401
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Stennett EMS, Ciuba MA, Levitus M. Photophysical processes in single molecule organic fluorescent probes. Chem Soc Rev 2014; 43:1057-75. [DOI: 10.1039/c3cs60211g] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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402
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Ast C, Draaijer A. Methods and Techniques to Measure Molecular Oxygen in Plants. LOW-OXYGEN STRESS IN PLANTS 2014. [DOI: 10.1007/978-3-7091-1254-0_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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403
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van de Linde S, Sauer M. How to switch a fluorophore: from undesired blinking to controlled photoswitching. Chem Soc Rev 2014; 43:1076-87. [DOI: 10.1039/c3cs60195a] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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404
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König SLB, Hadzic M, Fiorini E, Börner R, Kowerko D, Blanckenhorn WU, Sigel RKO. BOBA FRET: bootstrap-based analysis of single-molecule FRET data. PLoS One 2013; 8:e84157. [PMID: 24386343 PMCID: PMC3873958 DOI: 10.1371/journal.pone.0084157] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/12/2013] [Indexed: 01/18/2023] Open
Abstract
Time-binned single-molecule Förster resonance energy transfer (smFRET) experiments with surface-tethered nucleic acids or proteins permit to follow folding and catalysis of single molecules in real-time. Due to the intrinsically low signal-to-noise ratio (SNR) in smFRET time traces, research over the past years has focused on the development of new methods to extract discrete states (conformations) from noisy data. However, limited observation time typically leads to pronounced cross-sample variability, i.e., single molecules display differences in the relative population of states and the corresponding conversion rates. Quantification of cross-sample variability is necessary to perform statistical testing in order to assess whether changes observed in response to an experimental parameter (metal ion concentration, the presence of a ligand, etc.) are significant. However, such hypothesis testing has been disregarded to date, precluding robust biological interpretation. Here, we address this problem by a bootstrap-based approach to estimate the experimental variability. Simulated time traces are presented to assess the robustness of the algorithm in conjunction with approaches commonly used in thermodynamic and kinetic analysis of time-binned smFRET data. Furthermore, a pair of functionally important sequences derived from the self-cleaving group II intron Sc.ai5γ (d3'EBS1*/IBS1*) is used as a model system. Through statistical hypothesis testing, divalent metal ions are shown to have a statistically significant effect on both thermodynamic and kinetic aspects of their interaction. The Matlab source code used for analysis (bootstrap-based analysis of smFRET data, BOBA FRET), as well as a graphical user interface, is available via http://www.aci.uzh.ch/rna/.
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Affiliation(s)
- Sebastian L. B. König
- Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland
- * E-mail: (RKOS); (SLBK)
| | - Mélodie Hadzic
- Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland
| | - Erica Fiorini
- Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland
| | - Richard Börner
- Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland
| | - Danny Kowerko
- Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland
| | - Wolf U. Blanckenhorn
- Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Roland K. O. Sigel
- Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland
- * E-mail: (RKOS); (SLBK)
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405
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VanDelinder V, Bachand GD. Photodamage and the Importance of Photoprotection in Biomolecular-Powered Device Applications. Anal Chem 2013; 86:721-8. [DOI: 10.1021/ac403187g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Virginia VanDelinder
- Center
for Integrated Nanotechnologies,
Sandia National Laboratories, Albuquerque, NM 87185, United States
| | - George D. Bachand
- Center
for Integrated Nanotechnologies,
Sandia National Laboratories, Albuquerque, NM 87185, United States
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406
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Abstract
Single-molecule spectroscopy has developed into a widely used method for probing the structure, dynamics, and mechanisms of biomolecular systems, especially in combination with Förster resonance energy transfer (FRET). In this introductory tutorial, essential concepts and methods will be outlined, from the FRET process and the basic considerations for sample preparation and instrumentation to some key elements of data analysis and photon statistics. Different approaches for obtaining dynamic information over a wide range of timescales will be explained and illustrated with examples, including the quantitative analysis of FRET efficiency histograms, correlation spectroscopy, fluorescence trajectories, and microfluidic mixing.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057
Zurich, Switzerland
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407
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Klehs K, Spahn C, Endesfelder U, Lee SF, Fürstenberg A, Heilemann M. Increasing the brightness of cyanine fluorophores for single-molecule and superresolution imaging. Chemphyschem 2013; 15:637-41. [PMID: 24376142 DOI: 10.1002/cphc.201300874] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 01/12/2023]
Abstract
In spite of their relatively low fluorescence quantum yield, cyanine dyes such as Cy3, Cy5, or Cy7 are widely used in single-molecule fluorescence applications due to their high extinction coefficients and excellent photon yields. We show that the fluorescence quantum yield and lifetime of red-emitting cyanine dyes can be substantially increased in heavy water (D2 O) compared with water (H2 O). We find that the magnitude of the quantum yield increase in D2 O scales with the emission wavelength, reaching a particularly high value of 2.6-fold for the most red-emitting dye investigated, Cy7. We further demonstrate a higher photon yield in single-molecule superresolution experiments in D2 O compared to H2 O, which leads to an improved localization precision and hence better spatial resolution. This finding is especially beneficial for biological applications of fluorescence microscopy, which are typically carried out in aqueous media and which greatly profit from the red spectral range due to reduced cellular auto-fluorescence.
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Affiliation(s)
- Kathrin Klehs
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438 Frankfurt (Germany)
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408
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van der Velde JHM, Ploetz E, Hiermaier M, Oelerich J, de Vries JW, Roelfes G, Cordes T. Mechanism of intramolecular photostabilization in self-healing cyanine fluorophores. Chemphyschem 2013; 14:4084-93. [PMID: 24302532 DOI: 10.1002/cphc.201300785] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Indexed: 11/06/2022]
Abstract
Organic fluorophores, which are popular labels for microscopy applications, intrinsically suffer from transient and irreversible excursions to dark-states. An alternative to adding photostabilizers at high concentrations to the imaging buffer relies on the direct linkage to the fluorophore. However, the working principles of this approach are not yet fully understood. In this contribution, we investigate the mechanism of intramolecular photostabilization in self-healing cyanines, in which photodamage is automatically repaired. Experimental evidence is provided to demonstrate that a single photostabilizer, that is, the vitamin E derivative Trolox, efficiently heals the cyanine fluorophore Cy5 in the absence of any photostabilizers in solution. A plausible mechanism is that Trolox interacts with the fluorophore through intramolecular quenching of triplet-related dark-states, which is a mechanism that appears to be common for both triplet-state quenchers (cyclooctatetraene) and redox-active compounds (Trolox, ascorbic acid, methylviologen). Additionally, the influence of solution-additives, such as cysteamine and procatechuic acid, on the self-healing process are studied. The results suggest the potential applicability of self-healing fluorophores in stochastic optical reconstruction microscopy (STORM) with optical super-resolution. The presented data contributes to an improved understanding of the mechanism involved in intramolecular photostabilization and has high relevance for the future development of self-healing fluorophores, including their applications in various research fields.
