51
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Cheng X, Wang J, Li Q, Duan Y, Chen Y, Teng J, Chu S, Yang H, Wang S, Gong Q. Enhancing Weak-Signal Extraction for Single-Molecule Localization Microscopy. J Phys Chem A 2023; 127:329-338. [PMID: 36541035 DOI: 10.1021/acs.jpca.2c05164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-molecule localization microscopy (SMLM) has been widely used in biological imaging due to its ultrahigh spatial resolution. However, due to the strategy of reducing photodamage to living cells, the fluorescence signals of emitters are usually weak and the detector noises become non-negligible, which leads to localization misalignments and signal losses, thus deteriorating the imaging capability of SMLM. Here, we propose an active modulation method to control the fluorescence of the probe emitters. It actually marks the emitters with artificial blinking character, which directly distinguishes weak signals from multiple detector noises. We demonstrated from simulations and experiments that this method improves the signal-to-noise ratio by about 10 dB over the non-modulated method and boosts the sensitivity of single-molecule localization down to -4 dB, which significantly reduces localization misalignments and signal losses in SMLM. This signal-noise decoupling strategy is generally applicable to the super-resolution system with versatile labeled probes to improve their imaging capability. We also showed its application to the densely labeled sample, showing its flexibility in super-resolution nanoscopy.
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Affiliation(s)
- Xue Cheng
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Ju Wang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Qi Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing100871, China
| | - Yiqun Duan
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Yan Chen
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Junlin Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing100871, China
| | - Saisai Chu
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
| | - Hong Yang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
| | - Shufeng Wang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
| | - Qihuang Gong
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
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52
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Püntener S, Rivera-Fuentes P. Single-Molecule Peptide Identification Using Fluorescence Blinking Fingerprints. J Am Chem Soc 2023; 145:1441-1447. [PMID: 36603184 PMCID: PMC9853850 DOI: 10.1021/jacs.2c12561] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The ability to identify peptides with single-molecule sensitivity would lead to next-generation proteomics methods for basic research and clinical applications. Existing single-molecule peptide sequencing methods can read some amino acid sequences, but they are limited in their ability to distinguish between similar amino acids or post-translational modifications. Here, we demonstrate that the fluorescence intermittency of a peptide labeled with a spontaneously blinking fluorophore contains information about the structure of the peptide. Using a deep learning algorithm, this single-molecule blinking pattern can be used to identify the peptide. This method can distinguish between peptides with different sequences, peptides with the same sequence but different phosphorylation patterns, and even peptides that differ only by the presence of epimerized residues. This study builds the foundation for a targeted proteomics method with single-molecule sensitivity.
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Affiliation(s)
- Salome Püntener
- Institute
of Chemical Sciences and Engineering, Ecole
Polytechnique Fédéral de Lausanne, CH-1015 Lausanne, Switzerland,Department
of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Pablo Rivera-Fuentes
- Institute
of Chemical Sciences and Engineering, Ecole
Polytechnique Fédéral de Lausanne, CH-1015 Lausanne, Switzerland,Department
of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland,
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53
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Kikuchi K, Adair LD, Lin J, New EJ, Kaur A. Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy. Angew Chem Int Ed Engl 2023; 62:e202204745. [PMID: 36177530 PMCID: PMC10100239 DOI: 10.1002/anie.202204745] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 02/02/2023]
Abstract
Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.
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Affiliation(s)
- Kai Kikuchi
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liam D Adair
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jiarun Lin
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth J New
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Amandeep Kaur
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
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54
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Podh NK, Das A, Dey P, Paliwal S, Mehta G. Single-molecule tracking for studying protein dynamics and target-search mechanism in live cells of S. cerevisiae. STAR Protoc 2022; 3:101900. [PMID: 36595957 PMCID: PMC9732415 DOI: 10.1016/j.xpro.2022.101900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/22/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Single-molecule tracking (SMT) is a powerful approach to quantify the biophysical parameters of protein dynamics in live cells. Here, we describe a protocol for SMT in live cells of the budding yeast Saccharomyces cerevisiae. We detail how to genetically engineer yeast strains for SMT, how to set up image acquisition parameters, and how different software programs can be used to quantify a variety of biophysical parameters such as diffusion coefficient, residence time, bound fraction, jump angles, and target-search parameters. For complete details on the use and execution of this protocol, please refer to Mehta et al. 1 and Ball et al..2.
