201
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Basu S, Needham LM, Lando D, Taylor EJR, Wohlfahrt KJ, Shah D, Boucher W, Tan YL, Bates LE, Tkachenko O, Cramard J, Lagerholm BC, Eggeling C, Hendrich B, Klenerman D, Lee SF, Laue ED. FRET-enhanced photostability allows improved single-molecule tracking of proteins and protein complexes in live mammalian cells. Nat Commun 2018; 9:2520. [PMID: 29955052 PMCID: PMC6023872 DOI: 10.1038/s41467-018-04486-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/27/2018] [Indexed: 11/09/2022] Open
Abstract
A major challenge in single-molecule imaging is tracking the dynamics of proteins or complexes for long periods of time in the dense environments found in living cells. Here, we introduce the concept of using FRET to enhance the photophysical properties of photo-modulatable (PM) fluorophores commonly used in such studies. By developing novel single-molecule FRET pairs, consisting of a PM donor fluorophore (either mEos3.2 or PA-JF549) next to a photostable acceptor dye JF646, we demonstrate that FRET competes with normal photobleaching kinetic pathways to increase the photostability of both donor fluorophores. This effect was further enhanced using a triplet-state quencher. Our approach allows us to significantly improve single-molecule tracking of chromatin-binding proteins in live mammalian cells. In addition, it provides a novel way to track the localization and dynamics of protein complexes by labeling one protein with the PM donor and its interaction partner with the acceptor dye.
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Affiliation(s)
- Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lisa-Maria Needham
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David Lando
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Edward J R Taylor
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Kai J Wohlfahrt
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Devina Shah
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Yi Lei Tan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lawrence E Bates
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Olga Tkachenko
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Julie Cramard
- Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - B Christoffer Lagerholm
- Medical Research Council Human Immunology Unit and Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Christian Eggeling
- Medical Research Council Human Immunology Unit and Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Brian Hendrich
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.,Wellcome Trust - MRC Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Dave Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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202
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Hadzic MCAS, Börner R, König SLB, Kowerko D, Sigel RKO. Reliable State Identification and State Transition Detection in Fluorescence Intensity-Based Single-Molecule Förster Resonance Energy-Transfer Data. J Phys Chem B 2018; 122:6134-6147. [PMID: 29737844 DOI: 10.1021/acs.jpcb.7b12483] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique to probe biomolecular structure and dynamics. A popular implementation of smFRET consists of recording fluorescence intensity time traces of surface-immobilized, chromophore-tagged molecules. This approach generates large and complex data sets, the analysis of which is to date not standardized. Here, we address a key challenge in smFRET data analysis: the generation of thermodynamic and kinetic models that describe with statistical rigor the behavior of FRET trajectories recorded from surface-tethered biomolecules in terms of the number of FRET states, the corresponding mean FRET values, and the kinetic rates at which they interconvert. For this purpose, we first perform Monte Carlo simulations to generate smFRET trajectories, in which a relevant space of experimental parameters is explored. Then, we provide an account on current strategies to achieve such model selection, as well as a quantitative assessment of their performances. Specifically, we evaluate the performance of each algorithm (change-point analysis, STaSI, HaMMy, vbFRET, and ebFRET) with respect to accuracy, reproducibility, and computing time, which yields a range of algorithm-specific referential benchmarks for various data qualities. Data simulation and analysis were performed with our MATLAB-based multifunctional analysis software for handling smFRET data (MASH-FRET).
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Affiliation(s)
| | | | | | - Danny Kowerko
- Department of Computer Science , Chemnitz University of Technology , 09111 Chemnitz , Germany
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203
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Wang C, Fukazawa A, Tanabe Y, Inai N, Yokogawa D, Yamaguchi S. Water-Soluble Phospholo[3,2-b
]phosphole-P
,P
′-Dioxide-Based Fluorescent Dyes with High Photostability. Chem Asian J 2018; 13:1616-1624. [DOI: 10.1002/asia.201800533] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Chenguang Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Aiko Fukazawa
- Department of Chemistry; Graduate School of Science and Integrated Research Consortium on Chemical Sciences (IRCCS); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Yoshiyuki Tanabe
- Department of Chemistry; Graduate School of Science and Integrated Research Consortium on Chemical Sciences (IRCCS); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Naoto Inai
- Department of Chemistry; Graduate School of Science and Integrated Research Consortium on Chemical Sciences (IRCCS); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Daisuke Yokogawa
- Institute of Transformative Bio-Molecules (WPI-ITbM); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
- Department of Chemistry; Graduate School of Science and Integrated Research Consortium on Chemical Sciences (IRCCS); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Shigehiro Yamaguchi
- Institute of Transformative Bio-Molecules (WPI-ITbM); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
- Department of Chemistry; Graduate School of Science and Integrated Research Consortium on Chemical Sciences (IRCCS); Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
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204
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Dey SK, Pettersson JR, Topacio AZ, Das SR, Peteanu LA. Eliminating Spurious Zero-Efficiency FRET States in Diffusion-Based Single-Molecule Confocal Microscopy. J Phys Chem Lett 2018; 9:2259-2265. [PMID: 29570297 DOI: 10.1021/acs.jpclett.8b00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) of freely diffusing biomolecules using confocal microscopy is a simple and powerful technique for measuring conformation and dynamics. However, a spurious zero-FRET population can significantly distort the measured histograms and lead to incorrect results, particularly in measurements of intrinsically low-FRET systems. Using a model system consisting of duplex DNAs, we show that there are two important contributions to the zero-FRET state: (1) formation of a dark triplet state of the acceptor dye and (2) the presence of donor-only strands due to incomplete hybridization between donor- and acceptor-labeled strands. The combined strategy of using Trolox as a triplet-state quencher and labeling the same DNA strand with donor and acceptor dyes effectively eliminates the zero-FRET population, even for constructs with intrinsically low FRET efficiencies. This strategy allows us to perform smFRET experiments using a simple confocal microscope with improved accuracy.
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Affiliation(s)
- Sourav K Dey
- Department of Chemistry and Center for Nucleic Acids Science & Technology , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - John R Pettersson
- Department of Chemistry and Center for Nucleic Acids Science & Technology , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Andrea Z Topacio
- Department of Chemistry and Center for Nucleic Acids Science & Technology , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Subha R Das
- Department of Chemistry and Center for Nucleic Acids Science & Technology , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
| | - Linda A Peteanu
- Department of Chemistry and Center for Nucleic Acids Science & Technology , Carnegie Mellon University , 4400 Fifth Avenue , Pittsburgh , Pennsylvania 15213 , United States
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205
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Čechová L, Kind J, Dračínský M, Filo J, Janeba Z, Thiele CM, Cigáň M, Procházková E. Photoswitching Behavior of 5-Phenylazopyrimidines: In Situ Irradiation NMR and Optical Spectroscopy Combined with Theoretical Methods. J Org Chem 2018; 83:5986-5998. [DOI: 10.1021/acs.joc.8b00569] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lucie Čechová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Jonas Kind
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, Darmstadt 64287, Germany
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Juraj Filo
- Institute of Chemistry, Comenius University, Ilkovičova 6, Bratislava 84215, Slovakia
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Christina M. Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 16, Darmstadt 64287, Germany
| | - Marek Cigáň
- Institute of Chemistry, Comenius University, Ilkovičova 6, Bratislava 84215, Slovakia
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
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206
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Zuo J, Tu L, Li Q, Feng Y, Que I, Zhang Y, Liu X, Xue B, Cruz LJ, Chang Y, Zhang H, Kong X. Near Infrared Light Sensitive Ultraviolet-Blue Nanophotoswitch for Imaging-Guided "Off-On" Therapy. ACS NANO 2018; 12:3217-3225. [PMID: 29489327 DOI: 10.1021/acsnano.7b07393] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Photoswitchable materials are important in broad applications. Recently appeared inorganic photoswitchable upconversion nanoparticles (PUCNPs) become a competitive candidate to surmount the widespread issue of the organic counterparts -photobleaching. However, current PUCNPs follow solely Yb3+/Nd3+ cosensitizing mode, which results in complex multilayer doping patterns and imperfectness of switching in UV-blue region. In this work, we have adopted a new strategy to construct Nd3+ free PUCNPs-NaErF4@NaYF4@NaYbF4:0.5%Tm@NaYF4. These PUCNPs demonstrate the superior property of photoswitching. A prominent UV-blue emission from Tm3+ is turned on upon 980 nm excitation, which can be completely turned off by 800 nm light. The quasi-monochromatic red upconversion emission upon 800 nm excitation-a distinct feature of undoping NaErF4 upconversion system-endows the PUCNPs with promising image-guided photoinduced "off-on" therapy in biomedicine. As a proof-of-concept we have demonstrated the imaging-guided photodynamic therapy (PDT) of cancer, where 800 nm excitation turns off the UV-blue emission and leaves the emission at 660 nm for imaging. Once the tumor site is targeted, excitation switching to 980 nm results in UV-blue emission and the red emission. The former is used to induce PDT, whereas the latter is to monitor the therapeutic process. Our study implies that this upconversion photoswitching material is suitable for real-time imaging and image-guided therapy under temporal and spatial control.