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Affiliation(s)
- Jasper H M van der Velde
- Molecular Microscopy Research Group & Single-molecule Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands), Fax: (+31) 50-363-9199
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409
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Zheng Q, Jockusch S, Zhou Z, Blanchard SC. The contribution of reactive oxygen species to the photobleaching of organic fluorophores. Photochem Photobiol 2013; 90:448-454. [PMID: 24188468 DOI: 10.1111/php.12204] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/31/2013] [Indexed: 12/12/2022]
Abstract
Photoexcitation of fluorophores commonly used for biological imaging applications generates reactive oxygen species (ROS) which can cause bleaching of the fluorophore and damage to the biological system under investigation. In this study, we show that singlet oxygen contributes relatively little to Cy5 and ATTO 647N photobleaching at low concentrations in aqueous solution. We also show that Cy5 generates significantly less ROS when covalently linked to the protective agents, cyclooctatetraene (COT), nitrobenzyl alcohol (NBA) or Trolox. Such fluorophores exhibit enhanced photostability both in bulk solutions and in single-molecule fluorescence measurements. While the fluorophores ATTO 647N and ATTO 655 showed greater photostability than Cy5 and the protective-agent-linked Cy5 derivatives investigated here, both of ATTO 647N and ATTO 655 generated singlet oxygen and hydroxyl radicals at relatively rapid rates, suggesting that they may be substantially more phototoxic than Cy5 and its derivatives.
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Affiliation(s)
- Qinsi Zheng
- Department of Physiology and Biophysics, Weill Medical College of Cornell University.,Tri-Institutional Training Program in Chemical Biology, 1300 York Avenue, New York, NY 10065, USA
| | - Steffen Jockusch
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Medical College of Cornell University
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Medical College of Cornell University.,Tri-Institutional Training Program in Chemical Biology, 1300 York Avenue, New York, NY 10065, USA
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410
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Nishimura H, Ritchie K, Kasai RS, Goto M, Morone N, Sugimura H, Tanaka K, Sase I, Yoshimura A, Nakano Y, Fujiwara TK, Kusumi A. Biocompatible fluorescent silicon nanocrystals for single-molecule tracking and fluorescence imaging. ACTA ACUST UNITED AC 2013; 202:967-83. [PMID: 24043702 PMCID: PMC3776351 DOI: 10.1083/jcb.201301053] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Fluorescence microscopy is used extensively in cell-biological and biomedical research, but it is often plagued by three major problems with the presently available fluorescent probes: photobleaching, blinking, and large size. We have addressed these problems, with special attention to single-molecule imaging, by developing biocompatible, red-emitting silicon nanocrystals (SiNCs) with a 4.1-nm hydrodynamic diameter. Methods for producing SiNCs by simple chemical etching, for hydrophilically coating them, and for conjugating them to biomolecules precisely at a 1:1 ratio have been developed. Single SiNCs neither blinked nor photobleached during a 300-min overall period observed at video rate. Single receptor molecules in the plasma membrane of living cells (using transferrin receptor) were imaged for ≥10 times longer than with other probes, making it possible for the first time to observe the internalization process of receptor molecules at the single-molecule level. Spatial variations of molecular diffusivity in the scale of 1-2 µm, i.e., a higher level of domain mosaicism in the plasma membrane, were revealed.
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Affiliation(s)
- Hirohito Nishimura
- Institute for Integrated Cell-Material Sciences, 2 Institute for Frontier Medical Sciences, and 3 Department of Materials Science and Engineering, Kyoto University, Kyoto 606-8501, Japan
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411
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Single molecule FRET data analysis procedures for FRET efficiency determination: Probing the conformations of nucleic acid structures. Methods 2013; 64:36-42. [DOI: 10.1016/j.ymeth.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 11/23/2022] Open
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412
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Kwakowsky A, Potapov D, Abrahám IM. Tracking of single receptor molecule mobility in neuronal membranes: a quick theoretical and practical guide. J Neuroendocrinol 2013; 25:1231-7. [PMID: 23927034 DOI: 10.1111/jne.12083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/29/2013] [Accepted: 08/03/2013] [Indexed: 11/28/2022]
Abstract
Single-molecule detection enables us to visualise the real-time dynamics of individual molecules in live cells. We review the recent advancements in single-molecule fluorescence tracking of receptor protein mobility in the neuronal membrane. First, we discuss the practical consideration of single-molecule tracking in neurones, including the choice of cells and possible fluorescent labelling, as well as the appropriate optical set-up and imaging technology. We then describe the analysis of the single-molecule imaging data, including its theoretical and practical aspects of and relevant estimations of the biophysical parameters. Finally, we provide an example of a single-molecule tracking study in neuroendocrinology and highlight the next frontiers of single-molecule detection technologies.
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Affiliation(s)
- A Kwakowsky
- Centre for Neuroendocrinology and Department of Physiology, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
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413
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Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling. Proc Natl Acad Sci U S A 2013; 110:18519-24. [PMID: 24158481 DOI: 10.1073/pnas.1318188110] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The RAF serine/threonine kinases regulate cell growth through the MAPK pathway, and are targeted by small-molecule RAF inhibitors (RAFis) in human cancer. It is now apparent that protein multimers play an important role in RAF activation and tumor response to RAFis. However, the exact stoichiometry and cellular location of these multimers remain unclear because of the lack of technologies to visualize them. In the present work, we demonstrate that photoactivated localization microscopy (PALM), in combination with quantitative spatial analysis, provides sufficient resolution to directly visualize protein multimers in cells. Quantitative PALM imaging showed that CRAF exists predominantly as cytoplasmic monomers under resting conditions but forms dimers as well as trimers and tetramers at the cell membrane in the presence of active RAS. In contrast, N-terminal truncated CRAF (CatC) lacking autoinhibitory domains forms constitutive dimers and occasional tetramers in the cytoplasm, whereas a CatC mutant with a disrupted CRAF-CRAF dimer interface does not. Finally, artificially forcing CRAF to the membrane by fusion to a RAS CAAX motif induces multimer formation but activates RAF/MAPK only if the dimer interface is intact. Together, these quantitative results directly confirm the existence of RAF dimers and potentially higher-order multimers and their involvement in cell signaling, and showed that RAF multimer formation can result from multiple mechanisms and is a critical but not sufficient step for RAF activation.
