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Lauritsen L, Szomek M, Hornum M, Reinholdt P, Kongsted J, Nielsen P, Brewer JR, Wüstner D. Ratiometric fluorescence nanoscopy and lifetime imaging of novel Nile Red analogs for analysis of membrane packing in living cells. Sci Rep 2024; 14:13748. [PMID: 38877068 PMCID: PMC11178856 DOI: 10.1038/s41598-024-64180-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024] Open
Abstract
Subcellular membranes have complex lipid and protein compositions, which give rise to organelle-specific membrane packing, fluidity, and permeability. Due to its exquisite solvent sensitivity, the lipophilic fluorescence dye Nile Red has been used extensively to study membrane packing and polarity. Further improvement of Nile Red can be achieved by introducing electron-donating or withdrawing functional groups. Here, we compare the potential of derivatives of Nile Red with such functional substitutions for super-resolution fluorescence microscopy of lipid packing in model membranes and living cells. All studied Nile Red derivatives exhibit cholesterol-dependent fluorescence changes in model membranes, as shown by spectrally resolved stimulated emission depletion (STED) microscopy. STED imaging of Nile Red probes in cells reveals lower membrane packing in fibroblasts from healthy subjects compared to those from patients suffering from Niemann Pick type C1 (NPC1) disease, a lysosomal storage disorder with accumulation of cholesterol and sphingolipids in late endosomes and lysosomes. We also find small but consistent changes in the fluorescence lifetime of the Nile Red derivatives in NPC1 cells, suggesting altered hydrogen-bonding capacity in their membranes. All Nile Red derivatives are essentially non-fluorescent in water but increase their brightness in membranes, allowing for their use in MINFLUX single molecule tracking experiments. Our study uncovers the potential of Nile Red probes with functional substitutions for nanoscopic membrane imaging.
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Affiliation(s)
- Line Lauritsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Maria Szomek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Mick Hornum
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Jonathan R Brewer
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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2
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Ichikawa S, Ishikawa K, Miyakawa H, Kodama Y. Live-cell imaging of the chloroplast outer envelope membrane using fluorescent dyes. PLANT DIRECT 2022; 6:e462. [PMID: 36398034 PMCID: PMC9666008 DOI: 10.1002/pld3.462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/15/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED Chloroplasts are organelles composed of sub-organellar compartments-stroma, thylakoids, and starch granules-and are surrounded by outer and inner envelope membranes (OEM and IEM, respectively). The chloroplast OEM and IEM play key roles not only as a barrier separating the chloroplast components from the cytosol but also in the interchange of numerous metabolites and proteins between the chloroplast interior and the cytosol. Fluorescent protein markers for the chloroplast OEM have been widely used to visualize the outermost border of chloroplasts. However, the use of marker proteins requires an established cellular genetic transformation method, which limits the plant species in which marker proteins can be used. Moreover, the high accumulation of OEM marker proteins often elicits abnormal morphological phenotypes of the OEM. Because the OEM can currently only be visualized using exogenous marker proteins, the behaviors of the chloroplast and/or its OEM remain unknown in wild-type cells of various plant species. Here, we visualized the OEM using live-cell staining with the fluorescent dyes rhodamine B and Nile red in several plant species, including crops. We propose rhodamine B and Nile red as new tools for visualizing the chloroplast OEM in living plant cells that do not require genetic transformation. SIGNIFICANCE STATEMENT We established a live-cell imaging method to visualize the chloroplast outer envelope membrane by staining living cells with fluorescent dyes. This method does not require genetic transformation and allows the observation of the chloroplast outer envelope membrane in various plant species.
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Affiliation(s)
- Shintaro Ichikawa
- Center for Bioscience Research and EducationUtsunomiya UniversityTochigiJapan
- Graduate School of Regional Development and CreativityUtsunomiya UniversityTochigiJapan
| | - Kazuya Ishikawa
- Center for Bioscience Research and EducationUtsunomiya UniversityTochigiJapan
| | - Hitoshi Miyakawa
- Center for Bioscience Research and EducationUtsunomiya UniversityTochigiJapan
- Graduate School of Regional Development and CreativityUtsunomiya UniversityTochigiJapan
| | - Yutaka Kodama
- Center for Bioscience Research and EducationUtsunomiya UniversityTochigiJapan
- Graduate School of Regional Development and CreativityUtsunomiya UniversityTochigiJapan
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3
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Alsamsam MN, Kopūstas A, Jurevičiūtė M, Tutkus M. The miEye: Bench-top super-resolution microscope with cost-effective equipment. HARDWAREX 2022; 12:e00368. [PMID: 36248253 PMCID: PMC9556790 DOI: 10.1016/j.ohx.2022.e00368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/23/2022] [Accepted: 10/02/2022] [Indexed: 06/01/2023]
Abstract
Commercial super-resolution (SR) imaging systems require a high budget, while current more affordable open source microscopy systems lack modularity and sometimes are too complex or lack reliability. We present miEye - a cost-effective microscope designed for high-resolution wide-field fluorescence imaging. The build is constructed using a CNC milled aluminum microscope body and commercially available optomechanics, with open-source Python-based microscope control, data visualization, and analysis software integration. The data acquisition software works robustly with commonly used industrial-grade complementary metal oxide semiconductor (iCMOS) cameras, performs IR beam back-reflection-based automatic focus stabilization, and allows for laser control via an Arduino-based laser relay. The open-source nature of the design is aimed to facilitate adaptation by the community. The build can be constructed for a cost of roughly 50 k €. It contains SM-fiber and MM-fiber excitation paths that are easy to interchange and an adaptable emission path. Also, it ensures <5 nm/min stability of the sample on all axes, and allows achieving <30 nm lateral resolution for dSTORM and DNA-PAINT single-molecule localization microscopy (SMLM) experiments. Thus it serves as a cost-effective and adaptable addition to the open source microscopy community and potentially will allow high-quality SR imaging even for limited-budget research groups.