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Affiliation(s)
- Jing Zuo
- State Key Laboratory of Luminescence and Applications , Changchun Institute of Optics, FineMechanics and Physics, Chinese Academy of Sciences , Changchun , 130033 Jilin , China
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098XH Amsterdam , The Netherlands
| | - Langping Tu
- State Key Laboratory of Luminescence and Applications , Changchun Institute of Optics, FineMechanics and Physics, Chinese Academy of Sciences , Changchun , 130033 Jilin , China
| | - Qiqing Li
- State Key Laboratory of Luminescence and Applications , Changchun Institute of Optics, FineMechanics and Physics, Chinese Academy of Sciences , Changchun , 130033 Jilin , China
| | - Yansong Feng
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098XH Amsterdam , The Netherlands
| | - Ivo Que
- Translational Nanobiomaterials and Imaging, Department of Radiology , Leiden University Medical Center , 2333ZA Leiden , The Netherlands
| | - Youlin Zhang
- State Key Laboratory of Luminescence and Applications , Changchun Institute of Optics, FineMechanics and Physics, Chinese Academy of Sciences , Changchun , 130033 Jilin , China
| | - Xiaomin Liu
- State Key Laboratory of Luminescence and Applications , Changchun Institute of Optics, FineMechanics and Physics, Chinese Academy of Sciences , Changchun , 130033 Jilin , China
| | - Bin Xue
- State Key Laboratory of Luminescence and Applications , Changchun Institute of Optics, FineMechanics and Physics, Chinese Academy of Sciences , Changchun , 130033 Jilin , China
| | - Luis J Cruz
- Translational Nanobiomaterials and Imaging, Department of Radiology , Leiden University Medical Center , 2333ZA Leiden , The Netherlands
| | - Yulei Chang
- State Key Laboratory of Luminescence and Applications , Changchun Institute of Optics, FineMechanics and Physics, Chinese Academy of Sciences , Changchun , 130033 Jilin , China
| | - Hong Zhang
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098XH Amsterdam , The Netherlands
| | - Xianggui Kong
- State Key Laboratory of Luminescence and Applications , Changchun Institute of Optics, FineMechanics and Physics, Chinese Academy of Sciences , Changchun , 130033 Jilin , China
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207
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Isbaner S, Karedla N, Kaminska I, Ruhlandt D, Raab M, Bohlen J, Chizhik A, Gregor I, Tinnefeld P, Enderlein J, Tsukanov R. Axial Colocalization of Single Molecules with Nanometer Accuracy Using Metal-Induced Energy Transfer. NANO LETTERS 2018; 18:2616-2622. [PMID: 29562123 DOI: 10.1021/acs.nanolett.8b00425] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule localization based super-resolution microscopy has revolutionized optical microscopy and routinely allows for resolving structural details down to a few nanometers. However, there exists a rather large discrepancy between lateral and axial localization accuracy, the latter typically three to five times worse than the former. Here, we use single-molecule metal-induced energy transfer (smMIET) to localize single molecules along the optical axis, and to measure their axial distance with an accuracy of 5 nm. smMIET relies only on fluorescence lifetime measurements and does not require additional complex optical setups.
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Affiliation(s)
- Sebastian Isbaner
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
| | - Narain Karedla
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
- DFG Research Center "Nanoscale Microscopy and Molecular Physiology of the Brain" (CNMPB) , 37077 Göttingen , Germany
| | - Izabela Kaminska
- Institute for Physical and Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA) , Braunschweig University of Technology , 38106 Braunschweig , Germany
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics , Nicolaus Copernicus University , 87-100 Torun , Poland
| | - Daja Ruhlandt
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
| | - Mario Raab
- Institute for Physical and Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA) , Braunschweig University of Technology , 38106 Braunschweig , Germany
- Department of Chemistry and Center for NanoScience , Ludwig-Maximilians-Universität München , 80539 München , Germany
| | - Johann Bohlen
- Institute for Physical and Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA) , Braunschweig University of Technology , 38106 Braunschweig , Germany
- Department of Chemistry and Center for NanoScience , Ludwig-Maximilians-Universität München , 80539 München , Germany
| | - Alexey Chizhik
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
| | - Ingo Gregor
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
| | - Philip Tinnefeld
- Institute for Physical and Theoretical Chemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA) , Braunschweig University of Technology , 38106 Braunschweig , Germany
- Department of Chemistry and Center for NanoScience , Ludwig-Maximilians-Universität München , 80539 München , Germany
| | - Jörg Enderlein
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
- DFG Research Center "Nanoscale Microscopy and Molecular Physiology of the Brain" (CNMPB) , 37077 Göttingen , Germany
| | - Roman Tsukanov
- Third Institute of Physics - Biophysics , Georg August University , 37077 Göttingen , Germany
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208
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Flat-Field Super-Resolution Localization Microscopy with a Low-Cost Refractive Beam-Shaping Element. Sci Rep 2018; 8:5630. [PMID: 29618762 PMCID: PMC5884788 DOI: 10.1038/s41598-018-24052-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/14/2018] [Indexed: 11/08/2022] Open
Abstract
Super-resolution single-molecule localization microscopy, often referred to as PALM/STORM, works by ensuring that fewer than one fluorophore in a diffraction-limited volume is emitting at any one time, allowing the observer to infer that the emitter is located at the center of the point-spread function. This requires careful control over the incident light intensity in order to control the rate at which fluorophores are switched on; if too many fluorophores are activated, their point-spread functions overlap, which impedes efficient localization. If too few are activated, the imaging time is impractically long. There is therefore considerable recent interest in constructing so-called 'top-hat' illumination profiles that provide a uniform illumination over the whole field of view. We present the use of a single commercially-available low-cost refractive beamshaping element that can be retrofitted to almost any existing microscope; the illumination profile created by this element demonstrates a marked improvement in the power efficiency of dSTORM microscopy, as well as a significant reduction in the propensity for reconstruction artifacts, compared to conventional Gaussian illumination.