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414
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Abstract
Coimmunoprecipitation (co-IP) analysis is a useful method for studying protein-protein interactions. It currently involves electrophoresis and western blotting, which are not optimized for detecting weak and transient interactions. In this protocol we describe an advanced version of co-IP analysis that uses real-time, single-molecule fluorescence imaging as its detection scheme. Bait proteins are pulled down onto the imaging plane of a total internal reflection (TIR) microscope. With unpurified cells or tissue extracts kept in reaction chambers, we observe single protein-protein interactions between the surface-immobilized bait and the fluorescent protein-labeled prey proteins in real time. Such direct recording provides an improvement of five orders of magnitude in the time resolution of co-IP analysis. With the single-molecule sensitivity and millisecond time resolution, which distinguish our method from other methods for measuring weak protein-protein interactions, it is possible to quantify the interaction kinetics and active fraction of native, unlabeled bait proteins. Real-time single-molecule co-IP analysis, which takes ∼4 h to complete from lysate preparation to kinetic analysis, provides a general avenue for revealing the rich kinetic picture of target protein-protein interactions, and it can be used, for example, to investigate the molecular lesions that drive individual cancers at the level of protein-protein interactions.
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415
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Dendrimer probes for enhanced photostability and localization in fluorescence imaging. Biophys J 2013; 104:1566-75. [PMID: 23561533 DOI: 10.1016/j.bpj.2013.01.052] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 01/21/2013] [Accepted: 01/28/2013] [Indexed: 01/08/2023] Open
Abstract
Recent advances in fluorescence microscopy have enabled high-resolution imaging and tracking of single proteins and biomolecules in cells. To achieve high spatial resolutions in the nanometer range, bright and photostable fluorescent probes are critically required. From this view, there is a strong need for development of advanced fluorescent probes with molecular-scale dimensions for fluorescence imaging. Polymer-based dendrimer nanoconjugates hold strong potential to serve as versatile fluorescent probes due to an intrinsic capacity for tailored spectral properties such as brightness and emission wavelength. In this work, we report a new, to our knowledge, class of molecular probes based on dye-conjugated dendrimers for fluorescence imaging and single-molecule fluorescence microscopy. We engineered fluorescent dendritic nanoprobes (FDNs) to contain multiple organic dyes and reactive groups for target-specific biomolecule labeling. The photophysical properties of dye-conjugated FDNs (Cy5-FDNs and Cy3-FDNs) were characterized using single-molecule fluorescence microscopy, which revealed greatly enhanced photostability, increased probe brightness, and improved localization precision in high-resolution fluorescence imaging compared to single organic dyes. As proof-of-principle demonstration, Cy5-FDNs were used to assay single-molecule nucleic acid hybridization and for immunofluorescence imaging of microtubules in cytoskeletal networks. In addition, Cy5-FDNs were used as reporter probes in a single-molecule protein pull-down assay to characterize antibody binding and target protein capture. In all cases, the photophysical properties of FDNs resulted in enhanced fluorescence imaging via improved brightness and/or photostability.
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416
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Millis BA, Burnette DT, Lippincott-Schwartz J, Kachar B. Superresolution imaging with standard fluorescent probes. ACTA ACUST UNITED AC 2013; 60:21.8.1-21.8.17. [PMID: 24510788 DOI: 10.1002/0471143030.cb2108s60] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
For more than 100 years, the ultimate resolution of a light microscope (∼ 200 nm) has been constrained by the fundamental physical phenomenon of diffraction, as described by Ernst Abbe in 1873. While this limitation is just as applicable to today's light microscopes, it is the combination of high-end optics, clever methods of sample illumination, and computational techniques that has enabled researchers to access information at an order of magnitude greater resolution than once thought possible. This combination, broadly termed superresolution microscopy, has been increasingly practical for many labs to implement from both a hardware and software standpoint, but, as with many cutting-edge techniques, it also comes with limitations. One of the current drawbacks to superresolution microscopy is the limited number of probes and conditions that have been suitable for imaging. Here, a technique termed bleaching/blinking-assisted localization microscopy (BaLM) makes use of the inherent blinking and bleaching properties of almost all fluorophores as a means to generate superresolution images.
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Affiliation(s)
- Bryan A Millis
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Dylan T Burnette
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Jennifer Lippincott-Schwartz
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
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417
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Affiliation(s)
- Jens Michaelis
- Biophysics
Institute, Faculty of Natural Sciences, Ulm University, Albert-Einstein-Allee
11, 89081 Ulm, Germany
- Center
for Integrated Protein Science Munich (CIPSM), Department
of Chemistry and Biochemistry, Munich University, Butenandtstrasse 5-13, 81377 München, Germany
| | - Barbara Treutlein
- Department
of Bioengineering, Stanford University, James H. Clark Center, E-300, 318
Campus Drive, Stanford, California 94305-5432, United States
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418
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Christensen AL, Lohr C, Christensen SM, Stamou D. Single vesicle biochips for ultra-miniaturized nanoscale fluidics and single molecule bioscience. LAB ON A CHIP 2013; 13:3613-3625. [PMID: 23856986 DOI: 10.1039/c3lc50492a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
One of the major bottlenecks in the development of biochips is maintaining the structure and function of biomolecules when interfacing them with hard matter (glass, plastics, metals, etc.), a challenge that is exacerbated during miniaturization that inevitably increases the interface to volume ratio of these devices. Biochips based on immobilized vesicles circumvent this problem by encapsulating biomolecules in the protective environment of a lipid bilayer, thus minimizing interactions with hard surfaces. Here we review the development of biochips based on arrays of single nanoscale vesicles, their fabrication via controlled self-assembly, and their characterization using fluorescence microscopy. We also highlight their applications in selected fields such as nanofluidics and single molecule bioscience. Despite their great potential for improved biocompatibility, extreme miniaturization and high throughput, single vesicle biochips are still a niche technology that has yet to establish its commercial relevance.