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Affiliation(s)
- Mohammad Nour Alsamsam
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Aurimas Kopūstas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Meda Jurevičiūtė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Marijonas Tutkus
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
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4
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Mondal D, Mandal RP, De S. Addressing the Superior Drug Delivery Performance of Bilosomes─A Microscopy and Fluorescence Study. ACS APPLIED BIO MATERIALS 2022; 5:3896-3911. [PMID: 35924346 DOI: 10.1021/acsabm.2c00435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The global health scenario in present times has raised human awareness about drug delivery strategies. Among colloidal drug delivery vehicles, vesicular nanocarriers such as liposomes and niosomes are popular. However, liposomes and niosomes get disrupted in the harsh environment of the gastrointestinal tract. In this context, the drug delivery community has reported the superior performance of vesicles containing bile salts, that is, bilosomes. The present work attempts to examine the structural/morphological aspects underlying the superior performance of bilosomes. Optical microscopy, electron microscopy, and light scattering give a definite proof of the enhanced stability of bilosomes compared to niosomes, both prepared from the same amphiphilic molecule. Fluorescence probing of the vesicles provides detailed insight into the bilayer characteristics and the differences between bilosomes and niosomes. Fluorescence resonance energy transfer studies lend further support to the findings that bilosomes have a more flexible bilayer structure than niosomes. The entrapment efficiency of the vesicles for the well-known antioxidant curcumin (whose bioavailability is a matter of concern due to low water solubility) was also studied. Bilosomes show higher curcumin entrapment efficiency than niosomes. For use in drug delivery, one needs to establish a trade-off between cargo/drug entrapment and release. Thus, a flexible bilayer structure is an advantage.
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Affiliation(s)
- Durga Mondal
- Department of Chemistry, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Ranju Prasad Mandal
- Scientist Novel Hair Dyes, Henkel Beauty Care, Henkel AG & Co. KGaA, Henkelstraße 67, 40589 Düsseldorf, Germany
| | - Swati De
- Department of Chemistry, University of Kalyani, Kalyani 741235, West Bengal, India
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5
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Lee HS, Kim Y. Myricetin Disturbs the Cell Wall Integrity and Increases the Membrane Permeability of Candida albicans. J Microbiol Biotechnol 2022; 32:37-45. [PMID: 34750288 PMCID: PMC9628827 DOI: 10.4014/jmb.2110.10014] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022]
Abstract
The fungal cell wall and membrane are the principal targets of antifungals. Herein, we report that myricetin exerts antifungal activity against Candida albicans by damaging the cell wall integrity and notably enhancing the membrane permeability. In the presence of sorbitol, an osmotic protectant, the minimum inhibitory concentration (MIC) of myricetin against C. albicans increased from 20 to 40 and 80 μg/ml in 24 and 72 h, respectively, demonstrating that myricetin disturbs the cell wall integrity of C. albicans. Fluorescence microscopic images showed the presence of propidium iodidestained C. albicans cells, indicating the myricetin-induced initial damage of the cell membrane. The effects of myricetin on the membrane permeability of C. albicans cells were assessed using crystal violet-uptake and intracellular material-leakage assays. The percentage uptakes of crystal violet for myricetin-treated C. albicans cells at 1×, 2×, and 4× the MIC of myricetin were 36.5, 60.6, and 79.4%, respectively, while those for DMSO-treated C. albicans cells were 28.2, 28.9, and 29.7%, respectively. Additionally, myricetin-treated C. albicans cells showed notable DNA and protein leakage, compared with the DMSO-treated controls. Furthermore, treatment of C. albicans cells with 1× the MIC of myricetin showed a 17.2 and 28.0% reduction in the binding of the lipophilic probes diphenylhexatriene and Nile red, respectively, indicating that myricetin alters the lipid components or order in the C. albicans cell membrane, leading to increased membrane permeability. Therefore, these data will provide insights into the pharmacological worth of myricetin as a prospective antifungal for treating C. albicans infections.
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Affiliation(s)
- Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejongsi 30019, Republic of Korea
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, Jecheon 27136, Republic of Korea,Corresponding author Phone: +82-43-649-1346 Fax: +82-43-649-1341 E-mail:
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6
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Carravilla P, Dasgupta A, Zhurgenbayeva G, Danylchuk DI, Klymchenko AS, Sezgin E, Eggeling C. Long-term STED imaging of membrane packing and dynamics by exchangeable polarity-sensitive dyes. BIOPHYSICAL REPORTS 2021; 1:None. [PMID: 34939048 PMCID: PMC8651516 DOI: 10.1016/j.bpr.2021.100023] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/08/2021] [Indexed: 12/28/2022]
Abstract
Understanding the plasma membrane nanoscale organization and dynamics in living cells requires microscopy techniques with high spatial and temporal resolution that permit for long acquisition times and allow for the quantification of membrane biophysical properties, such as lipid ordering. Among the most popular super-resolution techniques, stimulated emission depletion (STED) microscopy offers one of the highest temporal resolutions, ultimately defined by the scanning speed. However, monitoring live processes using STED microscopy is significantly limited by photobleaching, which recently has been circumvented by exchangeable membrane dyes that only temporarily reside in the membrane. Here, we show that NR4A, a polarity-sensitive exchangeable plasma membrane probe based on Nile red, permits the super-resolved quantification of membrane biophysical parameters in real time with high temporal and spatial resolution as well as long acquisition times. The potential of this polarity-sensitive exchangeable dye is showcased by live-cell real-time three-dimensional STED recordings of bleb formation and lipid exchange during membrane fusion as well as by STED-fluorescence correlation spectroscopy experiments for the simultaneous quantification of membrane dynamics and lipid packing that correlate in model and live-cell membranes.
