state. We demonstrate the practical applicability of this approach by quantifying the oligomerization states of membrane proteins tagged with the mEos2 fluorescent protein. We find that the model parameters, obtained by likelihood maximization, are transferable. With the counting statistics being independent of the detailed photophysics and its parameters being transferable, the method should be robust and broadly applicable to counting colocalized molecules in vivo and in vitro.
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Affiliation(s)
- Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Franziska Fricke
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
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88
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Mateos-Gil P, Letschert S, Doose S, Sauer M. Super-Resolution Imaging of Plasma Membrane Proteins with Click Chemistry. Front Cell Dev Biol 2016; 4:98. [PMID: 27668214 PMCID: PMC5016519 DOI: 10.3389/fcell.2016.00098] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/24/2016] [Indexed: 12/30/2022] Open
Abstract
Besides its function as a passive cell wall, the plasma membrane (PM) serves as a platform for different physiological processes such as signal transduction and cell adhesion, determining the ability of cells to communicate with the exterior, and form tissues. Therefore, the spatial distribution of PM components, and the molecular mechanisms underlying it, have important implications in various biological fields including cell development, neurobiology, and immunology. The existence of confined compartments in the plasma membrane that vary on many length scales from protein multimers to micrometer-size domains with different protein and lipid composition is today beyond all questions. As much as the physiology of cells is controlled by the spatial organization of PM components, the study of distribution, size, and composition remains challenging. Visualization of the molecular distribution of PM components has been impeded mainly due to two problems: the specific labeling of lipids and proteins without perturbing their native distribution and the diffraction-limit of fluorescence microscopy restricting the resolution to about half the wavelength of light. Here, we present a bioorthogonal chemical reporter strategy based on click chemistry and metabolic labeling for efficient and specific visualization of PM proteins and glycans with organic fluorophores in combination with super-resolution fluorescence imaging by direct stochastic optical reconstruction microscopy (dSTORM) with single-molecule sensitivity.
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Affiliation(s)
- Pablo Mateos-Gil
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
| | - Sebastian Letschert
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
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89
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Cheng HB, Hu GF, Zhang ZH, Gao L, Gao X, Wu HC. Photocontrolled Reversible Luminescent Lanthanide Molecular Switch Based on a Diarylethene–Europium Dyad. Inorg Chem 2016; 55:7962-8. [DOI: 10.1021/acs.inorgchem.6b01009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hong-Bo Cheng
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Guo-Fei Hu
- College of Chemistry & Material Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Zhan-Hui Zhang
- College of Chemistry & Material Science, Hebei Normal University, Shijiazhuang 050024, China
| | - Liang Gao
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Xingfa Gao
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
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90
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Bittel AM, Nickerson A, Saldivar IS, Dolman NJ, Nan X, Gibbs SL. Methodology for Quantitative Characterization of Fluorophore Photoswitching to Predict Superresolution Microscopy Image Quality. Sci Rep 2016; 6:29687. [PMID: 27412307 PMCID: PMC4944197 DOI: 10.1038/srep29687] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/23/2016] [Indexed: 01/05/2023] Open
Abstract
Single-molecule localization microscopy (SMLM) image quality and resolution strongly depend on the photoswitching properties of fluorophores used for sample labeling. Development of fluorophores with optimized photoswitching will considerably improve SMLM spatial and spectral resolution. Currently, evaluating fluorophore photoswitching requires protein-conjugation before assessment mandating specific fluorophore functionality, which is a major hurdle for systematic characterization. Herein, we validated polyvinyl alcohol (PVA) as a single-molecule environment to efficiently quantify the photoswitching properties of fluorophores and identified photoswitching properties predictive of quality SMLM images. We demonstrated that the same fluorophore photoswitching properties measured in PVA films and using antibody adsorption, a protein-conjugation environment analogous to labeled cells, were significantly correlated to microtubule width and continuity, surrogate measures of SMLM image quality. Defining PVA as a fluorophore photoswitching screening platform will facilitate SMLM fluorophore development and optimal image buffer assessment through facile and accurate photoswitching property characterization, which translates to SMLM fluorophore imaging performance.