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Affiliation(s)
- Andreas L Christensen
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
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419
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Berthelot V, Steinmetz V, Alvarez LA, Houée-Levin C, Merola F, Rusconi F, Erard M. An analytical workflow for the molecular dissection of irreversibly modified fluorescent proteins. Anal Bioanal Chem 2013; 405:8789-98. [PMID: 24026516 DOI: 10.1007/s00216-013-7326-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/08/2013] [Accepted: 07/11/2013] [Indexed: 12/01/2022]
Abstract
Owing to their ability to be genetically expressed in live cells, fluorescent proteins have become indispensable markers in cellular and biochemical studies. These proteins can undergo a number of covalent chemical modifications that may affect their photophysical properties. Among other mechanisms, such covalent modifications may be induced by reactive oxygen species (ROS), as generated along a variety of biological pathways or through the action of ionizing radiations. In a previous report [1], we showed that the exposure of cyan fluorescent protein (ECFP) to amounts of (•)OH that mimic the conditions of intracellular oxidative bursts (associated with intense ROS production) leads to observable changes in its photophysical properties in the absence of any direct oxidation of the ECFP chromophore. In the present work, we analyzed the associated structural modifications of the protein in depth. Following the quantified production of (•)OH, we devised a complete analytical workflow based on chromatography and mass spectrometry that allowed us to fully characterize the oxidation events. While methionine, tyrosine, and phenylalanine were the only amino acids that were found to be oxidized, semi-quantitative assessment of their oxidation levels showed that the protein is preferentially oxidized at eight residue positions. To account for the preferred oxidation of a few, poorly accessible methionine residues, we propose a multi-step reaction pathway supported by data from pulsed radiolysis experiments. The described experimental workflow is widely generalizable to other fluorescent proteins, and opens the door to the identification of crucial covalent modifications that affect their photophysics.
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Affiliation(s)
- Vivien Berthelot
- Laboratoire de Chimie Physique, UMR CNRS 8000, Building 350, 91405, Orsay Cedex, France
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420
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Ciuba MA, Levitus M. Manganese-Induced Triplet Blinking and Photobleaching of Single Molecule Cyanine Dyes. Chemphyschem 2013; 14:3495-502. [DOI: 10.1002/cphc.201300634] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 07/24/2013] [Indexed: 11/09/2022]
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421
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Hensel M, Klingauf J, Piehler J. Imaging the invisible: resolving cellular microcompartments by superresolution microscopy techniques. Biol Chem 2013; 394:1097-113. [DOI: 10.1515/hsz-2012-0324] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 04/18/2013] [Indexed: 12/20/2022]
Abstract
Abstract
Unraveling the spatio-temporal organization of dynamic cellular microcompartments requires live cell imaging techniques capable of resolving submicroscopic structures. While the resolution of traditional far-field fluorescence imaging techniques is limited by the diffraction barrier, several fluorescence-based microscopy techniques providing sub-100 nm resolution have become available during the past decade. Here, we briefly introduce the optical principles of these techniques and compare their capabilities and limitations with respect to spatial and temporal resolution as well as live cell capabilities. Moreover, we summarize how these techniques contributed to a better understanding of plasma membrane microdomains, the dynamic nanoscale organization of neuronal synapses and the sub-compartmentation of microorganisms. Based on these applications, we highlight complementarity of these techniques and their potential to address specific challenges in the context of dynamic cellular microcompartments, as well as the perspectives to overcome current limitations of these methods.
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422
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Chung HS, Cellmer T, Louis JM, Eaton WA. Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories. Chem Phys 2013; 422:229-237. [PMID: 24443626 PMCID: PMC3892999 DOI: 10.1016/j.chemphys.2012.08.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Folding and unfolding rates for the ultrafast folding villin subdomain were determined from a photon-by-photon analysis of fluorescence trajectories in single molecule FRET experiments. One of the obstacles to measuring fast kinetics in single molecule fluorescence experiments is blinking of the fluorophores on a timescale that is not well separated from the process of interest. By incorporating acceptor blinking into a two-state kinetics model, we show that it is possible to extract accurate rate coefficients on the microsecond time scale for folding and unfolding using the maximum likelihood method of I.V. Gopich and A. Szabo. This method yields the most likely parameters of a given model that can reproduce the observed photon trajectories. The extracted parameters agree with both the decay rate of the donor-acceptor cross correlation function and the results of ensemble equilibrium and kinetic experiments using nanosecond laser temperature jump.
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Affiliation(s)
- Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Troy Cellmer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - William A Eaton
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
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423
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Acuña AU, Álvarez-Pérez M, Liras M, Coto PB, Amat-Guerri F. Synthesis and photophysics of novel biocompatible fluorescent oxocines and azocines in aqueous solution. Phys Chem Chem Phys 2013; 15:16704-12. [PMID: 23986088 DOI: 10.1039/c3cp52228h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The spectroscopic properties in water solution of the different prototropic forms of the strongly fluorescent hemiacetal 4,9-dihydroxy-1,2-dihydro-4,11a-methanooxocino[4,5-b]benzofuran-5(4H)-one (1a, monardine), the aza analogue 4,9-dihydroxy-3,4-dihydro-1H-4,11a-methanobenzofuro[2,3-d]azocin-5(2H)-one (2a, azamonardine) and the respective 2-carboxyl derivatives (1b, 2b) have been studied by experimental and quantum-chemical methods. Monardine and carboxymonardine are the major products of new fluorogenic, room-temperature reactions of hydroxytyrosol or salvianic acid in aqueous solution, respectively, and present unique photophysical properties. Near neutral pH (pKa = 7.2) monardine switches from a weakly emitting, UV-absorbing (382 nm) neutral species to a VIS-absorbing (426 nm), blue emitting (464 nm) anion form, with a fluorescence quantum yield ϕF = 1 and single-exponential decay τF = 2.74 ns. This binary-like spectroscopic change from the neutral to the anionic form was interpreted based on time-dependent density functional theory (TDDFT) calculations as due to (i) the reversal of (n,π*) and (π,π*) lowest-lying singlet excited states, and (ii) a change in the triplet-state distribution accompanying monardine ionization which may abolish de-excitation via intersystem crossing. A similar fluorogenic reaction takes place with catecholamines such as dopamine and DOPA, to yield fluorescent azocines 2a and 2b which, depending on pH, may be present as cationic, neutral or anionic species. TDDFT computations of these forms were also carried out to assign the corresponding excitation transitions and emission properties. Besides the analytical interest of the fluorogenic reactions, the photochemical stability and biocompatibility of the bright-dark pH-controlled molecular switches 1a and 1b may facilitate novel labels and probes to be developed for superresolution fluorescence microscopy.
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Affiliation(s)
- A Ulises Acuña
- Instituto de Química Física "Rocasolano", C.S.I.C., Serrano 119, 28006 Madrid, Spain.