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Affiliation(s)
- Pablo Carravilla
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
| | - Anindita Dasgupta
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
| | - Gaukhar Zhurgenbayeva
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Dmytro I. Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Christian Eggeling
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Jena Center for Soft Matter, Jena, Germany
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7
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Hornum M, Mulberg MW, Szomek M, Reinholdt P, Brewer JR, Wüstner D, Kongsted J, Nielsen P. Substituted 9-Diethylaminobenzo[ a]phenoxazin-5-ones (Nile Red Analogues): Synthesis and Photophysical Properties. J Org Chem 2021; 86:1471-1488. [PMID: 33370098 DOI: 10.1021/acs.joc.0c02346] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nile Red is a benzo[a]phenoxazone dye containing a diethylamino substituent at the 9-position. In recent years, it has become a popular histological stain for cellular membranes and lipid droplets due to its unrivaled fluorescent properties in lipophilic environments. This makes it an attractive lead for chemical decoration to tweak its attributes and optimize it for more specialized microscopy techniques, e.g., fluorescence lifetime imaging or two-photon excited fluorescence microscopy, to which Nile Red has never been optimized. Herein, we present synthesis approaches to a series of monosubstituted Nile Red derivatives (9-diethylbenzo[a]phenoxazin-5-ones) starting from 1-naphthols or 1,3-naphthalenediols. The solvatochromic responsiveness of these fluorophores is reported with focus on how the substituents affect the absorption and emission spectra, luminosity, fluorescence lifetimes, and two-photon absorptivity. Several of the analogues emerge as strong candidates for reporting the polarity of their local environment. Specifically, the one- and two-photon excited fluorescence of Nile Red turns out to be very responsive to substitution, and the spectroscopic features can be finely tuned by judiciously introducing substituents of distinct electronic character at specific positions. This new toolkit of 9-diethylbenzo[a]phenoxazine-5-ones constitutes a step toward the next generation of optical molecular probes for advancing the understanding of lipid structures and cellular processes.
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8
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Yan R, Chen K, Xu K. Probing Nanoscale Diffusional Heterogeneities in Cellular Membranes through Multidimensional Single-Molecule and Super-Resolution Microscopy. J Am Chem Soc 2020; 142:18866-18873. [PMID: 33084318 DOI: 10.1021/jacs.0c08426] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diffusion properties notably determine the behavior of biomembranes. Here we report the concurrent nanoscale fine-mapping of membrane topography, diffusivity, and packing order in live mammalian cells through a synergy of single-molecule and super-resolution methods. By identifying a bright, lipophilic fluorescence turn-on probe that enables sustained single-molecule imaging of cellular membranes under stroboscopic excitation, we accumulate the positions and transient displacements of >106 probe molecules to achieve super-resolution topography and diffusivity mapping. We thus determine a trend that the membrane diffusivity drops with increased lipid packing order when comparing the endoplasmic reticulum (ER) membrane, plasma membrane, and nanodomains induced by cholera toxin B. Utilizing our nanoscale mapping capability, we further unveil reduced diffusivity in the ER membrane at ER-plasma membrane contact sites. By next integrating spectrally resolved single-molecule imaging, we show that this localized diffusion slowdown is not due to altered lipid packing order but may instead be attributed to local protein crowding. Our integrated multidimensional single-molecule approach thus unveils and differentiates between nanoscale diffusional heterogeneities of different origins in live-cell membranes.
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Affiliation(s)
- Rui Yan
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Kun Chen
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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9
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Contini C, Hindley JW, Macdonald TJ, Barritt JD, Ces O, Quirke N. Size dependency of gold nanoparticles interacting with model membranes. Commun Chem 2020; 3:130. [PMID: 33829115 PMCID: PMC7610534 DOI: 10.1038/s42004-020-00377-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The rapid development of nanotechnology has led to an increase in the number and variety of engineered nanomaterials in the environment. Gold nanoparticles (AuNPs) are an example of a commonly studied nanomaterial whose highly tailorable properties have generated significant interest through a wide range of research fields. In the present work, we characterise the AuNP-lipid membrane interaction by coupling qualitative data with quantitative measurements of the enthalpy change of interaction. We investigate the interactions between citrate-stabilised AuNPs ranging from 5 to 60 nm in diameter and large unilamellar vesicles acting as a model membrane system. Our results reveal the existence of two critical AuNP diameters which determine their fate when in contact with a lipid membrane. The results provide new insights into the size dependent interaction between AuNPs and lipid bilayers which is of direct relevance to nanotoxicology and to the design of NP vectors.
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Affiliation(s)
- Claudia Contini
- grid.7445.20000 0001 2113 8111Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, W12 0BZ London, UK
| | - James W. Hindley
- grid.7445.20000 0001 2113 8111Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, W12 0BZ London, UK ,grid.7445.20000 0001 2113 8111Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, W12 0BZ London, UK
| | - Thomas J. Macdonald
- grid.7445.20000 0001 2113 8111Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, W12 0BZ London, UK ,grid.83440.3b0000000121901201Department of Chemistry, University College London, Gordon Street, WC1H 0AJ London, UK
| | - Joseph D. Barritt
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ London, UK
| | - Oscar Ces
- grid.7445.20000 0001 2113 8111Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, W12 0BZ London, UK ,grid.7445.20000 0001 2113 8111Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, W12 0BZ London, UK
| | - Nick Quirke
- grid.7445.20000 0001 2113 8111Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, W12 0BZ London, UK
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10
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Kroetz T, dos Santos MC, Beal R, Zanotto GM, Santos FS, Giacomelli FC, Gonçalves PFB, de Lima VR, Dal-Bó AG, Rodembusch FS. Proton transfer in fluorescent secondary amines: synthesis, photophysics, theoretical calculation and preparation of photoactive phosphatidylcholine-based liposomes. Photochem Photobiol Sci 2019; 18:1171-1184. [DOI: 10.1039/c9pp00017h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New proton-transfer lipophilic based benzazoles.