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209
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Peterson EM, Harris JM. Identification of Individual Immobilized DNA Molecules by Their Hybridization Kinetics Using Single-Molecule Fluorescence Imaging. Anal Chem 2018; 90:5007-5014. [DOI: 10.1021/acs.analchem.7b04512] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Eric M. Peterson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M. Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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210
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Vandenberk N, Barth A, Borrenberghs D, Hofkens J, Hendrix J. Evaluation of Blue and Far-Red Dye Pairs in Single-Molecule Förster Resonance Energy Transfer Experiments. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.8b00108] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Niels Vandenberk
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Anders Barth
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science, Nanosystems Initiative Munich and Centre for Nanoscience, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Doortje Borrenberghs
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Agoralaan C (BIOMED), Diepenbeek, B-3590, Belgium
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211
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Zhao D, Liu S, Gao Y. Single-molecule manipulation and detection. Acta Biochim Biophys Sin (Shanghai) 2018; 50:231-237. [PMID: 29377975 DOI: 10.1093/abbs/gmx146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/23/2017] [Indexed: 11/13/2022] Open
Abstract
Compared to conventional ensemble methods, studying macromolecules at single-molecule level can reveal extraordinary clear and even surprising views for a biological reaction. In the past 20 years, single-molecule techniques have been undergoing a very rapid development, and these cutting edge technologies have revolutionized the biological research by facilitating single-molecule manipulation and detection. Here we give a brief review about these advanced techniques, including optical tweezers, magnetic tweezers, atomic force microscopy (AFM), hydrodynamic flow-stretching assay, and single-molecule fluorescence resonance energy transfer (smFRET). We are trying to describe their basic principles and provide a few examples of applications for each technique. This review aims to give a rather introductory survey of single-molecule techniques for audiences with biological or biophysical background.
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Affiliation(s)
- Deyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Siyun Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Ying Gao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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212
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Byrdin M, Duan C, Bourgeois D, Brettel K. A Long-Lived Triplet State Is the Entrance Gateway to Oxidative Photochemistry in Green Fluorescent Proteins. J Am Chem Soc 2018; 140:2897-2905. [PMID: 29394055 DOI: 10.1021/jacs.7b12755] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Though ubiquitously used as selective fluorescence markers in cellular biology, fluorescent proteins (FPs) still have not disclosed all of their surprising properties. One important issue, notably for single-molecule applications, is the nature of the triplet state, suggested to be the starting point for many possible photochemical reactions leading to phenomena such as blinking or bleaching. Here, we applied transient absorption spectroscopy to characterize dark states in the prototypical enhanced green fluorescent protein (EGFP) of hydrozoan origin and, for comparison, in IrisFP, a representative phototransformable FP of anthozoan origin. We identified a long-lived (approximately 5 ms) dark state that is formed with a quantum yield of approximately 1% and has pronounced absorption throughout the visible-NIR range (peak at around 900 nm). Detection of phosphorescence emission with identical kinetics and excitation spectrum allowed unambiguous identification of this state as the first excited triplet state of the deprotonated chromophore. This triplet state was further characterized by determining its phosphorescence emission spectrum, the temperature dependence of its decay kinetics and its reactivity toward oxygen and electron acceptors and donors. It is suggested that it is this triplet state that lies at the origin of oxidative photochemistry in green FPs, leading to phenomena such as so-called "oxidative redding", "primed photoconversion", or, in a manner similar to that previously observed for organic dyes, redox induced blinking control with the reducing and oxidizing system ("ROXS").
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Affiliation(s)
- Martin Byrdin
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS , 38044 Grenoble, France
| | - Chenxi Duan
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS , 38044 Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS , 38044 Grenoble, France
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay , F-91198 Gif-sur-Yvette cedex, France
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213
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Steffen FD, Sigel RKO, Börner R. An atomistic view on carbocyanine photophysics in the realm of RNA. Phys Chem Chem Phys 2018; 18:29045-29055. [PMID: 27783069 DOI: 10.1039/c6cp04277e] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Carbocyanine dyes have a long-standing tradition in fluorescence imaging and spectroscopy, due to their photostability and large spectral separation between individual dye species. Herein, we explore the versatility of cyanine dyes to probe the dynamics of nucleic acids and we report on the interrelation of fluorophores, RNA, and metal ions, namely K+ and Mg2+. Photophysical parameters including the fluorescence lifetime, quantum yield and dynamic anisotropy are monitored as a function of the nucleic acid composition, conformation, and metal ion abundance. Occasional excursions to a non-fluorescent cis-state hint at the remarkable sensitivity of carbocyanines to their local environment. Comparison of time-correlated single photon experiments with all-atom molecular dynamics simulations demonstrate that the propensity of photoisomerization is dictated by sterical constraints imposed on the fluorophore. Structural features in the vicinity of the dye play a crucial role in RNA recognition and have far-reaching implications on the mobility of the fluorescent probe. An atomic level description of the mutual interactions will ultimately benefit the quantitative interpretation of single-molecule FRET measurements on large RNA systems.
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Affiliation(s)
- Fabio D Steffen
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Richard Börner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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214
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Mamontova AV, Grigoryev AP, Tsarkova AS, Lukyanov KA, Bogdanov AM. Struggle for photostability: Bleaching mechanisms of fluorescent proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162017060085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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215
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Lerner E, Cordes T, Ingargiol A, Alhadid Y, Chung S, Michalet X, Weiss S. Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science 2018; 359:eaan1133. [PMID: 29348210 PMCID: PMC6200918 DOI: 10.1126/science.aan1133] [Citation(s) in RCA: 323] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.
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Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Antonino Ingargiol
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yazan Alhadid
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
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216
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Andreoni A, Sen S, Hagedoorn PL, Buma WJ, Aartsma TJ, Canters GW. Fluorescence Correlation Spectroscopy of Labeled Azurin Reveals Photoinduced Electron Transfer between Label and Cu Center. Chemistry 2018; 24:646-654. [PMID: 29064125 DOI: 10.1002/chem.201703733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 11/06/2022]
Abstract
Fluorescent labeling of biomacromolecules enjoys increasing popularity for structural, mechanistic, and microscopic investigations. Its success hinges on the ability of the dye to alternate between bright and dark states. Förster resonance energy transfer (FRET) is an important source of fluorescence modulation. Photo-induced electron transfer (PET) may occur as well, but is often considered only when donor and acceptor are in van der Waals contact. In this study, PET is shown between a label and redox centers in oxidoreductases, which may occur over large distances. In the small blue copper protein azurin, labeled with ATTO655, PET is observed when the label is at 18.5 Å, but not when it is at 29.1 Å from the Cu. For CuII , PET from label to Cu occurs at a rate of (4.8±0.3)×104 s-1 and back at (0.7±0.1)×103 s-1 . With CuI the numbers are (3.3±0.7)×106 s-1 and (1.0±0.1)×104 s-1 . Reorganization energies and electronic coupling elements are in the range of 0.8-1.2 eV and 0.02-0.5 cm-1 , respectively. These data are compatible with electron transfer (ET) along a through-bond pathway although transient complex formation followed by ET cannot be ruled out. The outcome of this study is a useful guideline for experimental designs in which oxidoreductases are labelled with fluorescent dyes, with particular attention to single molecule investigations. The labelling position for FRET can be optimized to avoid reactions like PET by evaluating the structure and thermodynamics of protein and label.