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424
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Demchenko AP, Dekaliuk MO. Novel fluorescent carbonic nanomaterials for sensing and imaging. Methods Appl Fluoresc 2013; 1:042001. [DOI: 10.1088/2050-6120/1/4/042001] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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425
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van de Linde S, Aufmkolk S, Franke C, Holm T, Klein T, Löschberger A, Proppert S, Wolter S, Sauer M. Investigating cellular structures at the nanoscale with organic fluorophores. ACTA ACUST UNITED AC 2013; 20:8-18. [PMID: 23352135 DOI: 10.1016/j.chembiol.2012.11.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 09/10/2012] [Accepted: 11/02/2012] [Indexed: 01/31/2023]
Abstract
Super-resolution fluorescence imaging can provide insights into cellular structure and organization with a spatial resolution approaching virtually electron microscopy. Among all the different super-resolution methods single-molecule-based localization microscopy could play an exceptional role in the future because it can provide quantitative information, for example, the absolute number of biomolecules interacting in space and time. Here, small organic fluorophores are a decisive factor because they exhibit high fluorescence quantum yields and photostabilities, thus enabling their localization with nanometer precision. Besides past progress, problems with high-density and specific labeling, especially in living cells, and the lack of suited standards and long-term continuous imaging methods with minimal photodamage render the exploitation of the full potential of the method currently challenging.
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Affiliation(s)
- Sebastian van de Linde
- Department of Biotechnology and Biophysics, Biozentrum, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany
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426
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Lenn T, Leake MC. Experimental approaches for addressing fundamental biological questions in living, functioning cells with single molecule precision. Open Biol 2013; 2:120090. [PMID: 22773951 PMCID: PMC3390795 DOI: 10.1098/rsob.120090] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 05/16/2012] [Indexed: 12/25/2022] Open
Abstract
In recent years, single molecule experimentation has allowed researchers to observe biological processes at the sensitivity level of single molecules in actual functioning, living cells, thereby allowing us to observe the molecular basis of the key mechanistic processes in question in a very direct way, rather than inferring these from ensemble average data gained from traditional molecular and biochemical techniques. In this short review, we demonstrate the impact that the application of single molecule bioscience experimentation has had on our understanding of various cellular systems and processes, and the potential that this approach has for the future to really address very challenging and fundamental questions in the life sciences.
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Affiliation(s)
- Tchern Lenn
- Lawrence Berkeley National Laboratory, Physical Biosciences Division, 1 Cyclotron Road, Berkeley, CA 94720 , USA
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427
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Xu J, Chang J, Yan Q, Dertinger T, Bruchez M, Weiss S. Labeling Cytosolic Targets in Live Cells with Blinking Probes. J Phys Chem Lett 2013; 4:2138-2146. [PMID: 23930154 PMCID: PMC3733402 DOI: 10.1021/jz400682m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
With the advent of superresolution imaging methods, fast dynamic imaging of biological processes in live cells remains a challenge. A subset of these methods requires the cellular targets to be labeled with spontaneously blinking probes. The delivery and specific targeting of cytosolic targets and the control of the probes' blinking properties are reviewed for three types of blinking probes: quantum dots, synthetic dyes, and fluorescent proteins.
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Affiliation(s)
- Jianmin Xu
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles CA 90095
| | - Jason Chang
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles CA 90095
| | - Qi Yan
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh PA 15213
| | | | - Marcel Bruchez
- Department of Chemistry, Carnegie Mellon University, Pittsburgh PA 15213
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh PA 15213
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles CA 90095
- Department of Physiology, University of California Los Angeles, Los Angeles CA 90095
- Molecular Biology Institute, University of California Los Angeles, Los Angeles CA 90095
- California NanoSystems Institute, University of California Los Angeles, Los Angeles CA 90095
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428
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Feng Z, Zhang W, Xu J, Gauron C, Ducos B, Vriz S, Volovitch M, Jullien L, Weiss S, Bensimon D. Optical control and study of biological processes at the single-cell level in a live organism. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2013; 76:072601. [PMID: 23764902 PMCID: PMC3736146 DOI: 10.1088/0034-4885/76/7/072601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Living organisms are made of cells that are capable of responding to external signals by modifying their internal state and subsequently their external environment. Revealing and understanding the spatio-temporal dynamics of these complex interaction networks is the subject of a field known as systems biology. To investigate these interactions (a necessary step before understanding or modelling them) one needs to develop means to control or interfere spatially and temporally with these processes and to monitor their response on a fast timescale (< minute) and with single-cell resolution. In 2012, an EMBO workshop on 'single-cell physiology' (organized by some of us) was held in Paris to discuss those issues in the light of recent developments that allow for precise spatio-temporal perturbations and observations. This review will be largely based on the investigations reported there. We will first present a non-exhaustive list of examples of cellular interactions and developmental pathways that could benefit from these new approaches. We will review some of the novel tools that have been developed for the observation of cellular activity and then discuss the recent breakthroughs in optical super-resolution microscopy that allow for optical observations beyond the diffraction limit. We will review the various means to photo-control the activity of biomolecules, which allow for local perturbations of physiological processes. We will end up this review with a report on the current status of optogenetics: the use of photo-sensitive DNA-encoded proteins as sensitive reporters and efficient actuators to perturb and monitor physiological processes.
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Affiliation(s)
- Zhiping Feng
- Department of Molecular, Cellular and Integrative Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
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429
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Yang SK, Shi X, Park S, Ha T, Zimmerman SC. A dendritic single-molecule fluorescent probe that is monovalent, photostable and minimally blinking. Nat Chem 2013; 5:692-7. [PMID: 23881501 PMCID: PMC4104187 DOI: 10.1038/nchem.1706] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 06/05/2013] [Indexed: 12/17/2022]
Abstract
Single-molecule fluorescence techniques have emerged as a powerful approach to understand complex biological systems. However, a challenge researchers still face is the limited photostability of nearly all organic fluorophores, including the cyanine and Alexa dyes. We report a new, monovalent probe that emits in the far-red region of the visible spectrum with properties desirable for single-molecule optical imaging. This probe is based on a ring-fused boron-dipyrromethene (BODIPY) core that is conjugated to a polyglycerol dendrimer (PGD). The dendrimer makes the hydrophobic fluorophore water-soluble. This probe exhibits excellent brightness, with an emission maximum of 705 nm. We observed strikingly long and stable emission from individual PGD-BODIPY probes even in the absence of anti-fading agents such as Trolox, a combined oxidizing-reducing agent often used in single-molecule studies for improving the photostability of common imaging probes. These interesting properties greatly simplify use of the fluorophore.