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Affiliation(s)
- Amy M Bittel
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA
| | - Andrew Nickerson
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA
| | - Isaac S Saldivar
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA
| | | | - Xiaolin Nan
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA.,Knight Cancer Institute, Oregon Health &Science University, Portland, OR 97201, USA.,OHSU Center for Spatial Systems Biomedicine, Oregon Health &Science University, Portland, OR 97201, USA
| | - Summer L Gibbs
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA.,Knight Cancer Institute, Oregon Health &Science University, Portland, OR 97201, USA.,OHSU Center for Spatial Systems Biomedicine, Oregon Health &Science University, Portland, OR 97201, USA
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91
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Nizamov S, Sednev MV, Bossi ML, Hebisch E, Frauendorf H, Lehnart SE, Belov VN, Hell SW. "Reduced" Coumarin Dyes with an O-Phosphorylated 2,2-Dimethyl-4-(hydroxymethyl)-1,2,3,4-tetrahydroquinoline Fragment: Synthesis, Spectra, and STED Microscopy. Chemistry 2016; 22:11631-42. [PMID: 27385071 DOI: 10.1002/chem.201601252] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Indexed: 11/11/2022]
Abstract
Large Stokes-shift coumarin dyes with an O-phosphorylated 4-(hydroxymethyl)-2,2-dimethyl-1,2,3,4-tetrahydroquinoline fragment emitting in the blue, green, and red regions of the visible spectrum were synthesized. For this purpose, N-substituted and O-protected 1,2-dihydro-7-hydroxy-2,2,4-trimethylquinoline was oxidized with SeO2 to the corresponding α,β-unsaturated aldehyde and then reduced with NaBH4 in a "one-pot" fashion to yield N-substituted and 7-O-protected 4-(hydroxymethyl)-7-hydroxy-2,2-dimethyl-1,2,3,4-tetrahydroquinoline as a common precursor to all the coumarin dyes reported here. The photophysical properties of the new dyes ("reduced coumarins") and 1,2-dihydroquinoline analogues (formal precursors) with a trisubstituted C=C bond were compared. The "reduced coumarins" were found to be more photoresistant and brighter than their 1,2-dihydroquinoline counterparts. Free carboxylate analogues, as well as their antibody conjugates (obtained from N-hydroxysuccinimidyl esters) were also prepared. All studied conjugates with secondary antibodies afforded high specificity and were suitable for fluorescence microscopy. The red-emitting coumarin dye bearing a betaine fragment at the C-3-position showed excellent performance in stimulation emission depletion (STED) microscopy.
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Affiliation(s)
- Shamil Nizamov
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Maksim V Sednev
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Mariano L Bossi
- Laboratorio de Nanoscopias Fotonicas, INQUIMAE-DQIAyQF (FCEyN), Universidad de Buenos Aires & Conicet, Buenos Aires, Argentina
| | - Elke Hebisch
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Holm Frauendorf
- Institute for Organic and Biomolecular Chemistry, Georg-August University, Tammannstrasse 2, 37077, Göttingen, Germany
| | - Stephan E Lehnart
- Heart Research Center Göttingen, Department of Cardiology & Pulmonology, University Medical Center Göttingen, 37077, Göttingen, Germany
| | - Vladimir N Belov
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Stefan W Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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92
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Huang M, Yu R, Xu K, Ye S, Kuang S, Zhu X, Wan Y. An arch-bridge-type fluorophore for bridging the gap between aggregation-caused quenching (ACQ) and aggregation-induced emission (AIE). Chem Sci 2016; 7:4485-4491. [PMID: 30155095 PMCID: PMC6016330 DOI: 10.1039/c6sc01254j] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 03/29/2016] [Indexed: 12/11/2022] Open
Abstract
Solution and solid dual photoluminescence (PL) molecules fill the substantial gap between ACQ and AIE molecules to explore the mechanism of molecular luminescence in greater detail and to facilitate practical applications. A unique arch-bridge-like thiazolo[5,4-b]thieno[3,2-e]pyridine moiety is obtained as a stator after the rigidification of rotor 1 by intramolecular H-bonding of ortho -OH or -NH2 to afford two classes of solid and solution dual PL molecules. As a typical example, DF5 is dual PL active. Moreover, the large Stokes shift with high dual PL efficiency (ΦF up to 51% in the solid state, 80% in DMF, 74% in DMSO, and 100% in water), together with the good thermal stability (Tm > 200 °C and T05 > 200 °C), make it more practical for promising optoelectronic and biological applications.