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Affiliation(s)
- Alessio Andreoni
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands.,Present address: National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Saptaswa Sen
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands.,Present address: AlbaNova University Center, Department of Applied Physics, KTH-Royal Institute of, Technology, 10691, Stockholm, Sweden
| | - Peter-Leon Hagedoorn
- TU Delft, Applied Sciences, Biotechnology, Building 58, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Wybren J Buma
- Van't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD, Amsterdam, The Netherlands
| | - Thijs J Aartsma
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands
| | - Gerard W Canters
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands
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217
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Lefler S, Vizel R, Yeor E, Granot E, Heifler O, Kwiat M, Krivitsky V, Weil M, Yaish YE, Patolsky F. Multicolor Spectral-Specific Silicon Nanodetectors based on Molecularly Embedded Nanowires. NANO LETTERS 2018; 18:190-201. [PMID: 29202247 DOI: 10.1021/acs.nanolett.7b03873] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Silicon-based photodetectors cannot distinguish between different wavelengths. Therefore, these detectors relay on color-specific filters to achieve color separation. Color filters add complexity to color sensitive device fabrication, and hinder miniaturization of such devices. Here, we report an ultrasmall (as small as ∼20 nm by 300 nm), red-green-blue-violet (RGBV) filter-free spectrally gated field effect transistor (SGFET) detectors. These photodetectors are based on organic-silicon nanowire hybrid FET devices, capable of detecting specific visible wavelength spectrum with full width at half-maxima (fwhm) under 100 nm. Each SGFET is controlled by a distinctive RGBV spectral range, according to its specific organic fluorophore functionalization. The spectral-specific RGBV detection is accomplished via covalent attachment of different fluorophores. The fluorophore molecules inject electrons into the nanowire structure as a result of light absorption at the appropriate RGBV spectral range. These photoinduced electrons modify the occupancies of the oxide's surface states, shifting the device threshold voltage, thus changing its conductivity, and functioning as a negative stress bias in a p-type SiNW FETs. A positive biasing can be achieved via UV light-induced ionization, which leads to detrapping and translocation of electrons at the oxide layer. Furthermore, a novel theoretical model on the mechanism of action of these devices was developed. Also, we show that suspended SGFETs can function as nonvolatile memory elements, which unlike fast-relaxing on-surface SGFETs, can store discrete "on" (RGBV illumination) and "off" (UV illumination) states for several days at ambient conditions. We also demonstrate a unique single-nanowire multicolor photodetector, enabling in principle a broad spectral detection over a single silicon nanowire element. These highly compact, spectral-controlled nanodevices have the potential to serve in various future novel optoelectric applications.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yuval E Yaish
- Andrew and Erna Viterbi Faculty of Electrical Engineering, Technion , Haifa 3200003, Israel
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218
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Kocks C, Boltengagen A, Piwecka M, Rybak-Wolf A, Rajewsky N. Single-Molecule Fluorescence In Situ Hybridization (FISH) of Circular RNA CDR1as. Methods Mol Biol 2018; 1724:77-96. [PMID: 29322442 DOI: 10.1007/978-1-4939-7562-4_7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Individual mRNA molecules can be imaged in fixed cells by hybridization with multiple, singly labeled oligonucleotide probes, followed by computational identification of fluorescent signals. This approach, called single-molecule RNA fluorescence in situ hybridization (smRNA FISH), allows subcellular localization and absolute quantification of RNA molecules in individual cells. Here, we describe a simple smRNA FISH protocol for two-color imaging of a circular RNA, CDR1as, simultaneously with an unrelated messenger RNA. The protocol can be adapted to circRNAs that coexist with overlapping, noncircular mRNA isoforms produced from the same genetic locus.
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Affiliation(s)
- Christine Kocks
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
| | - Anastasiya Boltengagen
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Monika Piwecka
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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219
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Abstract
Chemical activity of single nanoparticles can be imaged and determined by monitoring the optical signal of each individual during chemical reactions with advanced optical microscopes. It allows for clarifying the functional heterogeneity among individuals, and for uncovering the microscopic reaction mechanisms and kinetics that could otherwise be averaged out in ensemble measurements.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
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220
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Abstract
Human RAD51 promotes accurate DNA repair by homologous recombination and is involved in protection and repair of damaged DNA replication forks. The active species of RAD51 and related recombinases in all organisms is a nucleoprotein filament assembled on single-stranded DNA (ssDNA). The formation of a nucleoprotein filament competent for the recombination reaction, or for DNA replication support, is a delicate and strictly regulated process, which occurs through filament nucleation followed by filament extension. The rates of these two phases of filament formation define the capacity of RAD51 to compete with the ssDNA-binding protein RPA, as well as the lengths of the resulting filament segments. Single-molecule approaches can provide a wealth of quantitative information on the kinetics of RAD51 nucleoprotein filament assembly, internal dynamics, and disassembly. In this chapter, we describe how to set up a single-molecule total internal reflection fluorescence microscopy experiment to monitor the initial steps of RAD51 nucleoprotein filament formation in real-time and at single-monomer resolution. This approach is based on the unique, stretched-ssDNA conformation within the recombinase nucleoprotein filament and follows the efficiency of Förster resonance energy transfer (EFRET) between two DNA-conjugated fluorophores. We will discuss the practical aspects of the experimental setup, extraction of the FRET trajectories, and how to analyze and interpret the data to obtain information on RAD51 nucleation kinetics, the mechanism of nucleation, and the oligomeric species involved in filament formation.
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221
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Holmstrom ED, Nesbitt DJ. Biophysical Insights from Temperature-Dependent Single-Molecule Förster Resonance Energy Transfer. Annu Rev Phys Chem 2017; 67:441-65. [PMID: 27215819 DOI: 10.1146/annurev-physchem-040215-112544] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Single-molecule fluorescence microscopy techniques can be used in combination with micrometer length-scale temperature control and Förster resonance energy transfer (FRET) in order to gain detailed information about fundamental biophysical phenomena. In particular, this combination of techniques has helped foster the development of remarkable quantitative tools for studying both time- and temperature-dependent structural kinetics of biopolymers. Over the past decade, multiple research efforts have successfully incorporated precise spatial and temporal control of temperature into single-molecule FRET (smFRET)-based experiments, which have uncovered critical thermodynamic information on a wide range of biological systems such as conformational dynamics of nucleic acids. This review provides an overview of various temperature-dependent smFRET approaches from our laboratory and others, highlighting efforts in which such methods have been successfully applied to studies of single-molecule nucleic acid folding.
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Affiliation(s)
- Erik D Holmstrom
- JILA, National Institute of Standards and Technology, University of Colorado, Boulder, Colorado 80309;
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology, University of Colorado, Boulder, Colorado 80309;
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222
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Yoshimura H. Live Cell Imaging of Endogenous RNAs Using Pumilio Homology Domain Mutants: Principles and Applications. Biochemistry 2017; 57:200-208. [PMID: 29164876 DOI: 10.1021/acs.biochem.7b00983] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recently, dynamic changes in the location of RNA in space and time in living cells have become a target of interest in biology because of their essential roles in controlling physiological phenomena. To visualize RNA, methods for the fluorescent labeling of RNA in living cells have been developed. For RNA labeling, oligonucleotide-based RNA probes have mainly been used because of their high selectivity for target RNAs. By contrast, protein-based RNA probes have not been used widely because of their lack of design flexibility, although they have various potential advantages compared with nucleotide-based probes, such as controllability of intracellular localization, high detectability, and ease of introduction into cells and transgenic organisms in a cell type and tissue specific manner by genetic engineering techniques. This Perspective focuses on a possible approach to the development of protein-based RNA probes using Pumilio homology domain (PUM-HD) mutants. The PUM-HD is a domain of an RNA binding protein that allows custom-made modifications to recognize a given eight-base RNA sequence. PUM-HD-based RNA probes have been applied to visualize various RNAs in living cells. Here, the techniques and RNA imaging results obtained using the PUM-HD are introduced.
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Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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223
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Huh H, Lee J, Kim HJ, Hohng S, Kim SK. Morphological analysis of oligomeric vs. fibrillar forms of α-synuclein aggregates with super-resolution BALM imaging. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.10.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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224
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Hori Y, Hirayama S, Kikuchi K. Development of cyanine probes with dinitrobenzene quencher for rapid fluorogenic protein labelling. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2017.0018. [PMID: 29038376 PMCID: PMC5647265 DOI: 10.1098/rsta.2017.0018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/08/2017] [Indexed: 06/07/2023]
Abstract
A multicolour protein labelling technique using a protein tag and fluorogenic probes is a powerful approach for spatio-temporal analyses of proteins in living cells. Since cyanine fluorophores have attractive properties for multicolour imaging of proteins, there is a huge demand to develop fluorogenic cyanine probes for specific protein labelling in living cells. Herein, we develop fluorogenic cyanine probes for labelling a protein tag by using a dinitrobenzene fluorescence quencher. The probes enhanced fluorescence intensity upon labelling reactions and emitted orange or far-red fluorescence. Intramolecular interactions between the cyanine fluorophores and the dinitrobenzene quencher led not only to fluorescence quenching of the probes in the free state but also to promotion of labelling reactions. Furthermore, the probes successfully imaged cell-surface proteins without a washing process. These findings offer valuable information on the design of fluorogenic cyanine probes and indicate that the probes are useful as novel live-cell imaging tools.This article is part of the themed issue 'Challenges for chemistry in molecular imaging'.