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Affiliation(s)
- Si Kyung Yang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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430
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Kisley L, Chang WS, Cooper D, Mansur AP, Landes CF. Extending single molecule fluorescence observation time by amplitude-modulated excitation. Methods Appl Fluoresc 2013; 1:037001-37001. [PMID: 24587894 DOI: 10.1088/2050-6120/1/3/037001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present a hardware-based method that can improve single molecule fluorophore observation time by up to 1500% and super-localization by 47% for the experimental conditions used. The excitation was modulated using an acousto-optic modulator (AOM) synchronized to the data acquisition and inherent data conversion time of the detector. The observation time and precision in super-localization of four commonly used fluorophores were compared under modulated and traditional continuous excitation, including direct total internal reflectance excitation of Alexa 555 and Cy3, non-radiative Förster resonance energy transfer (FRET) excited Cy5, and direct epi-fluorescence wide field excitation of Rhodamine 6G. The proposed amplitude-modulated excitation does not perturb the chemical makeup of the system or sacrifice signal and is compatible with multiple types of fluorophores. Amplitude-modulated excitation has practical applications for any fluorescent study utilizing an instrumental setup with time-delayed detectors.
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431
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Davis LM, Lubbeck JL, Dean KM, Palmer AE, Jimenez R. Microfluidic cell sorter for use in developing red fluorescent proteins with improved photostability. LAB ON A CHIP 2013; 13:2320-7. [PMID: 23636097 PMCID: PMC4047792 DOI: 10.1039/c3lc50191d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
This paper presents a novel microfluidic cytometer for mammalian cells that rapidly measures the irreversible photobleaching of red fluorescent proteins expressed within each cell and achieves high purity (>99%) selection of individual cells based on these measurements. The selection is achieved by using sub-millisecond timed control of a piezo-tilt mirror to steer a focused 1064-nm laser spot for optical gradient force switching following analysis of the fluorescence signals from passage of the cell through a series of 532-nm laser beams. In transit through each beam, the fluorescent proteins within the cell undergo conversion to dark states, but the microfluidic chip enables the cell to pass sufficiently slowly that recovery from reversible dark states occurs between beams, thereby enabling irreversible photobleaching to be quantified separately from the reversible dark-state conversion. The microfluidic platform achieves sorting of samples down to sub-millilitre volumes with minimal loss, wherein collected cells remain alive and can subsequently proliferate. The instrument provides a unique first tool for rapid selection of individual mammalian cells on the merits of photostability and is likely to form the basis of subsequent lab-on-a-chip platforms that combine photobleaching with other spectroscopic measurements for on-going research to develop advanced red fluorescent proteins by screening of genetic libraries.
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Affiliation(s)
- Lloyd M. Davis
- Visiting Fellow at JILA; Permanent address: Department of Physics, University of Tennessee Knoxville, and Center for Laser Applications, University of Tennessee Space Institute, 411 B.H. Goethert Parkway, Tullahoma, Tennessee 37388, USA
| | - Jennifer L. Lubbeck
- Department of Chemistry & Biochemistry, University of Colorado Boulder, 215 UCB, Boulder, Colorado 80309, USA
- JILA, University of Colorado Boulder, 440 UCB, Boulder, Colorado 80309, USA
| | - Kevin M. Dean
- Department of Chemistry & Biochemistry, University of Colorado Boulder, 215 UCB, Boulder, Colorado 80309, USA
| | - Amy E. Palmer
- Department of Chemistry & Biochemistry, University of Colorado Boulder, 215 UCB, Boulder, Colorado 80309, USA
- BioFrontiers Institute, University of Colorado Boulder, 596 UCB, Boulder, Colorado 80309, USA
| | - Ralph Jimenez
- Department of Chemistry & Biochemistry, University of Colorado Boulder, 215 UCB, Boulder, Colorado 80309, USA
- JILA, University of Colorado Boulder, 440 UCB, Boulder, Colorado 80309, USA
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432
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Mazouchi A, Bahram A, Gradinaru CC. Sub-diffusion decays in fluorescence correlation spectroscopy: dye photophysics or protein dynamics? J Phys Chem B 2013; 117:11100-11. [PMID: 23675915 DOI: 10.1021/jp4010746] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transitions between bright and dark fluorescent states of several rhodamine dyes were investigated by fluorescence correlation spectroscopy. We resolved two sub-diffusion exponential decays for free rhodamines in aqueous solutions, of which the slower component scales linearly with the viscosity of the solution. Correlation data for proteins and DNA labeled with tetramethylrhodamine were fitted with three to four exponential decays describing flickering dynamics on a time scale between 0.5 and 100 μs. We investigated the nature of these processes by performing experiments under different experimental conditions and for different samples. On the basis of how their population and lifetime change with viscosity, the oxygen content of the solution, the laser irradiance, and the detection geometry, we assigned these states, in the order of increasing lifetimes, to a triplet state, a hybrid between twisted-intramolecular-charge-transfer state and a ground state lactonic state, a lactonic state, and a photoionized state, respectively. Our data suggests that none of the observed sub-diffusion correlation decays can be directly assigned to the intramolecular dynamics of the labeled biomolecules. However, we found evidence that the intrinsic conformational dynamics of the biomolecule appears in the correlation curves as a modulation of the photophysics of the dye label. This shows the importance of accurate control measurements and appropriate modeling of the dye photophysics in fluorescence correlation studies, and it cautions against direct assignments of dark-state relaxation times to folding kinetics in proteins and nucleic acids.
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Affiliation(s)
- Amir Mazouchi
- Department of Physics, University of Toronto , and Department of Chemical and Physical Sciences, University of Toronto Mississauga , Mississauga, Ontario L5L 1C6, Canada
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433
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Shaban Ragab S, Swaminathan S, Deniz E, Captain B, Raymo FM. Fluorescence photoactivation by ligand exchange around the boron center of a BODIPY chromophore. Org Lett 2013; 15:3154-7. [PMID: 23738708 DOI: 10.1021/ol401380n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Chelation of the boron center of the borondipyrromethene (BODIPY) platform by a catecholate ligand results in effective fluorescence suppression. Electron transfer from the chelating unit to the adjacent chromophore upon excitation is responsible for fluorescence quenching. Under the influence of a photoacid generator, the catecholate chelator can be exchanged with a pair of methoxide ligands. This photoinduced transformation prevents electron transfer and efficiently activates the fluorescence of the BODIPY chromophore.