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Affiliation(s)
- Thais Kroetz
- Grupo de Pesquisa em Fotoquímica Orgânica Aplicada
- Universidade Federal do Rio Grande do Sul – Instituto de Química
- CEP 91501-970 Porto Alegre-RS
- Brazil
| | | | - Roiney Beal
- Grupo de Química Teórica
- Instituto de Química
- Universidade Federal do Rio Grande do Sul
- Porto Alegre-RS
- Brazil
| | - Gabriel Modernell Zanotto
- Grupo de Química Teórica
- Instituto de Química
- Universidade Federal do Rio Grande do Sul
- Porto Alegre-RS
- Brazil
| | | | | | - Paulo F. B. Gonçalves
- Grupo de Química Teórica
- Instituto de Química
- Universidade Federal do Rio Grande do Sul
- Porto Alegre-RS
- Brazil
| | | | | | - Fabiano S. Rodembusch
- Grupo de Pesquisa em Fotoquímica Orgânica Aplicada
- Universidade Federal do Rio Grande do Sul – Instituto de Química
- CEP 91501-970 Porto Alegre-RS
- Brazil
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11
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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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12
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Singh G, Chamberlin AC, Zhekova HR, Noskov SY, Tieleman DP. Two-Dimensional Potentials of Mean Force of Nile Red in Intact and Damaged Model Bilayers. Application to Calculations of Fluorescence Spectra. J Chem Theory Comput 2015; 12:364-71. [PMID: 26579726 DOI: 10.1021/acs.jctc.5b00520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fluorescent dyes revolutionized and expanded our understanding of biological membranes. The interpretation of experimental fluorescence data in terms of membrane structure, however, requires detailed information about the molecular environment of the dyes. Nile red is a fluorescent molecule whose excitation and emission maxima depend on the polarity of the solvent. It is mainly used as a probe to study lipid microenvironments, for example in imaging the progression of damage to the myelin sheath in multiple sclerosis. In this study, we determine the position and orientation of Nile red in lipid bilayers by calculating two-dimensional Potential of Mean Force (2D-PMF) profiles in a defect-free 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer and in damaged bilayers containing two mixtures of the oxidized lipid 1-palmitoyl-2-(9'-oxo-nonanoyl)-sn-glycero-3-phosphocholine and POPC. From 2D-PMF simulations we obtain positions and orientations of Nile Red corresponding to the minimum on the binding free energy surface in three different membrane environments with increasing amounts of water, mimicking damage in biological tissue. Using representative snapshots from the simulations, we use combined quantum mechanical/molecular mechanical (QM/MM) models to calculate the emission spectrum of Nile red as a function of its local solvation environment. The results of QM and QM/MM computations are in qualitative agreement with the experimentally observed shift in fluorescence for the dye moving from aqueous solution to the more hydrophobic environment of the lipid interiors. The range of the conformation dependent values of the computed absorption-emission spectra and the lack of solvent relaxation effects in the QM/MM calculations made it challenging to delineate specific differences between the intact and damaged bilayers.
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Affiliation(s)
- Gurpreet Singh
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada
| | - Adam C Chamberlin
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada
| | - Hristina R Zhekova
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada
| | - Sergei Y Noskov
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary , 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada
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13
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Gao F, Kight AD, Henderson R, Jayanthi S, Patel P, Murchison M, Sharma P, Goforth RL, Kumar TKS, Henry RL, Heyes CD. Regulation of Structural Dynamics within a Signal Recognition Particle Promotes Binding of Protein Targeting Substrates. J Biol Chem 2015; 290:15462-15474. [PMID: 25918165 DOI: 10.1074/jbc.m114.624346] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Indexed: 11/06/2022] Open
Abstract
Protein targeting is critical in all living organisms and involves a signal recognition particle (SRP), an SRP receptor, and a translocase. In co-translational targeting, interactions among these proteins are mediated by the ribosome. In chloroplasts, the light-harvesting chlorophyll-binding protein (LHCP) in the thylakoid membrane is targeted post-translationally without a ribosome. A multidomain chloroplast-specific subunit of the SRP, cpSRP43, is proposed to take on the role of coordinating the sequence of targeting events. Here, we demonstrate that cpSRP43 exhibits significant interdomain dynamics that are reduced upon binding its SRP binding partner, cpSRP54. We showed that the affinity of cpSRP43 for the binding motif of LHCP (L18) increases when cpSRP43 is complexed to the binding motif of cpSRP54 (cpSRP54pep). These results support the conclusion that substrate binding to the chloroplast SRP is modulated by protein structural dynamics in which a major role of cpSRP54 is to improve substrate binding efficiency to the cpSRP.
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Affiliation(s)
- Feng Gao
- Departments of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Alicia D Kight
- Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Rory Henderson
- Departments of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Srinivas Jayanthi
- Departments of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Parth Patel
- Departments of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Marissa Murchison
- Departments of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Priyanka Sharma
- Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Robyn L Goforth
- Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | | | - Ralph L Henry
- Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701.
| | - Colin D Heyes
- Departments of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701.
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14
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Location, dynamics and solvent relaxation of a nile red-based phase-sensitive fluorescent membrane probe. Chem Phys Lipids 2014; 183:1-8. [DOI: 10.1016/j.chemphyslip.2014.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/22/2014] [Accepted: 04/27/2014] [Indexed: 11/20/2022]
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15
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Cooper JT, Harris JM. Imaging Fluorescence-Correlation Spectroscopy for Measuring Fast Surface Diffusion at Liquid/Solid Interfaces. Anal Chem 2014; 86:7618-26. [DOI: 10.1021/ac5014354] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Justin T. Cooper
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0805, United States
| | - Joel M. Harris
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0805, United States
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16
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Felbeck T, Behnke T, Hoffmann K, Grabolle M, Lezhnina MM, Kynast UH, Resch-Genger U. Nile-Red-nanoclay hybrids: red emissive optical probes for use in aqueous dispersion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:11489-11497. [PMID: 23941582 DOI: 10.1021/la402165q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Water-dispersible and (bio)functionalizable nanoclays have a considerable potential as inexpensive carriers for organic molecules like drugs and fluorophores. Aiming at simple design strategies for red-emissive optical probes for the life sciences from commercial precursors with minimum synthetic effort, we systematically studied the dye loading behavior and stability of differently functionalized laponites. Here, we present a comprehensive study of the absorption and emission properties of the red emissive hydrophobic and neutral dye Nile Red, a well-known polarity probe, which is almost insoluble and nonemissive in water. Adsorption of this probe onto disk-shaped nanoclays was studied in aqueous dispersion as function of dye concentration, in the absence and presence of the cationic surfactant cetyltrimethylammonium bromide (CTAB) assisting dye loading, and as a function of pH. This laponite loading strategy yields strongly fluorescent nanoclay suspensions with a fluorescence quantum yield of 0.34 at low dye loading concentration. The dye concentration-, CTAB-, and pH-dependent absorption, fluorescence emission, and fluorescence excitation spectra of the Nile-Red-nanoclay suspensions suggest the formation of several Nile Red species including emissive Nile Red monomers facing a polar environment, nonemissive H-type dimers, and protonated Nile Red molecules that are also nonfluorescent. Formation of all nonemissive Nile Red species could be suppressed by modification of the laponite with CTAB. This underlines the great potential of properly modified and functionalized laponite nanodisks as platform for optical probes with drug delivery capacities, for example, for tumor and therapy imaging. Moreover, comparison of the Nile Red dimer absorption spectra with absorption spectra of previously studied Nile Red aggregates in dendrimer systems and micelles and other literature systems reveals a considerable dependence of the dimer absorption band on microenvironment polarity which has not yet been reported so far for H-type dye aggregates.