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Affiliation(s)
- Nitesh Kumar Podh
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Ayan Das
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Partha Dey
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Sheetal Paliwal
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Gunjan Mehta
- Laboratory of Chromosome Dynamics and Gene Regulation, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India,Corresponding author
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55
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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56
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Gandin V, English BP, Freeman M, Leroux LP, Preibisch S, Walpita D, Jaramillo M, Singer RH. Cap-dependent translation initiation monitored in living cells. Nat Commun 2022; 13:6558. [PMID: 36323665 PMCID: PMC9630388 DOI: 10.1038/s41467-022-34052-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 10/06/2022] [Indexed: 11/19/2022] Open
Abstract
mRNA translation is tightly regulated to preserve cellular homeostasis. Despite extensive biochemical, genetic, and structural studies, a detailed understanding of mRNA translation regulation is lacking. Imaging methodologies able to resolve the binding dynamics of translation factors at single-cell and single-mRNA resolution were necessary to fully elucidate regulation of this paramount process. Here live-cell spectroscopy and single-particle tracking were combined to interrogate the binding dynamics of endogenous initiation factors to the 5'cap. The diffusion of initiation factors (IFs) changed markedly upon their association with mRNA. Quantifying their diffusion characteristics revealed the sequence of IFs assembly and disassembly in cell lines and the clustering of translation in neurons. This approach revealed translation regulation at high spatial and temporal resolution that can be applied to the formation of any endogenous complex that results in a measurable shift in diffusion.
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Affiliation(s)
- Valentina Gandin
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Brian P. English
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Melanie Freeman
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Louis-Philippe Leroux
- grid.418084.10000 0000 9582 2314Institut National de la Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie (CAFSB), Laval, QC Canada
| | - Stephan Preibisch
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Deepika Walpita
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
| | - Maritza Jaramillo
- grid.418084.10000 0000 9582 2314Institut National de la Recherche Scientifique (INRS)-Centre Armand-Frappier Santé Biotechnologie (CAFSB), Laval, QC Canada
| | - Robert H. Singer
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA
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57
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Vecchia MD, Conte-Daban A, Cappe B, Vandenberg W, Vandenabeele P, Riquet FB, Dedecker P. Spectrally Tunable Förster Resonance Energy Transfer-Based Biosensors Using Organic Dye Grafting. ACS Sens 2022; 7:2920-2927. [PMID: 36162130 DOI: 10.1021/acssensors.2c00066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Biosensors based on Förster resonance energy transfer (FRET) have revolutionized cellular biology by allowing the direct measurement of biochemical processes in situ. Many genetically encoded sensors make use of fluorescent proteins that are limited in spectral versatility and that allow few ways to change the spectral properties once the construct has been created. In this work, we developed genetically encoded FRET biosensors based on the chemigenetic SNAP and HaloTag domains combined with matching organic fluorophores. We found that the resulting constructs can display comparable responses, kinetics, and reversibility compared to their fluorescent protein-based ancestors, but with the added advantage of spectral versatility, including the availability of red-shifted dye pairs. However, we also find that the introduction of these tags can alter the sensor readout, showing that careful validation is required before applying such constructs in practice. Overall, our approach delivers an innovative methodology that can readily expand the spectral variety and versatility of FRET-based biosensors.
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Affiliation(s)
- Marco Dalla Vecchia
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium.,Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | | | - Benjamin Cappe
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Wim Vandenberg
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Franck B Riquet
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Peter Dedecker
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
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58
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Abstract
Strategies to visualize cellular membranes with light microscopy are restricted by the diffraction limit of light, which far exceeds the dimensions of lipid bilayers. Here, we describe a method for super-resolution imaging of metabolically labeled phospholipids within cellular membranes. Guided by the principles of expansion microscopy, we develop an all-small molecule approach that enables direct chemical anchoring of bioorthogonally labeled phospholipids into a hydrogel network and is capable of super-resolution imaging of cellular membranes. We apply this method, termed lipid expansion microscopy (LExM), to visualize organelle membranes with precision, including a unique class of membrane-bound structures known as nuclear invaginations. Compatible with standard confocal microscopes, LExM will be widely applicable for super-resolution imaging of phospholipids and cellular membranes in numerous physiological contexts.