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Affiliation(s)
- Yuichiro Hori
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shinya Hirayama
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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225
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Tornmalm J, Widengren J. Label-free monitoring of ambient oxygenation and redox conditions using the photodynamics of flavin compounds and transient state (TRAST) spectroscopy. Methods 2017; 140-141:178-187. [PMID: 29179988 DOI: 10.1016/j.ymeth.2017.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022] Open
Abstract
Transient state (TRAST) monitoring can determine population dynamics of long-lived, dark transient states of fluorescent molecules, detecting only the average fluorescence intensity from a sample, when subject to different excitation pulse trains. Like Fluorescence Correlation Spectroscopy (FCS), TRAST unites the detection sensitivity of fluorescence with the environmental sensitivity of long-lived non-fluorescent states, but does not rely on detection of stochastic fluorescence fluctuations from individual molecules. Relaxed requirements on noise suppression, detection quantum yield and time-resolution of the instrument, as well as on fluorescence brightness of the molecules studied, make TRAST broadly applicable, opening also for investigations based on less bright, auto-fluorescent molecules. In this work, we applied TRAST to study the transient state population dynamics within the auto-fluorescent coenzymes flavin adenine dinucleotide (FAD) and flavin-mononucleotide (FMN). From the experimental TRAST data, we defined state models, and determined rate parameters for triplet state and redox transitions within FMN and FAD, stacking and un-stacking rates of external redox active quenching agents and by the adenine moiety of FAD itself. TRAST experiments were found to be well capable to resolve these transitions in FMN and FAD, and to track how the transitions are influenced by ambient oxygenation and redox conditions. This work demonstrates that TRAST provides a useful tool to follow local oxygenation and redox conditions via FMN and FAD fluorescence, and forms the basis for measurements on flavo-proteins and of redox and metabolic conditions in more complex environments, such as in live cells.
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Affiliation(s)
- Johan Tornmalm
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Albanova University Center, 106 91 Stockholm, Sweden.
| | - Jerker Widengren
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Albanova University Center, 106 91 Stockholm, Sweden.
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226
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Freidus LG, Pradeep P, Kumar P, Choonara YE, Pillay V. Alternative fluorophores designed for advanced molecular imaging. Drug Discov Today 2017; 23:115-133. [PMID: 29111179 DOI: 10.1016/j.drudis.2017.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 08/11/2017] [Accepted: 09/12/2017] [Indexed: 01/09/2023]
Abstract
Fluorescent molecular imaging has advanced drastically over the past decade. With the development of high-resolution microscopy techniques and the ability to visualize intracellular molecular events, there is a growing need for new fluorophores to accompany these fast-developing techniques. Therefore, there has been substantial development of alternative fluorophores for single-molecule detection and molecular imaging. These rationally designed fluorophores have infinite possibilities and novel fluorophores are constantly being produced for different applications. This review focuses on the recent developments in novel fluorophores designed for molecular imaging and single-molecule detection. Here, single-molecule imaging, smart fluorescent probes, two-photon microscopy, Förster resonance energy transfer (FRET) and super-resolution microscopy are discussed in detail.
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Affiliation(s)
- Lara G Freidus
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg, South Africa
| | - Priyamvada Pradeep
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg, South Africa
| | - Pradeep Kumar
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg, South Africa
| | - Yahya E Choonara
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg, South Africa
| | - Viness Pillay
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, Johannesburg, South Africa.
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227
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Tang J, Sun Y, Pang S, Han KY. Spatially encoded fast single-molecule fluorescence spectroscopy with full field-of-view. Sci Rep 2017; 7:10945. [PMID: 28887471 PMCID: PMC5591195 DOI: 10.1038/s41598-017-10837-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/15/2017] [Indexed: 11/09/2022] Open
Abstract
We report a simple single-molecule fluorescence imaging method that increases the temporal resolution of any type of array detector by >5-fold with full field-of-view. We spread single-molecule spots to adjacent pixels by rotating a mirror in the detection path during the exposure time of a single frame, which encodes temporal information into the spatial domain. Our approach allowed us to monitor fast blinking of an organic dye, the dissociation kinetics of very short DNA and conformational changes of biomolecules with much improved temporal resolution than the conventional method. Our technique is useful when a large field-of-view is required, for example, in the case of weakly interacting biomolecules or cellular imaging.
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Affiliation(s)
- Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
| | - Yangyang Sun
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
| | - Shuo Pang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA.
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228
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Wang L, Li B, Xu F, Li Y, Xu Z, Wei D, Feng Y, Wang Y, Jia D, Zhou Y. Visual in vivo degradation of injectable hydrogel by real-time and non-invasive tracking using carbon nanodots as fluorescent indicator. Biomaterials 2017; 145:192-206. [PMID: 28869865 DOI: 10.1016/j.biomaterials.2017.08.039] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/23/2017] [Accepted: 08/26/2017] [Indexed: 12/27/2022]
Abstract
Visual in vivo degradation of hydrogel by fluorescence-related tracking and monitoring is crucial for quantitatively depicting the degradation profile of hydrogel in a real-time and non-invasive manner. However, the commonly used fluorescent imaging usually encounters limitations, such as intrinsic photobleaching of organic fluorophores and uncertain perturbation of degradation induced by the change in molecular structure of hydrogel. To address these problems, we employed photoluminescent carbon nanodots (CNDs) with low photobleaching, red emission and good biocompatibility as fluorescent indicator for real-time and non-invasive visual in vitro/in vivo degradation of injectable hydrogels that are mixed with CNDs. The in vitro/in vivo toxicity results suggested that CNDs were nontoxic. The embedded CNDs in hydrogels did not diffuse outside in the absence of hydrogel degradation. We had acquired similar degradation kinetics (PBS-Enzyme) between gravimetric and visual determination, and established mathematical equation to quantitatively depict in vitro degradation profile of hydrogels for the predication of in vivo hydrogel degradation. Based on the in vitro data, we developed a visual platform that could quantitatively depict in vivo degradation behavior of new injectable biomaterials by real-time and non-invasive fluorescence tracking. This fluorescence-related visual imaging methodology could be applied to subcutaneous degradation of injectable hydrogel with down to 7 mm depth in small animal trials so far. This fluorescence-related visual imaging methodology holds great potentials for rational design and convenient in vivo screening of biocompatible and biodegradable injectable hydrogels in tissue engineering.