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Affiliation(s)
- Tom Felbeck
- BAM Federal Institute for Materials Research and Testing , Richard-Willstaetter-Str. 11, 12489 Berlin, Germany
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17
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Hamm P, Zewail AH, Fleming GR. A tribute to Robin Hochstrasser. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Sasaki DY, Zawada N, Gilmore SF, Narasimmaraj P, Sanchez MAA, Stachowiak JC, Hayden CC, Wang HL, Parikh AN, Shreve AP. Lipid membrane domains for the selective adsorption and surface patterning of conjugated polyelectrolytes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:5214-5221. [PMID: 23544969 DOI: 10.1021/la400454c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Conjugated polyelectrolytes (CPEs) are promising materials for generating optoelectronics devices under environmentally friendly processing conditions, but challenges remain to develop methods to define lateral features for improved junction interfaces and direct optoelectronic pathways. We describe here the potential to use a bottom-up approach that employs self-assembly in lipid membranes to form structures to template the selective adsorption of CPEs. Phase separation of gel phase anionic lipids and fluid phase phosphocholine lipids allowed the formation of negatively charged domain assemblies that selectively adsorb a cationic conjugated polyelectrolyte (P2). Spectroscopic studies found the adsorption of P2 to negatively charged membranes resulted in minimal structural change of the solution phase polymer but yielded an enhancement in fluorescence intensity (~50%) due to loss of quenching pathways. Fluorescence microscopy, dynamic light scattering, and AFM imaging were used to characterize the polymer-membrane interaction and the polymer-bound domain structures of the biphasic membranes. In addition to randomly formed circular gel phase domains, we also show that predefined features, such as straight lines, can be directed to form upon etched patterns on the substrate, thus providing potential routes toward the self-organization of optoelectronic architectures.
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Affiliation(s)
- Darryl Y Sasaki
- Sandia National Laboratories, Livermore, California 94550, USA.
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19
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Sloniec J, Schnurr M, Witte C, Resch-Genger U, Schröder L, Hennig A. Biomembrane interactions of functionalized cryptophane-A: combined fluorescence and 129Xe NMR studies of a bimodal contrast agent. Chemistry 2013; 19:3110-8. [PMID: 23319433 DOI: 10.1002/chem.201203773] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Indexed: 12/19/2022]
Abstract
Fluorescent derivatives of the (129)Xe NMR contrast agent cryptophane-A were obtained by functionalization with near infrared fluorescent dyes DY680 and DY682. The resulting conjugates were spectrally characterized, and their interaction with giant and large unilamellar vesicles of varying phospholipid composition was analyzed by fluorescence and NMR spectroscopy. In the latter, a chemical exchange saturation transfer with hyperpolarized (129)Xe (Hyper-CEST) was used to obtain sufficient sensitivity. To determine the partitioning coefficients, we developed a method based on fluorescence resonance energy transfer from Nile Red to the membrane-bound conjugates. This indicated that not only the hydrophobicity of the conjugates, but also the phospholipid composition, largely determines the membrane incorporation. Thereby, partitioning into the liquid-crystalline phase of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine was most efficient. Fluorescence depth quenching and flip-flop assays suggest a perpendicular orientation of the conjugates to the membrane surface with negligible transversal diffusion, and that the fluorescent dyes reside in the interfacial area. The results serve as a basis to differentiate biomembranes by analyzing the Hyper-CEST signatures that are related to membrane fluidity, and pave the way for dissecting different contributions to the Hyper-CEST signal.
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Affiliation(s)
- Jagoda Sloniec
- Division 1.10 Biophotonics, BAM Federal Institute for Materials Research and Testing, Richard-Willstaetter-Strasse 11, 12489 Berlin, Germany
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20
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Myers GA, Gacek DA, Peterson EM, Fox CB, Harris JM. Microscopic Rates of Peptide–Phospholipid Bilayer Interactions from Single-Molecule Residence Times. J Am Chem Soc 2012; 134:19652-60. [DOI: 10.1021/ja306074k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Grant A. Myers
- Department
of Chemistry, University of Utah, 315 South
1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Daniel A. Gacek
- Department
of Chemistry, University of Utah, 315 South
1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Eric M. Peterson
- Department
of Chemistry, University of Utah, 315 South
1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Christopher B. Fox
- Department
of Chemistry, University of Utah, 315 South
1400 East, Salt Lake
City, Utah 84112-0850, United States
- Department of Bioengineering, University of Utah, 50 South Central Campus Drive,
Salt Lake City, Utah 84112-9202, United States
| | - Joel M. Harris
- Department
of Chemistry, University of Utah, 315 South
1400 East, Salt Lake
City, Utah 84112-0850, United States
- Department of Bioengineering, University of Utah, 50 South Central Campus Drive,
Salt Lake City, Utah 84112-9202, United States
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21
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Mandal AK, Das DK, Das AK, Sen Mojumdar S, Bhattacharyya K. Study of γ-Cyclodextrin Host–Guest Complex and Nanotube Aggregate by Fluorescence Correlation Spectroscopy. J Phys Chem B 2011; 115:10456-61. [DOI: 10.1021/jp2053629] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amit Kumar Mandal
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Dibyendu Kumar Das
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Atanu Kumar Das
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Supratik Sen Mojumdar
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Kankan Bhattacharyya
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
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22
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Das DK, Mondal T, Mandal AK, Bhattacharyya K. Binding of organic dyes with human serum albumin: a single-molecule study. Chem Asian J 2011; 6:3097-103. [PMID: 21751404 DOI: 10.1002/asia.201100272] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Indexed: 11/10/2022]
Abstract
Kinetics of binding of dyes at different sites of human serum albumin (HSA) has been studied by single-molecule spectroscopy. The protein was immobilized on a glass surface. To probe different binding sites (hydrophobic and hydrophilic) two dyes, coumarin 153 (C153, neutral) and rhodamine 6G (R6G, cationic) were chosen. For both the dyes, a major (ca. 96-98%) and minor (ca. 3%) binding site were detected. Rate constants of association and dissociation were simultaneously determined from directly measuring fluctuations in fluorescence intensity (τ(off) and τ(on)) and from this the equilibrium (binding) constants were calculated. Fluorescence lifetimes at individual sites were obtained from burst-integrated lifetime analysis. Distributions of lifetime histograms for both the probes (C153 and R6G) exhibit two maxima, which indicates the presence of two binding domains in the protein. Unfolding of the protein has been studied by adding guanidinium hydrochloride (GdnHCl) to the solution. It is observed that addition of GdnHCl affects the dissociation and association kinetics and hence, binding equilibrium of the association of C153. However, the effect of binding of R6G is not affected much. It is proposed that GdnHCl affects the hydrophobic binding sites more than the hydrophilic site.