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Affiliation(s)
- Manna Huang
- School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , P. R. China .
| | - Ruina Yu
- School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , P. R. China .
| | - Ke Xu
- School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , P. R. China .
| | - Shuxian Ye
- School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , P. R. China .
| | - Shi Kuang
- School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , P. R. China .
| | - Xinhai Zhu
- School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , P. R. China .
| | - Yiqian Wan
- School of Chemistry and Chemical Engineering , Sun Yat-sen University , Guangzhou 510275 , P. R. China .
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93
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Laine RF, Kaminski Schierle GS, van de Linde S, Kaminski CF. From single-molecule spectroscopy to super-resolution imaging of the neuron: a review. Methods Appl Fluoresc 2016; 4:022004. [PMID: 28809165 PMCID: PMC5390958 DOI: 10.1088/2050-6120/4/2/022004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/09/2016] [Accepted: 05/19/2016] [Indexed: 12/03/2022]
Abstract
For more than 20 years, single-molecule spectroscopy has been providing invaluable insights into nature at the molecular level. The field has received a powerful boost with the development of the technique into super-resolution imaging methods, ca. 10 years ago, which overcome the limitations imposed by optical diffraction. Today, single molecule super-resolution imaging is routinely used in the study of macromolecular function and structure in the cell. Concomitantly, computational methods have been developed that provide information on numbers and positions of molecules at the nanometer-scale. In this overview, we outline the technical developments that have led to the emergence of localization microscopy techniques from single-molecule spectroscopy. We then provide a comprehensive review on the application of the technique in the field of neuroscience research.
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Affiliation(s)
- Romain F Laine
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Gabriele S Kaminski Schierle
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Sebastian van de Linde
- Department of Biotechnology and Biophysics, Julius-Maximilians-University, Am Hubland, D-97074 Würzburg, Germany
| | - Clemens F Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
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94
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Butkevich AN, Mitronova GY, Sidenstein SC, Klocke JL, Kamin D, Meineke DNH, D'Este E, Kraemer PT, Danzl JG, Belov VN, Hell SW. Fluorescent Rhodamines and Fluorogenic Carbopyronines for Super-Resolution STED Microscopy in Living Cells. Angew Chem Int Ed Engl 2016; 55:3290-4. [PMID: 26844929 PMCID: PMC4770443 DOI: 10.1002/anie.201511018] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 11/14/2022]
Abstract
A range of bright and photostable rhodamines and carbopyronines with absorption maxima in the range of λ=500–630 nm were prepared, and enabled the specific labeling of cytoskeletal filaments using HaloTag technology followed by staining with 1 μm solutions of the dye–ligand conjugates. The synthesis, photophysical parameters, fluorogenic behavior, and structure–property relationships of the new dyes are discussed. Light microscopy with stimulated emission depletion (STED) provided one‐ and two‐color images of living cells with an optical resolution of 40–60 nm.