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Affiliation(s)
- Lei Wang
- Institute for Advanced Ceramics, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, PR China
| | - Baoqiang Li
- Institute for Advanced Ceramics, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, PR China.
| | - Feng Xu
- MOE Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Ying Li
- Sino-Russian Institute of Hard Tissue Development and Regeneration, The Second Affiliated Hospital of Harbin Medical University, Heilongjiang Academy of Medical Sciences, Harbin 150001, PR China
| | - Zheheng Xu
- Institute for Advanced Ceramics, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, PR China
| | - Daqing Wei
- Institute for Advanced Ceramics, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, PR China
| | - Yujie Feng
- Institute for Advanced Ceramics, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, PR China
| | - Yaming Wang
- Institute for Advanced Ceramics, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, PR China
| | - Dechang Jia
- Institute for Advanced Ceramics, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, PR China
| | - Yu Zhou
- Institute for Advanced Ceramics, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, PR China
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229
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Hariri AA, Hamblin GD, Hardwick JS, Godin R, Desjardins JF, Wiseman PW, Sleiman HF, Cosa G. Stoichiometry and Dispersity of DNA Nanostructures Using Photobleaching Pair-Correlation Analysis. Bioconjug Chem 2017; 28:2340-2349. [DOI: 10.1021/acs.bioconjchem.7b00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | | | - Jean-Francois Desjardins
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 0B8, Canada
| | - Paul W. Wiseman
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 0B8, Canada
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230
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231
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Jenkinson DR, Cadby AJ, Jones S. The Synthesis and Photophysical Analysis of a Series of 4-Nitrobenzochalcogenadiazoles for Super-Resolution Microscopy. Chemistry 2017; 23:12585-12592. [PMID: 28703339 DOI: 10.1002/chem.201702289] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 11/07/2022]
Abstract
A series of 4-nitrobenzodiazoles with atomic substitution through the chalcogen group were synthesised and their photophysical properties analysed with a view for use in single-molecule localisation microscopy. Sub-diffraction resolution imaging was achieved for silica nanoparticles coated with each dye. Those containing larger atoms were favoured for super-resolution microscopy due to a reduced blink rate (required for stochastic events to be localised). The sulfur-containing molecule was deemed most amenable for widespread use due to the ease of synthetic manipulation compared to the selenium-containing derivative.
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Affiliation(s)
- Daniel Ray Jenkinson
- Department of Chemistry, University of Sheffield, Dainton Building, Brook Hill, Sheffield, S3 7HF, UK.,Department of Physics and Astronomy, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield, S3 7RH, UK
| | - Ashley James Cadby
- Department of Physics and Astronomy, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield, S3 7RH, UK
| | - Simon Jones
- Department of Chemistry, University of Sheffield, Dainton Building, Brook Hill, Sheffield, S3 7HF, UK
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232
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Wang C, Taki M, Sato Y, Fukazawa A, Higashiyama T, Yamaguchi S. Super-Photostable Phosphole-Based Dye for Multiple-Acquisition Stimulated Emission Depletion Imaging. J Am Chem Soc 2017; 139:10374-10381. [PMID: 28741935 DOI: 10.1021/jacs.7b04418] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As stimulated emission depletion (STED) microscopy can provide structural details of cells with an optical resolution beyond the diffraction limit, it has become an indispensable tool in cell biology. However, the intense STED laser beam usually causes rapid photobleaching of the employed fluorescent dyes, which significantly limits the utility of STED microscopy from a practical perspective. Herein we report a new design of super-photostable dye, PhoxBright 430 (PB430), comprising a fully ring-fused π-conjugated skeleton with an electron-accepting phosphole P-oxide unit. We previously developed a super-photostable dye C-Naphox by combining the phosphole unit with an electron-donating triphenylamine moiety. In PB430, removal of the amino group alters the transition type from intramolecular charge transfer character to π-π* transition character, which gives rise to intense fluorescence insensitive to molecular environment in terms of fluorescence colors and intensity, and bright fluorescence even in aqueous media. PB430 also furnishes high solubility in water, and is capable of labeling proteins with maintaining high fluorescence quantum yields. This dye exhibits outstanding resistance to photoirradiation even under the STED conditions and allows continuous acquisition of STED images. Indeed, using a PB430-conjugated antibody, we succeed in attaining a 3-D reconstruction of super-resolution STED images as well as photostability-based multicolor STED imaging of fluorescently labeled cytoskeletal structures.
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Affiliation(s)
- Chenguang Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan
| | - Masayasu Taki
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan
| | - Aiko Fukazawa
- Department of Chemistry, Graduate School of Science, Nagoya University , Furo, Chikusa, Nagoya 464-8602, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University , Furo, Chikusa, Nagoya 464-8602, Japan
| | - Shigehiro Yamaguchi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University , Furo, Chikusa, Nagoya 464-8501, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University , Furo, Chikusa, Nagoya 464-8602, Japan
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233
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Goudsmits JMH, van Oijen AM, Slotboom DJ. Single-Molecule Fluorescence Studies of Membrane Transporters Using Total Internal Reflection Microscopy. Methods Enzymol 2017; 594:101-121. [PMID: 28779837 DOI: 10.1016/bs.mie.2017.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Cells are delineated by a lipid bilayer that physically separates the inside from the outer environment. Most polar, charged, or large molecules require proteins to reduce the energetic barrier for passage across the membrane and to achieve transport rates that are relevant for life. Here, we describe techniques to visualize the functioning of membrane transport proteins with fluorescent probes at the single-molecule level. First, we explain how to produce membrane-reconstituted transporters with fluorescent labels. Next, we detail the construction of a microfluidic flow cell to image immobilized proteoliposomes on a total internal reflection fluorescence microscope. We conclude by describing the methods that are needed to analyze fluorescence movies and obtain useful single-molecule data.
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234
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Agarwal K, Prasad DK. Eigen-analysis reveals components supporting super-resolution imaging of blinking fluorophores. Sci Rep 2017; 7:4445. [PMID: 28667336 PMCID: PMC5493635 DOI: 10.1038/s41598-017-04544-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022] Open
Abstract
This paper presents eigen-analysis of image stack of blinking fluorophores to identify the components that enable super-resolved imaging of blinking fluorophores. Eigen-analysis reveals that the contributions of spatial distribution of fluorophores and their temporal photon emission characteristics can be completely separated. While cross-emitter cross-pixel information of spatial distribution that permits super-resolution is encoded in two matrices, temporal statistics weigh the contribution of these matrices to the measured data. The properties and conditions of exploitation of these matrices are investigated. Con-temporary super-resolution imaging methods that use blinking for super-resolution are studied in the context of the presented analysis. Besides providing insight into the capabilities and limitations of existing super-resolution methods, the analysis shall help in designing better super-resolution techniques that directly exploit these matrices.
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Affiliation(s)
- Krishna Agarwal
- BioSystems and Micromechanics Inter-Disciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore. .,Department of Physics and Technology, UiT-The Arctic University of Norway, 9037, Tromsø, Norway.
| | - Dilip K Prasad
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
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235
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Han D, Crouch GM, Fu K, Zaino Iii LP, Bohn PW. Single-molecule spectroelectrochemical cross-correlation during redox cycling in recessed dual ring electrode zero-mode waveguides. Chem Sci 2017; 8:5345-5355. [PMID: 28970913 PMCID: PMC5609146 DOI: 10.1039/c7sc02250f] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/18/2017] [Indexed: 11/21/2022] Open
Abstract
The ability of zero-mode waveguides (ZMW) to guide light into subwavelength-diameter nanoapertures has been exploited for studying electron transfer dynamics in zeptoliter-volume nanopores under single-molecule occupancy conditions. In this work, we report the spectroelectrochemical detection of individual molecules of the redox-active, fluorogenic molecule flavin mononucleotide (FMN) freely diffusing in solution. Our approach is based on an array of nanopore-confined recessed dual ring electrodes, wherein repeated reduction and oxidation of a single molecule at two closely spaced annular working electrodes yields amplified electrochemical signals. We have articulated these structures with an optically transparent bottom, so that the nanopores are bifunctional, exhibiting both nanophotonic and nanoelectrochemical behaviors allowing the coupling between electron transfer and fluorescence dynamics to be studied under redox cycling conditions. We also investigated the electric field intensity in electrochemical ZMWs (E-ZMW) through finite-element simulations, and the amplification of fluorescence by redox cycling agrees well with predictions based on optical confinement effects inside the E-ZMW. Proof-of-principle experiments are conducted showing that electrochemical and fluorescence signals may be correlated to reveal single molecule fluctuations in the array population. Cross-correlation of single molecule fluctuations in amperometric response and single photon emission provides unequivocal evidence of single molecule sensitivity.