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Affiliation(s)
- Dibyendu Kumar Das
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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23
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Heider EC, Peterson EM, Barhoum M, Gericke KH, Harris JM. Quantitative fluorescence microscopy to determine molecular occupancy of phospholipid vesicles. Anal Chem 2011; 83:5128-36. [PMID: 21648957 DOI: 10.1021/ac200129n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Encapsulation of molecules in phospholipid vesicles provides unique opportunities to study chemical reactions in small volumes as well as the behavior of individual proteins, enzymes, and ribozymes in a confined region without requiring a tether to immobilize the molecule to a surface. These experiments generally depend on generating a predictable loading of vesicles with small numbers of target molecules and thus raise a significant measurement challenge, namely, to quantify molecular occupancy of vesicles at the single-molecule level. In this work, we describe an imaging experiment to measure the time-dependent fluorescence from individual dye molecules encapsulated in ~130 nm vesicles that are adhered to a glass surface. For determining a fit of the molecular occupancy data to a Poisson model, it is critical to count empty vesicles in the population since these dominate the sample when the mean occupancy is small, λ ≤ ~1. Counting empty vesicles was accomplished by subsequently labeling all the vesicles with a lipophilic dye and reimaging the sample. By counting both the empty vesicles and those containing fluors, and quantifying the number of fluors present, we demonstrate a self-consistent Poisson distribution of molecular occupancy for well-solvated molecules, as well as anomalies due to aggregation of dye, which can arise even at very low solution concentrations. By observation of many vesicles in parallel in an image, this approach provides quantitative information about the distribution of molecular occupancy in a population of vesicles.
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Affiliation(s)
- Emily C Heider
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
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24
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Schibel AEP, Heider EC, Harris JM, White HS. Fluorescence microscopy of the pressure-dependent structure of lipid bilayers suspended across conical nanopores. J Am Chem Soc 2011; 133:7810-5. [PMID: 21542629 DOI: 10.1021/ja1117182] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Glass and fused-quartz nanopore membranes containing a single conically shaped pore are promising solid supports for lipid bilayer ion-channel recordings due to the high inherent stability of lipid bilayers suspended across the nanopore orifice, as well as the favorable electrical properties of glass and fused quartz. Fluorescence microscopy is used here to investigate the structure of the suspended lipid bilayer as a function of the pressure applied across a fused-quartz nanopore membrane. When a positive pressure is applied across the bilayer, from the nanopore interior relative to the exterior bulk solution, insertion or reconstitution of operative ion channels (e.g., α-hemolysin (α-HL) and gramicidin) in the bilayer is observed; conversely, reversing the direction of the applied pressure results in loss of all channel activity, although the bilayer remains intact. The dependence of the bilayer structure on pressure was explored by imaging the fluorescence intensity from Nile red dye doped into suspended 1,2-diphytanoyl-sn-glycero-3-phosphocholine bilayers, while simultaneously recording the activity of an α-HL channel. The fluorescence images suggest that a positive pressure results in compression of the bilayer leaflets and an increase in the bilayer curvature, making it suitable for ion-channel formation and activity. At negative pressure, the fluorescence images are consistent with separation of the lipid leaflets, resulting in the observed loss of the ion-channel activity. The fluorescence data indicate that the changes in the pressure-induced bilayer structure are reversible, consistent with the ability to repeatedly switch the ion-channel activity on and off by applying positive and negative pressures, respectively.
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Affiliation(s)
- Anna E P Schibel
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
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25
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Abstract
Sub-diffraction optical imaging with nanometer resolution of lipid phase-separated regions is reported. Merocyanine 540, a probe whose fluorescence is sensitive to the lipid phase, is combined with super-resolution imaging to distinguish the liquid- and gel-phase nanoscale domains of lipid bilayers supported on glass. The monomer-dimer equilibrium of MC540 in membranes is deemed responsible for the population difference of single-molecule fluorescence bursts in the different phase regions. The extension of this method to other binary or ternary lipid models or natural systems provides a promising new super-resolution strategy.
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Affiliation(s)
- Chinkuei Kuo
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104-6323
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104-6323
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26
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Chowdhury SA, Lim MH. Characterization of the Surface Contribution to Fluorescence Correlation Spectroscopy Measurements. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.2.583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Lu Y, Porterfield R, Thunder T, Paige MF. An ensemble and single-molecule fluorescence microscopy investigation of phase-separated monolayer films stained with Nile Red. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 78:216-223. [PMID: 21115390 DOI: 10.1016/j.saa.2010.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 09/08/2010] [Accepted: 09/29/2010] [Indexed: 05/30/2023]
Abstract
Phase-separated Langmuir-Blodgett monolayer films prepared from mixtures of arachidic acid (C19H39COOH) and perfluorotetradecanoic acid (C13F27COOH) were stained via spin-casting with the polarity sensitive phenoxazine dye Nile Red, and characterized using a combination of ensemble and single-molecule fluorescence microscopy measurements. Ensemble fluorescence microscopy and spectromicroscopy showed that Nile Red preferentially associated with the hydrogenated domains of the phase-separated films, and was strongly fluorescent in these areas of the film. These measurements, in conjunction with single-molecule fluorescence imaging experiments, also indicated that a small sub-population of dye molecules localizes on the perfluorinated regions of the sample, but that this sub-population is spectroscopically indistinguishable from that associated with the hydrogenated domains. The relative importance of selective dye adsorption and local polarity sensitivity of Nile Red for staining applications in phase-separated LB films as well as in cellular environments is discussed in context of the experimental results.