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Affiliation(s)
- Alexey N Butkevich
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Gyuzel Yu Mitronova
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Sven C Sidenstein
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Jessica L Klocke
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Dirk Kamin
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Dirk N H Meineke
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Elisa D'Este
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Philip-Tobias Kraemer
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Johann G Danzl
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Vladimir N Belov
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Stefan W Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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95
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Butkevich AN, Mitronova GY, Sidenstein SC, Klocke JL, Kamin D, Meineke DNH, D'Este E, Kraemer PT, Danzl JG, Belov VN, Hell SW. Fluoreszierende Rhodamine und fluorogene Carbopyronine für die STED-Mikroskopie lebender Zellen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Alexey N. Butkevich
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
| | - Gyuzel Yu. Mitronova
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
| | - Sven C. Sidenstein
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
| | - Jessica L. Klocke
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
| | - Dirk Kamin
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
| | - Dirk N. H. Meineke
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
| | - Elisa D'Este
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
| | - Philip-Tobias Kraemer
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
| | - Johann G. Danzl
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
| | - Vladimir N. Belov
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
| | - Stefan W. Hell
- Abteilung für NanoBiophotonik; Max-Planck-Institut für biophysikalische Chemie (MPIBPC); Am Faßberg 11 37077 Göttingen Deutschland
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96
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Lehmann M, Lichtner G, Klenz H, Schmoranzer J. Novel organic dyes for multicolor localization-based super-resolution microscopy. JOURNAL OF BIOPHOTONICS 2016; 9:161-70. [PMID: 25973835 DOI: 10.1002/jbio.201500119] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 05/07/2023]
Abstract
Precise multicolor single molecule localization-based microscopy (SMLM) requires bright probes with compatible photo-chemical and spectral properties to resolve distinct molecular species at the nanoscale. The accuracy of multicolor SMLM is further challenged by color channel crosstalk and chromatic alignment errors. These constrains limit the applicability of known reversibly switchable organic dyes for optimized multicolor SMLM. Here, we tested 28 commercially available dyes for their suitability to super-resolve a known cellular nanostructure. We identified eight novel dyes in different spectral regimes that enable high quality dSTORM imaging. Among those, the spectrally close dyes CF647 and CF680 comprise an optimal dye pair for spectral demixing-based, registration free multicolor dSTORM with low crosstalk. Combining this dye pair with the separately excited CF568 we performed 3-color dSTORM to image the relative nanoscale distribution of components of the endocytic machinery and the cytoskeleton.
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Affiliation(s)
- Martin Lehmann
- Leibniz Institut für Molekulare Pharmakologie (FMP) & Freie Universität Berlin, Robert-Roessle-Straße 10, 13125, Berlin, Germany
| | - Gregor Lichtner
- Leibniz Institut für Molekulare Pharmakologie (FMP) & Freie Universität Berlin, Robert-Roessle-Straße 10, 13125, Berlin, Germany
| | - Haider Klenz
- Leibniz Institut für Molekulare Pharmakologie (FMP) & Freie Universität Berlin, Robert-Roessle-Straße 10, 13125, Berlin, Germany
| | - Jan Schmoranzer
- Leibniz Institut für Molekulare Pharmakologie (FMP) & Freie Universität Berlin, Robert-Roessle-Straße 10, 13125, Berlin, Germany.
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97
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Zhang X, Chamberlayne CF, Kurimoto A, Frank NL, Harbron EJ. Visible light photoswitching of conjugated polymer nanoparticle fluorescence. Chem Commun (Camb) 2016; 52:4144-7. [DOI: 10.1039/c6cc00001k] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conjugated polymer nanoparticles doped with a reverse photochromic dye exhibit highly quenched fluorescence that can be reversibly activated by controlling the form of the photochrome with visible light.
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Affiliation(s)
- Xinzi Zhang
- Department of Chemistry
- The College of William and Mary
- Williamsburg
- USA
| | | | - Aiko Kurimoto
- Department of Chemistry
- University of Victoria
- Victoria
- Canada
| | - Natia L. Frank
- Department of Chemistry
- University of Victoria
- Victoria
- Canada
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98
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Zheng HR, Niu LY, Chen YZ, Wu LZ, Tung CH, Yang QZ. A multi-stimuli-responsive fluorescence switch based on E–Z isomerization of hydrazone. RSC Adv 2016. [DOI: 10.1039/c6ra01507g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We report a new strategy to construct fluorescence switches by taking advantage of the E–Z isomerization of the hydrazone group.