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Affiliation(s)
- Donghoon Han
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , IN 46556 , USA . ; ; Tel: +1 574 631 1849
| | - Garrison M Crouch
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , IN 46556 , USA . ; ; Tel: +1 574 631 1849
| | - Kaiyu Fu
- Departmemt of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN 46556 , USA
| | - Lawrence P Zaino Iii
- Departmemt of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN 46556 , USA
| | - Paul W Bohn
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , IN 46556 , USA . ; ; Tel: +1 574 631 1849.,Departmemt of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , IN 46556 , USA
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236
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Lee A, Tsekouras K, Calderon C, Bustamante C, Pressé S. Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis. Chem Rev 2017; 117:7276-7330. [PMID: 28414216 PMCID: PMC5487374 DOI: 10.1021/acs.chemrev.6b00729] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Super-resolution microscopy provides direct insight into fundamental biological processes occurring at length scales smaller than light's diffraction limit. The analysis of data at such scales has brought statistical and machine learning methods into the mainstream. Here we provide a survey of data analysis methods starting from an overview of basic statistical techniques underlying the analysis of super-resolution and, more broadly, imaging data. We subsequently break down the analysis of super-resolution data into four problems: the localization problem, the counting problem, the linking problem, and what we've termed the interpretation problem.
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Affiliation(s)
- Antony Lee
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, United States
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California at Berkeley, Berkeley, California 94720, United States
| | - Konstantinos Tsekouras
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | | | - Carlos Bustamante
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California at Berkeley, Berkeley, California 94720, United States
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, United States
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, United States
- Kavli Energy Nanosciences Institute, University of California at Berkeley, Berkeley, California 94720, United States
| | - Steve Pressé
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Department of Cell and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
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237
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Lu J, Zong S, Wang Z, Chen C, Zhang Y, Cui Y. Yolk-shell type nanoprobe with excellent fluorescence 'blinking' behavior for optical super resolution imaging. NANOTECHNOLOGY 2017; 28:265701. [PMID: 28593936 DOI: 10.1088/1361-6528/aa7536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A new yolk-shell type nanoprobe for super-resolution imaging is demonstrated. Using the proposed nanoprobe and single molecule localization based super resolution imaging strategy, intracellular nanoparticle tracking and super-resolution imaging are realized. The localization precision is about 50 nm and single-molecule localization microscopy using the proposed nanoprobe requires only one single excitation laser and no specific imaging buffer.
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Affiliation(s)
- Ju Lu
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, People's Republic of China
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238
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Klementieva NV, Bozhanova NG, Zagaynova EV, Lukyanov KA, Mishin AS. Fluorophores for single-molecule localization microscopy. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017030074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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239
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Bourgeois D. Deciphering Structural Photophysics of Fluorescent Proteins by Kinetic Crystallography. Int J Mol Sci 2017; 18:ijms18061187. [PMID: 28574447 PMCID: PMC5486010 DOI: 10.3390/ijms18061187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 01/02/2023] Open
Abstract
Because they enable labeling of biological samples in a genetically-encoded manner, Fluorescent Proteins (FPs) have revolutionized life sciences. Photo-transformable fluorescent proteins (PTFPs), in particular, recently attracted wide interest, as their fluorescence state can be actively modulated by light, a property central to the emergence of super-resolution microscopy. PTFPs, however, exhibit highly complex photophysical behaviours that are still poorly understood, hampering the rational engineering of variants with improved performances. We show that kinetic crystallography combined with in crystallo optical spectroscopy, modeling approaches and single-molecule measurements constitutes a powerful tool to decipher processes such as photoactivation, photoconversion, photoswitching, photoblinking and photobleaching. Besides potential applications for the design of enhanced PTFPs, these investigations provide fundamental insight into photoactivated protein dynamics.
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Affiliation(s)
- Dominique Bourgeois
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, CNRS, IBS, F-38000 Grenoble, France.
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240
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Woehrstein JB, Strauss MT, Ong LL, Wei B, Zhang DY, Jungmann R, Yin P. Sub-100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA. SCIENCE ADVANCES 2017; 3:e1602128. [PMID: 28691083 PMCID: PMC5479647 DOI: 10.1126/sciadv.1602128] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 04/28/2017] [Indexed: 05/21/2023]
Abstract
Fluorescence microscopy allows specific target detection down to the level of single molecules and has become an enabling tool in biological research. To transduce the biological information to an imageable signal, we have developed a variety of fluorescent probes, such as organic dyes or fluorescent proteins with different colors. Despite their success, a limitation on constructing small fluorescent probes is the lack of a general framework to achieve precise and programmable control of critical optical properties, such as color and brightness. To address this challenge, we introduce metafluorophores, which are constructed as DNA nanostructure-based fluorescent probes with digitally tunable optical properties. Each metafluorophore is composed of multiple organic fluorophores, organized in a spatially controlled fashion in a compact sub-100-nm architecture using a DNA nanostructure scaffold. Using DNA origami with a size of 90 × 60 nm2, substantially smaller than the optical diffraction limit, we constructed small fluorescent probes with digitally tunable brightness, color, and photostability and demonstrated a palette of 124 virtual colors. Using these probes as fluorescent barcodes, we implemented an assay for multiplexed quantification of nucleic acids. Additionally, we demonstrated the triggered in situ self-assembly of fluorescent DNA nanostructures with prescribed brightness upon initial hybridization to a nucleic acid target.
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Affiliation(s)
- Johannes B. Woehrstein
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Physics and Center for NanoScience, Ludwig Maximilian University, 80539 Munich, Germany
- Max Planck Institute of Biochemistry, 82152 Martinsried near Munich, Germany
| | - Maximilian T. Strauss
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Physics and Center for NanoScience, Ludwig Maximilian University, 80539 Munich, Germany
- Max Planck Institute of Biochemistry, 82152 Martinsried near Munich, Germany
| | - Luvena L. Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bryan Wei
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David Y. Zhang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ralf Jungmann
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Physics and Center for NanoScience, Ludwig Maximilian University, 80539 Munich, Germany
- Max Planck Institute of Biochemistry, 82152 Martinsried near Munich, Germany
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author. (P.Y.); (R.J.)
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author. (P.Y.); (R.J.)
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241
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Djorović A, Meyer M, Darby BL, Le Ru EC. Accurate Modeling of the Polarizability of Dyes for Electromagnetic Calculations. ACS OMEGA 2017; 2:1804-1811. [PMID: 31457544 PMCID: PMC6640948 DOI: 10.1021/acsomega.7b00171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/25/2017] [Indexed: 06/10/2023]
Abstract
The wavelength-dependent complex linear polarizability of a dye is a crucial input for the modeling of the optical properties of dye-containing systems. We here propose and discuss methods to obtain an accurate polarizability model by combining absorption spectrum measurements, Kramers-Kronig (KK) tranformations, and density functional theory (DFT) calculations. We focus, in particular, on the real part of the polarizability and its link with static polarizability. In addition, we introduce simple KK-consistent analytic functions based on the theory of critical points as a much more accurate approach to model dye polarizabilities compared with existing models based on Lorentz oscillators. Accurate polarizability models based on critical points and DFT calculations of the static polarizability are derived for five commonly used dyes: Rhodamine 6G, Rhodamine 700, Crystal Violet, Nile Blue A, and Methylene Blue. Finally, we demonstrate explicitly, using examples of Mie Theory calculations of nanoparticle-dye interactions, how an inaccurate polarizability model can result in fundamentally different predictions, further emphasizing the importance of accurate models, such as the one proposed here.