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Affiliation(s)
- Sherif Shaban Ragab
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami , 1301 Memorial Drive, Coral Gables, Florida 33146-0431, United States
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434
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Cooper D, Uhm H, Tauzin LJ, Poddar N, Landes CF. Photobleaching lifetimes of cyanine fluorophores used for single-molecule Förster resonance energy transfer in the presence of various photoprotection systems. Chembiochem 2013; 14:1075-80. [PMID: 23733413 DOI: 10.1002/cbic.201300030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Indexed: 12/19/2022]
Abstract
Lengthening smFRET lifetimes: We investigated various photoprotection system combinations to find the combination that optimally extended the photobleach lifetime of a Cy3/Cy5 smFRET pair attached to a DNA hairpin in a single-molecule environment. We found that the glucose/glucose oxygen-scavenging solution in combination with redox-based photostabilization solutions yielded the longest average photobleaching lifetimes.
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Affiliation(s)
- David Cooper
- Department of Chemistry, Rice University, 6100 Main St. Houston, TX 77005, USA
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435
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Guo L, Gai F. Simple method to enhance the photostability of the fluorescence reporter R6G for prolonged single-molecule studies. J Phys Chem A 2013; 117:6164-70. [PMID: 23641719 DOI: 10.1021/jp4003643] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For fluorescence-based single-molecule studies, photobleaching of the dye reporter often limits the time window over which individual molecules can be followed. As such, many strategies, for example, using a cocktail of chemical reagents, have been developed to decrease the rate of photobleaching. Herein, we introduce a new and highly effective method to enhance the photostability of one of the commonly used fluorescent dyes, rhodamine 6G (R6G). We show that micrometer-sized polydimethylsiloxane (PDMS) wells, when the PDMS surface is properly treated, not only provide a confined environment for single-molecule detection but can also significantly increase the survival time of individual R6G molecules before photobleaching. Moreover, our results suggest, consistent with several previous studies, that R6G photobleaching involves a radical state.
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Affiliation(s)
- Lin Guo
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA
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436
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Lv Y, Liu H, Zhao B, Tian Z, Li ADQ. Tuning Photoswitchable Dual-Color Fluorescence from Core-Shell Polymer Nanoparticles. Isr J Chem 2013. [DOI: 10.1002/ijch.201300015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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437
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Demchenko AP. Nanoparticles and nanocomposites for fluorescence sensing and imaging. Methods Appl Fluoresc 2013; 1:022001. [DOI: 10.1088/2050-6120/1/2/022001] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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438
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Lee JH, Cavagnero S. A novel tri-enzyme system in combination with laser-driven NMR enables efficient nuclear polarization of biomolecules in solution. J Phys Chem B 2013; 117:6069-81. [PMID: 23560683 DOI: 10.1021/jp4010168] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NMR is an extremely powerful, yet insensitive technique. Many available nuclear polarization methods that address sensitivity are not directly applicable to low-concentration biomolecules in liquids and are often too invasive. Photochemically induced dynamic nuclear polarization (photo-CIDNP) is no exception. It needs high-power laser irradiation, which often leads to sample degradation, and photosensitizer reduction. Here, we introduce a novel tri-enzyme system that significantly overcomes the above challenges, rendering photo-CIDNP a practically applicable technique for NMR sensitivity enhancement in solution. The specificity of the nitrate reductase (NR) enzyme is exploited to selectively in situ reoxidize the reduced photo-CIDNP dye FMNH2. At the same time, the oxygen-scavenging ability of glucose oxidase (GO) and catalase (CAT) is synergistically employed to prevent sample photodegradation. The resulting tri-enzyme system (NR-GO-CAT) enables prolonged sensitivity-enhanced data collection in 1D and 2D heteronuclear NMR, leading to the highest photo-CIDNP sensitivity enhancement (48-fold relative to SE-HSQC) achieved to date for amino acids and polypeptides in solution. NR-GO-CAT extends the concentration limit of photo-CIDNP NMR down to the low micromolar range. In addition, sensitivity (relative to the reference SE-HSQC) is found to be inversely proportional to sample concentration, paving the way for the future analysis of even more diluted samples.
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Affiliation(s)
- Jung Ho Lee
- Department of Chemistry and Biophysics Program, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
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439
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440
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Toseland CP. Fluorescent labeling and modification of proteins. J Chem Biol 2013; 6:85-95. [PMID: 24432126 PMCID: PMC3691395 DOI: 10.1007/s12154-013-0094-5] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/01/2013] [Indexed: 10/27/2022] Open
Abstract
This review provides an outline for fluorescent labeling of proteins. Fluorescent assays are very diverse providing the most sensitive and robust methods for observing biological processes. Here, different types of labels and methods of attachment are discussed in combination with their fluorescent properties. The advantages and disadvantages of these different methods are highlighted, allowing the careful selection for different applications, ranging from ensemble spectroscopy assays through to single-molecule measurements.
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Affiliation(s)
- Christopher P. Toseland
- Institut für Zelluläre Physiologie and Center for NanoScience (CeNS), Physiologisches Institut, Ludwig Maximilians Universität, Munich, 80336 Germany
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441
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Zooming in on biological processes with fluorescence nanoscopy. Curr Opin Biotechnol 2013; 24:646-53. [PMID: 23498844 DOI: 10.1016/j.copbio.2013.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 02/17/2013] [Accepted: 02/18/2013] [Indexed: 11/23/2022]
Abstract
Fluorescence nanoscopy enables the study of biological phenomena at nanometer scale spatial resolution. Recent biological studies using fluorescence nanoscopy have showcased the ability of these techniques to directly observe protein organization, subcellular molecular interactions, structural dynamics, electrical signaling, and diffusion of cytosolic proteins at unprecedented spatial resolution. Super-resolution imaging techniques critically rely on bright fluorescent probes such as organic dyes or fluorescent proteins. Recently, these methods have been extended to live cells and multicolor, three-dimensional imaging, thereby providing exquisite spatiotemporal resolutions of the order of 10-20 nm and 1-2 s for subcellular imaging. Further improvements in image processing algorithms, labeling techniques, correlative microscopy, and development of advanced fluorescent probes will be required to achieve true molecular-scale resolution using these techniques.