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Affiliation(s)
- Hai-Rong Zheng
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
- University of the Chinese Academy of Sciences
| | - Li-Ya Niu
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
- College of Chemistry
| | - Yu-Zhe Chen
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Li-Zhu Wu
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Chen-Ho Tung
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Qing-Zheng Yang
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
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Kawai K, Maruyama A. Triple helix conformation-specific blinking of Cy3 in DNA. Chem Commun (Camb) 2015; 51:4861-4. [PMID: 25697775 DOI: 10.1039/c5cc00607d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report that Cy3 undergoes triple helix conformation-specific blinking in DNA. Blinking patterns were affected by the stabilization of the Hoogsteen base-pair, suggesting that not only the presence but also the fluctuating behaviour of the triple helix can be monitored by the changes in the Cy3 blinking patterns.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 5670047, Japan.
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100
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Martínez-Carmona M, Colilla M, Vallet-Regí M. Smart Mesoporous Nanomaterials for Antitumor Therapy. NANOMATERIALS (BASEL, SWITZERLAND) 2015; 5:1906-1937. [PMID: 28347103 PMCID: PMC5304809 DOI: 10.3390/nano5041906] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 10/23/2015] [Accepted: 11/03/2015] [Indexed: 01/13/2023]
Abstract
The use of nanomaterials for the treatment of solid tumours is receiving increasing attention by the scientific community. Among them, mesoporous silica nanoparticles (MSNs) exhibit unique features that make them suitable nanocarriers to host, transport and protect drug molecules until the target is reached. It is possible to incorporate different targeting ligands to the outermost surface of MSNs to selectively drive the drugs to the tumour tissues. To prevent the premature release of the cargo entrapped in the mesopores, it is feasible to cap the pore entrances using stimuli-responsive nanogates. Therefore, upon exposure to internal (pH, enzymes, glutathione, etc.) or external (temperature, light, magnetic field, etc.) stimuli, the pore opening takes place and the release of the entrapped cargo occurs. These smart MSNs are capable of selectively reaching and accumulating at the target tissue and releasing the entrapped drug in a specific and controlled fashion, constituting a promising alternative to conventional chemotherapy, which is typically associated with undesired side effects. In this review, we overview the recent advances reported by the scientific community in developing MSNs for antitumor therapy. We highlight the possibility to design multifunctional nanosystems using different therapeutic approaches aimed at increasing the efficacy of the antitumor treatment.
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Affiliation(s)
- Marina Martínez-Carmona
- Department of Inorganic and Bioinorganic Chemistry, Faculty of Pharmacy, Complutense University of Madrid, Sanitary Research Institute "Hospital 12 de Octubre" i+12, Ramón y Cajal Square, S/N, Madrid 28040, Spain.
- Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid 28040, Spain.
- Campus of International Excellence, CEI Campus Moncloa, UCM-UPM, Madrid 28040, Spain.
| | - Montserrat Colilla
- Department of Inorganic and Bioinorganic Chemistry, Faculty of Pharmacy, Complutense University of Madrid, Sanitary Research Institute "Hospital 12 de Octubre" i+12, Ramón y Cajal Square, S/N, Madrid 28040, Spain.
- Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid 28040, Spain.
- Campus of International Excellence, CEI Campus Moncloa, UCM-UPM, Madrid 28040, Spain.
| | - Maria Vallet-Regí
- Department of Inorganic and Bioinorganic Chemistry, Faculty of Pharmacy, Complutense University of Madrid, Sanitary Research Institute "Hospital 12 de Octubre" i+12, Ramón y Cajal Square, S/N, Madrid 28040, Spain.
- Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid 28040, Spain.
- Campus of International Excellence, CEI Campus Moncloa, UCM-UPM, Madrid 28040, Spain.
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