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Affiliation(s)
- Yin Lu
- Department of Chemistry, University of Saskatchewan 110 Science Place, Saskatoon, SK S7N 5C9, Canada
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28
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Hosseiny Davarani SS, Kalate Bojdi M, Mehdinia A. A New Way for Synthesis of Phenoxazine and Diphenoxazine Derivatives via Electrochemical Method. Chem Pharm Bull (Tokyo) 2011; 59:1209-13. [DOI: 10.1248/cpb.59.1209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Majid Kalate Bojdi
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University
| | - Ali Mehdinia
- Department of Marine Living Resources, Iranian National Institute for Oceanography
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29
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Kucherak OA, Oncul S, Darwich Z, Yushchenko DA, Arntz Y, Didier P, Mély Y, Klymchenko AS. Switchable nile red-based probe for cholesterol and lipid order at the outer leaflet of biomembranes. J Am Chem Soc 2010; 132:4907-16. [PMID: 20225874 DOI: 10.1021/ja100351w] [Citation(s) in RCA: 290] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cholesterol and sphingomyelin form together a highly ordered membrane phase, which is believed to play important biological functions in plasma membranes of mammalian cells. Since sphingomyelin is present mainly at the outer leaflet of cell membranes, monitoring its lipid order requires molecular probes capable to bind specifically at this leaflet and exhibit negligibly slow flip-flop. In the present work, such a probe was developed by modifying the solvatochromic fluorescent dye Nile Red with an amphiphilic anchor group. To evaluate the flip-flop of the obtained probe (NR12S), we developed a methodology of reversible redox switching of its fluorescence at one leaflet using sodium dithionite. This method shows that NR12S, in contrast to parent Nile Red, binds exclusively the outer membrane leaflet of model lipid vesicles and living cells with negligible flip-flop in the time scale of hours. Moreover, the emission maximum of NR12S in model vesicles exhibits a significant blue shift in liquid ordered phase (sphingomyelin-cholesterol) as compared to liquid disordered phase (unsaturated phospholipids). As a consequence, these two phases could be clearly distinguished in NR12S-stained giant vesicles by fluorescence microscopy imaging of intensity ratio between the blue and red parts of the probe emission spectrum. Being added to living cells, NR12S binds predominantly, if not exclusively, their plasma membranes and shows an emission spectrum intermediate between those in liquid ordered and disordered phases of model membranes. Importantly, the emission color of NR12S correlates well with the cholesterol content in cell membranes, which allows monitoring the cholesterol depletion process with methyl-beta-cyclodextrin by fluorescence spectroscopy and microscopy. The attractive photophysical and switching properties of NR12S, together with its selective outer leaflet staining and sensitivity to cholesterol and lipid order, make it a new powerful tool for studying model and cell membranes.
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Affiliation(s)
- Oleksandr A Kucherak
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74, Route du Rhin, 67401 Illkirch Cedex, France
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30
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Ghosh S, Adhikari A, Sen Mojumdar S, Bhattacharyya K. A Fluorescence Correlation Spectroscopy Study of the Diffusion of an Organic Dye in the Gel Phase and Fluid Phase of a Single Lipid Vesicle. J Phys Chem B 2010; 114:5736-41. [DOI: 10.1021/jp911971p] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Subhadip Ghosh
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Aniruddha Adhikari
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Supratik Sen Mojumdar
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Kankan Bhattacharyya
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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31
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Nath A, Trexler AJ, Koo P, Miranker AD, Atkins WM, Rhoades E. Single-molecule fluorescence spectroscopy using phospholipid bilayer nanodiscs. Methods Enzymol 2010; 472:89-117. [PMID: 20580961 DOI: 10.1016/s0076-6879(10)72014-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nanodiscs are a new class of model membranes that are being used to solubilize and study a range of integral membrane proteins and membrane-associated proteins. Unlike other model membranes, the Nanodisc bilayer is bounded by a scaffold protein coat that confers enhanced stability and a narrow particle size distribution. The bilayer diameter can be precisely controlled by changing the diameter of the protein coat. All these properties make Nanodiscs excellent model membranes for single-molecule fluorescence applications. In this chapter, we describe our work using Nanodiscs to apply total internal reflection fluorescence microscopy (TIRFM), fluorescence correlation spectroscopy (FCS), and Förster resonance energy transfer (FRET) to study the integral membrane protein cytochrome P450 3A4 and the peripheral membrane-binding proteins islet amyloid polypeptide (IAPP) and alpha-synuclein, respectively. The monodisperse size distribution of Nanodiscs enhances control over the oligomeric state of the membrane protein of interest, and facilitates accurate solution-based measurements as well. Nanodiscs also comprise an excellent system to stably immobilize integral membrane proteins in a bilayer without covalent modification, enabling a range of surface-based experiments where accurate localization of the protein of interest is required.
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Affiliation(s)
- Abhinav Nath
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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32
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Guo L, Park J, Lee T, Chowdhury P, Lim M, Gai F. Probing the role of hydration in the unfolding transitions of carbonmonoxy myoglobin and apomyoglobin. J Phys Chem B 2009; 113:6158-63. [PMID: 19348439 DOI: 10.1021/jp900009x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We show that the equilibrium unfolding transition of horse carbonmonoxy myoglobin monitored by the stretching vibration of the CO ligand, a local environmental probe, is very sharp and, thus, quite different from those measured by global conformational reporters. In addition, the denatured protein exhibits an A(0)-like CO band. We hypothesize that this sharp transition reports penetration of water into the heme pocket of the protein. Parallel experiments on horse apomyoglobin, wherein an environment-sensitive fluorescent probe, nile red, was used, also reveals a similar putative hydration event. Given the importance of dehydration in protein folding and also the recent debate over the interpretation of probe-dependent unfolding transitions, these results have strong implications on the mechanism of protein folding.
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Affiliation(s)
- Lin Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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33
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Nath A, Koo PK, Rhoades E, Atkins WM. Allosteric effects on substrate dissociation from cytochrome P450 3A4 in nanodiscs observed by ensemble and single-molecule fluorescence spectroscopy. J Am Chem Soc 2009; 130:15746-7. [PMID: 18980315 DOI: 10.1021/ja805772r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochrome P450 (CYP) 3A4 is a major human drug-metabolizing enzyme and displays pharmacologically relevant allosteric kinetics caused by multiple substrate and/or effector binding. Here, in the first single-molecule (SM) fluorescence studies of CYPs, we use total internal reflection fluorescence microscopy to measure residence times of the fluorescent dye Nile Red in CYP3A4 incorporated in surface-immobilized lipid Nanodiscs, with and without the effector alpha-naphthoflavone. We find direct evidence that CYP3A4 effectors can decrease substrate off-rates, providing a possible mechanism for effector-mediated enhancement of substrate metabolism. These interesting results highlight the potential of SM methods in studies of CYP allosteric mechanisms.