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442
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Schäfer P, van de Linde S, Lehmann J, Sauer M, Doose S. Methylene Blue- and Thiol-Based Oxygen Depletion for Super-Resolution Imaging. Anal Chem 2013; 85:3393-400. [DOI: 10.1021/ac400035k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Philip Schäfer
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97075 Würzburg, Germany
| | - Sebastian van de Linde
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97075 Würzburg, Germany
| | - Julian Lehmann
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97075 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97075 Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology & Biophysics, Biocenter, Julius-Maximilians-University Würzburg, Am Hubland, 97075 Würzburg, Germany
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443
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Yu J. To unscramble an egg. Nat Methods 2013; 10:208-9. [DOI: 10.1038/nmeth.2379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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444
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Waichman S, Roder F, Richter CP, Birkholz O, Piehler J. Diffusion and interaction dynamics of individual membrane protein complexes confined in micropatterned polymer-supported membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:570-577. [PMID: 23109503 DOI: 10.1002/smll.201201530] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/12/2012] [Indexed: 06/01/2023]
Abstract
Micropatterned polymer-supported membranes (PSM) are established as a tool for confining the diffusion of transmembrane proteins for single molecule studies. To this end, a photochemical surface modification with hydrophobic tethers on a PEG polymer brush is implemented for capturing of lipid vesicles and subsequent fusion. Formation of contiguous membranes within micropatterns is confirmed by scanning force microscopy, fluorescence recovery after photobleaching (FRAP), and super-resolved single-molecule tracking and localization microscopy. Free diffusion of transmembrane proteins reconstituted into micropatterned PSM is demonstrated by FRAP and by single-molecule tracking. By exploiting the confinement of diffusion within micropatterned PSM, the diffusion and interaction dynamics of individual transmembrane receptors are quantitatively resolved.
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Affiliation(s)
- Sharon Waichman
- Department of Biology, University of Osnabrück, Osnabrück, Germany
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445
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Sengupta P, Van Engelenburg S, Lippincott-Schwartz J. Visualizing cell structure and function with point-localization superresolution imaging. Dev Cell 2013; 23:1092-102. [PMID: 23237943 DOI: 10.1016/j.devcel.2012.09.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fundamental to the success of cell and developmental biology is the ability to tease apart molecular organization in cells and tissues by localizing specific proteins with respect to one another in a native cellular context. However, many key cellular structures (from mitochondrial cristae to nuclear pores) lie below the diffraction limit of visible light, precluding analysis of their organization by conventional approaches. Point-localization superresolution microscopy techniques, such as PALM and STORM, are poised to resolve, with unprecedented clarity, the organizational principles of macromolecular complexes within cells, thus leading to deeper insights into cellular function in both health and disease.
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Affiliation(s)
- Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Sengupta P, Jovanovic-Talisman T, Lippincott-Schwartz J. Quantifying spatial organization in point-localization superresolution images using pair correlation analysis. Nat Protoc 2013; 8:345-54. [PMID: 23348362 PMCID: PMC3925398 DOI: 10.1038/nprot.2013.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The distinctive distributions of proteins within subcellular compartments both at steady state and during signaling events have essential roles in cell function. Here we describe a method for delineating the complex arrangement of proteins within subcellular structures visualized using point-localization superresolution (PL-SR) imaging. The approach, called pair correlation photoactivated localization microscopy (PC-PALM), uses a pair-correlation algorithm to precisely identify single molecules in PL-SR imaging data sets, and it is used to decipher quantitative features of protein organization within subcellular compartments, including the existence of protein clusters and the size, density and number of proteins in these clusters. We provide a step-by-step protocol for PC-PALM, illustrating its analysis capability for four plasma membrane proteins tagged with photoactivatable GFP (PAGFP). The experimental steps for PC-PALM can be carried out in 3 d and the analysis can be done in ∼6-8 h. Researchers need to have substantial experience in single-molecule imaging and statistical analysis to conduct the experiments and carry out this analysis.
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Affiliation(s)
- Prabuddha Sengupta
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tijana Jovanovic-Talisman
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jennifer Lippincott-Schwartz
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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447
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Schuler B, Hofmann H. Single-molecule spectroscopy of protein folding dynamics—expanding scope and timescales. Curr Opin Struct Biol 2013; 23:36-47. [DOI: 10.1016/j.sbi.2012.10.008] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
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448
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Kim H, Ha T. Single-molecule nanometry for biological physics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2013; 76:016601. [PMID: 23249673 PMCID: PMC3549428 DOI: 10.1088/0034-4885/76/1/016601] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Precision measurement is a hallmark of physics but the small length scale (∼nanometer) of elementary biological components and thermal fluctuations surrounding them challenge our ability to visualize their action. Here, we highlight the recent developments in single-molecule nanometry where the position of a single fluorescent molecule can be determined with nanometer precision, reaching the limit imposed by the shot noise, and the relative motion between two molecules can be determined with ∼0.3 nm precision at ∼1 ms time resolution, as well as how these new tools are providing fundamental insights into how motor proteins move on cellular highways. We will also discuss how interactions between three and four fluorescent molecules can be used to measure three and six coordinates, respectively, allowing us to correlate the movements of multiple components. Finally, we will discuss recent progress in combining angstrom-precision optical tweezers with single-molecule fluorescent detection, opening new windows for multi-dimensional single-molecule nanometry for biological physics.
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Affiliation(s)
- Hajin Kim
- Howard Hughes Medical Institute, Urbana, IL 61801, USA
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449
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Ziemniak M, Szabelski M, Lukaszewicz M, Nowicka A, Darzynkiewicz E, Rhoads RE, Wieczorek Z, Jemielity J. Synthesis and evaluation of fluorescent cap analogues for mRNA labelling. RSC Adv 2013; 3. [PMID: 24273643 DOI: 10.1039/c3ra42769b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We describe the synthesis and properties of five dinucleotide fluorescent cap analogues labelled at the ribose of the 7-methylguanosine moiety with either anthraniloyl (Ant) or N-methylanthraniloyl (Mant), which have been designed for the preparation of fluorescent mRNAs via transcription in vitro. Two of the analogues bear a methylene modification in the triphosphate bridge, providing resistance against either the Dcp2 or DcpS decapping enzymes. All these compounds were prepared by ZnCl2-mediated coupling of a nucleotide P-imidazolide with a fluorescently labelled mononucleotide. To evaluate the utility of these compounds for studying interactions with cap-binding proteins and cap-related cellular processes, both biological and spectroscopic features of those compounds were determined. The results indicate acceptable quantum yields of fluorescence, pH independence, environmental sensitivity, and photostability. The cap analogues are incorporated by RNA polymerase into mRNA transcripts that are efficiently translated in vitro. Transcripts containing fluorescent caps but unmodified in the triphosphate chain are hydrolysed by Dcp2 whereas those containing a α-β methylene modification are resistant. Model studies exploiting sensitivity of Mant to changes of local environment demonstrated utility of the synthesized compounds for studying cap-related proteins.
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Affiliation(s)
- Marcin Ziemniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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