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242
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Woodford O, Harriman A, McFarlane W, Wills C. Dramatic Effect of Solvent on the Rate of Photobleaching of Organic Pyrrole-BF2(BOPHY) Dyes. CHEMPHOTOCHEM 2017. [DOI: 10.1002/cptc.201600061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Owen Woodford
- Molecular Photonics Laboratory, School of Chemistry; Newcastle University; Newcastle upon Tyne NE1 7RU UK
| | - Anthony Harriman
- Molecular Photonics Laboratory, School of Chemistry; Newcastle University; Newcastle upon Tyne NE1 7RU UK
| | - William McFarlane
- NMR Laboratory, School of Chemistry; Newcastle University; Newcastle upon Tyne NE1 7RU UK
| | - Corinne Wills
- NMR Laboratory, School of Chemistry; Newcastle University; Newcastle upon Tyne NE1 7RU UK
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243
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Zheng Q, Lavis LD. Development of photostable fluorophores for molecular imaging. Curr Opin Chem Biol 2017; 39:32-38. [PMID: 28544971 DOI: 10.1016/j.cbpa.2017.04.017] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/18/2017] [Accepted: 04/25/2017] [Indexed: 10/19/2022]
Abstract
Advances in fluorescence microscopy promise to unlock details of biological systems with high spatiotemporal precision. These new techniques also place a heavy demand on the 'photon budget'-the number of photons one can extract from a sample. Improving the photostability of small molecule fluorophores using chemistry is a straightforward method for increasing the photon budget. Here, we review the (sometimes sparse) efforts to understand the mechanism of fluorophore photobleaching and recent advances to improve photostability through reducing the propensity for oxidation or through intramolecular triplet-state quenching. Our intent is to inspire a more thorough mechanistic investigation of photobleaching and the use of precise chemistry to improve fluorescent probes.
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Affiliation(s)
- Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr., Ashburn, VA 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr., Ashburn, VA 20147, USA.
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244
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245
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Shen H, Tauzin LJ, Baiyasi R, Wang W, Moringo N, Shuang B, Landes CF. Single Particle Tracking: From Theory to Biophysical Applications. Chem Rev 2017; 117:7331-7376. [PMID: 28520419 DOI: 10.1021/acs.chemrev.6b00815] [Citation(s) in RCA: 277] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
After three decades of developments, single particle tracking (SPT) has become a powerful tool to interrogate dynamics in a range of materials including live cells and novel catalytic supports because of its ability to reveal dynamics in the structure-function relationships underlying the heterogeneous nature of such systems. In this review, we summarize the algorithms behind, and practical applications of, SPT. We first cover the theoretical background including particle identification, localization, and trajectory reconstruction. General instrumentation and recent developments to achieve two- and three-dimensional subdiffraction localization and SPT are discussed. We then highlight some applications of SPT to study various biological and synthetic materials systems. Finally, we provide our perspective regarding several directions for future advancements in the theory and application of SPT.
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Affiliation(s)
- Hao Shen
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Lawrence J Tauzin
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Rashad Baiyasi
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Wenxiao Wang
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Nicholas Moringo
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Bo Shuang
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Christy F Landes
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
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246
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Nickels PC, Wünsch B, Holzmeister P, Bae W, Kneer LM, Grohmann D, Tinnefeld P, Liedl T. Molecular force spectroscopy with a DNA origami-based nanoscopic force clamp. Science 2017; 354:305-307. [PMID: 27846560 DOI: 10.1126/science.aah5974] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/06/2016] [Indexed: 11/02/2022]
Abstract
Forces in biological systems are typically investigated at the single-molecule level with atomic force microscopy or optical and magnetic tweezers, but these techniques suffer from limited data throughput and their requirement for a physical connection to the macroscopic world. We introduce a self-assembled nanoscopic force clamp built from DNA that operates autonomously and allows massive parallelization. Single-stranded DNA sections of an origami structure acted as entropic springs and exerted controlled tension in the low piconewton range on a molecular system, whose conformational transitions were monitored by single-molecule Förster resonance energy transfer. We used the conformer switching of a Holliday junction as a benchmark and studied the TATA-binding protein-induced bending of a DNA duplex under tension. The observed suppression of bending above 10 piconewtons provides further evidence of mechanosensitivity in gene regulation.
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Affiliation(s)
- Philipp C Nickels
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Bettina Wünsch
- Institut für Physikalische und Theoretische Chemie, Braunschweig Integrated Centre of Systems Biology, and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Phil Holzmeister
- Institut für Physikalische und Theoretische Chemie, Braunschweig Integrated Centre of Systems Biology, and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Wooli Bae
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Luisa M Kneer
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Dina Grohmann
- Institut für Physikalische und Theoretische Chemie, Braunschweig Integrated Centre of Systems Biology, and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Philip Tinnefeld
- Institut für Physikalische und Theoretische Chemie, Braunschweig Integrated Centre of Systems Biology, and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany.
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany.
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Zhang Z, Yomo D, Gradinaru C. Choosing the right fluorophore for single-molecule fluorescence studies in a lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1242-1253. [PMID: 28392350 DOI: 10.1016/j.bbamem.2017.04.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/14/2017] [Accepted: 04/05/2017] [Indexed: 10/19/2022]
Abstract
Nonspecific interactions between lipids and fluorophores can alter the outcomes of single-molecule spectroscopy of membrane proteins in live cells, liposomes or lipid nanodiscs and of cytosolic proteins encapsulated in liposomes or tethered to supported lipid bilayers. To gain insight into these effects, we examined interactions between 9 dyes that are commonly used as labels for single-molecule fluorescence (SMF) and 6 standard lipids including cationic, zwitterionic and anionic types. The diffusion coefficients of dyes in the absence and presence of set amounts of lipid vesicles were measured by fluorescence correlation spectroscopy (FCS). The partition coefficients and the free energies of partitioning for different fluorophore-lipid pairs were obtained by global fitting of the titration FCS curves. Lipids with different charges, head groups and degrees of chain saturation were investigated, and interactions with dyes are discussed in terms of hydrophobic, electrostatic and steric contributions. Fluorescence imaging of individual fluorophores adsorbed on supported lipid bilayers provides visualization and additional quantification of the strength of dye-lipid interaction in the context of single-molecule measurements. By dissecting fluorophore-lipid interactions, our study provides new insights into setting up single-molecule fluorescence spectroscopy experiments with minimal interference from interactions between fluorescent labels and lipids in the environment.
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Affiliation(s)
- Zhenfu Zhang
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Dan Yomo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Claudiu Gradinaru
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada.
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248
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SPAD imagers for super resolution localization microscopy enable analysis of fast fluorophore blinking. Sci Rep 2017; 7:44108. [PMID: 28287122 PMCID: PMC5347095 DOI: 10.1038/srep44108] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/01/2017] [Indexed: 11/16/2022] Open
Abstract
sCMOS imagers are currently utilized (replacing EMCCD imagers) to increase the acquisition speed in super resolution localization microscopy. Single-photon avalanche diode (SPAD) imagers feature frame rates per bit depth comparable to or higher than sCMOS imagers, while generating microsecond 1-bit-frames without readout noise, thus paving the way to in-depth time-resolved image analysis. High timing resolution can also be exploited to explore fluorescent dye blinking and other photophysical properties, which can be used for dye optimization. We present the methodology for the blinking analysis of fluorescent dyes on experimental data. Furthermore, the recent use of microlenses has enabled a substantial increase of SPAD imager overall sensitivity (12-fold in our case), reaching satisfactory values for sensitivity-critical applications. This has allowed us to record the first super resolution localization microscopy results obtained with a SPAD imager, with a localization uncertainty of 20 nm and a resolution of 80 nm.
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249
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Abstract
Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology & Biophysics, Julius-Maximilian-University of Würzburg , 97074 Würzburg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt , 60438 Frankfurt, Germany
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Chamma I, Rossier O, Giannone G, Thoumine O, Sainlos M. Optimized labeling of membrane proteins for applications to super-resolution imaging in confined cellular environments using monomeric streptavidin. Nat Protoc 2017; 12:748-763. [DOI: 10.1038/nprot.2017.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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