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Affiliation(s)
- Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
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Lowry M, Fakayode SO, Geng ML, Baker GA, Wang L, McCarroll ME, Patonay G, Warner IM. Molecular Fluorescence, Phosphorescence, and Chemiluminescence Spectrometry. Anal Chem 2008; 80:4551-74. [DOI: 10.1021/ac800749v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Mark Lowry
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Sayo O. Fakayode
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Maxwell L. Geng
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Gary A. Baker
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Lin Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Matthew E. McCarroll
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Gabor Patonay
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
| | - Isiah M. Warner
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, Department of Chemistry, Nanoscience and Nanotechnology Institute and the Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale,
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Frade VH, Sousa MJ, Moura JC, Gonçalves MST. Synthesis, characterisation and antimicrobial activity of new benzo[a]phenoxazine based fluorophores. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.09.108] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mukherjee S, Kombrabail M, Krishnamoorthy G, Chattopadhyay A. Dynamics and heterogeneity of bovine hippocampal membranes: role of cholesterol and proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2130-44. [PMID: 17618864 DOI: 10.1016/j.bbamem.2007.05.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 05/05/2007] [Accepted: 05/29/2007] [Indexed: 12/14/2022]
Abstract
The structural and dynamic consequence of alterations in membrane lipid composition (specifically cholesterol) in neuronal membranes is poorly understood. Previous work from our laboratory has established bovine hippocampal membranes as a convenient natural source for studying neuronal receptors. In this paper, we have explored the role of cholesterol and proteins in the dynamics and heterogeneity of bovine hippocampal membranes using fluorescence lifetime distribution analysis of the environment-sensitive fluorescent probe Nile Red incorporated into such membranes by the maximum entropy method (MEM), and time-resolved fluorescence anisotropy measurements. The peak position and the width of the lifetime distribution of Nile Red show a progressive reduction with increasing cholesterol depletion from native hippocampal membranes indicating that the extent of heterogeneity decreases with decrease in membrane cholesterol content. This is accompanied by a concomitant decrease of the fluorescence anisotropy and rotational correlation time. Our results point out that the microenvironment experienced by Nile Red is relatively insensitive to the presence of proteins in hippocampal membranes. Interestingly, Nile Red lifetime distribution in liposomes of lipid extracts is similar to that of native membranes indicating that proteins do not contribute significantly to the high level of heterogeneity observed in native membranes. These results could be relevant in understanding the neuronal diseases characterized by defective membrane lipid metabolism.
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Affiliation(s)
- Soumi Mukherjee
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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Mukherjee S, Raghuraman H, Chattopadhyay A. Membrane localization and dynamics of Nile Red: Effect of cholesterol. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:59-66. [PMID: 16934217 DOI: 10.1016/j.bbamem.2006.07.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Revised: 07/07/2006] [Accepted: 07/14/2006] [Indexed: 11/29/2022]
Abstract
The organization and dynamics of the hydrophobic fluorescent probe Nile Red incorporated in DOPC vesicles containing varying amounts of cholesterol has been monitored utilizing fluorescence-based approaches which include the red edge excitation shift (REES) approach and the parallax method for depth determination. Our results show that the fluorescence emission maximum, intensity, polarization, and lifetime of Nile Red vary with the cholesterol content of the membrane. Interestingly, Nile Red exhibits significant REES independent of the presence of cholesterol. This indicates that Nile Red is localized in a motionally restricted environment in the membrane. This is supported by analysis of membrane penetration depth of Nile Red using the parallax method which points out to a membrane interfacial localization of Nile Red. These results could be useful in analyzing membrane organization and heterogeneity in natural membranes using Nile Red.
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Affiliation(s)
- Soumi Mukherjee
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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Sharonov A, Hochstrasser RM. Wide-field subdiffraction imaging by accumulated binding of diffusing probes. Proc Natl Acad Sci U S A 2006; 103:18911-6. [PMID: 17142314 PMCID: PMC1748151 DOI: 10.1073/pnas.0609643104] [Citation(s) in RCA: 682] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A method is introduced for subdiffraction imaging that accumulates points by collisional flux. It is based on targeting the surface of objects by fluorescent probes diffusing in the solution. Because the flux of probes at the object is essentially constant over long time periods, the examination of an almost unlimited number of individual probe molecules becomes possible. Each probe that hits the object and that becomes immobilized is located with high precision by replacing its point-spread function by a point at its centroid. Images of lipid bilayers, contours of these bilayers, and large unilamellar vesicles are shown. A spatial resolution of approximately 25 nm is readily achieved. The ability of the method to effect rapid nanoscale imaging and spatial resolution below Rayleigh criterion and without the necessity for labeling with fluorescent probes is proven.
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Affiliation(s)
- Alexey Sharonov
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
- *To whom correspondence should be addressed. E-mail:
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Mei E, Gao F, Hochstrasser RM. Controlled bimolecular collisions allow sub-diffraction limited microscopy of lipid vesicles. Phys Chem Chem Phys 2006; 8:2077-82. [PMID: 16633697 DOI: 10.1039/b601670g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The concentration and vesicle size-controlled collisions of single molecules with target biological assemblies allow sub-diffraction limited optical images to be obtained that are not subject to the usual photobleaching problems with single molecule experiments. For example, single molecules of the probe Nile Red in aqueous solution emit a burst of fluorescence when they collide with a 50 nm hydrophobic vesicle situated on the surface in the laser focus. The bimolecular kinetics of the bursts is defined by their on- and off-time distribution functions which depend on the concentration and diffusion of the probe and the vesicle size. The mean burst frequency changes much more sharply than does the fluorescence intensity when a vesicle is raster scanned through the laser focus. This sharpness allows the spatial resolution of two objects to be improved and separations less than the diffraction limited resolution of the conventional optical microscope to be measured. The principle of this method of trajectory time distribution optical microscopy (TTDOM) could be used in a far field optical microscopic system with a resolution of several nanometers.
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Affiliation(s)
- Erwen Mei
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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