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Affiliation(s)
- Brittany M White
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Pratik Kumar
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, United States
| | - Amanda N Conwell
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kane Wu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
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59
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Aparin IO, Yan R, Pelletier R, Choi AA, Danylchuk DI, Xu K, Klymchenko AS. Fluorogenic Dimers as Bright Switchable Probes for Enhanced Super-Resolution Imaging of Cell Membranes. J Am Chem Soc 2022; 144:18043-18053. [PMID: 36153973 DOI: 10.1021/jacs.2c07542] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Super-resolution fluorescence imaging based on single-molecule localization microscopy (SMLM) enables visualizing cellular structures with nanometric precision. However, its spatial and temporal resolution largely relies on the brightness of ON/OFF switchable fluorescent dyes. Moreover, in cell plasma membranes, the single-molecule localization is hampered by the fast lateral diffusion of membrane probes. Here, to address these two fundamental problems, we propose a concept of ON/OFF switchable probes for SMLM (points accumulation for imaging in nanoscale topography, PAINT) based on fluorogenic dimers of bright cyanine dyes. In these probes, the two cyanine units connected with a linker were modified at their extremities with low-affinity membrane anchors. Being self-quenched in water due to intramolecular dye H-aggregation, they displayed light up on reversible binding to lipid membranes. The charged group in the linker further decreased the probe affinity to the lipid membranes, thus accelerating its dynamic reversible ON/OFF switching. The concept was validated on cyanines 3 and 5. SMLM of live cells revealed that the new probes provided higher brightness and ∼10-fold slower diffusion at the cell surface, compared to reference probes Nile Red and DiD, which boosted axial localization precision >3-fold down to 31 nm. The new probe allowed unprecedented observation of nanoscale fibrous protrusions on plasma membranes of live cells with 40 s time resolution, revealing their fast dynamics. Thus, going beyond the brightness limit of single switchable dyes by cooperative dequenching in fluorogenic dimers and slowing down probe diffusion in biomembranes open the route to significant enhancement of super-resolution fluorescence microscopy of live cells.
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Affiliation(s)
- Ilya O Aparin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Alexander A Choi
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
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60
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Mo J, Chen J, Shi Y, Sun J, Wu Y, Liu T, Zhang J, Zheng Y, Li Y, Chen Z. Third-Generation Covalent TMP-Tag for Fast Labeling and Multiplexed Imaging of Cellular Proteins. Angew Chem Int Ed Engl 2022; 61:e202207905. [PMID: 35816052 DOI: 10.1002/anie.202207905] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Indexed: 11/10/2022]
Abstract
Self-labeling protein tags can introduce advanced molecular motifs to specific cellular proteins. Here we introduce the third-generation covalent TMP-tag (TMP-tag3) and showcase its comparison with HaloTag and SNAP-tag. TMP-tag3 is based on a proximity-induced covalent Michael addition between an engineered Cys of E. coli dihydrofolate reductase (eDHFR) and optimized trimethoprim (TMP)-acrylamide conjugates with minimal linkers. Compared to previous versions, the TMP-tag3 features an enhanced permeability when conjugated to fluorogenic spirocyclic rhodamines. As a small protein, the 18-kD eDHFR is advantageous in tagging selected mitochondrial proteins which are less compatible with bulkier HaloTag fusions. The proximal N-C termini of eDHFR also enable facile insertion into various protein loops. TMP-tag3, HaloTag, and SNAP-tag are orthogonal to each other, collectively forming a toolbox for multiplexed live-cell imaging of cellular proteins under fluorescence nanoscopy.
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Affiliation(s)
- Jiaming Mo
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Jingting Chen
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Yabo Shi
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Jingfu Sun
- PKU-Nanjing Institute of Translational Medicine, Nanjing, 211800, Jiangsu, China
| | - Yunxiang Wu
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Tianyan Liu
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China
| | - Junwei Zhang
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Yu Zheng
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China.,State Key Laboratory of Membrane Biology, PKU-IDG/McGovern Institute for Brain Research, School of Life Science, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Yulong Li
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China.,State Key Laboratory of Membrane Biology, PKU-IDG/McGovern Institute for Brain Research, School of Life Science, Peking University, Yiheyuan Road No.5, Beijing, 100871, China.,Chinese Institute for Brain Research, Beijing, 102206, China
| | - Zhixing Chen
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China.,PKU-Nanjing Institute of Translational Medicine, Nanjing, 211800, Jiangsu, China.,Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China
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61
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A serotonergic axon-cilium synapse drives nuclear signaling to alter chromatin accessibility. Cell 2022; 185:3390-3407.e18. [PMID: 36055200 PMCID: PMC9789380 DOI: 10.1016/j.cell.2022.07.026] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 05/16/2022] [Accepted: 07/25/2022] [Indexed: 12/27/2022]
Abstract
Chemical synapses between axons and dendrites mediate neuronal intercellular communication. Here, we describe a synapse between axons and primary cilia: the axo-ciliary synapse. Using enhanced focused ion beam-scanning electron microscopy on samples with optimally preserved ultrastructure, we discovered synapses between brainstem serotonergic axons and the primary cilia of hippocampal CA1 pyramidal neurons. Functionally, these cilia are enriched in a ciliary-restricted serotonin receptor, the 5-hydroxytryptamine receptor 6 (5-HTR6). Using a cilia-targeted serotonin sensor, we show that opto- and chemogenetic stimulation of serotonergic axons releases serotonin onto cilia. Ciliary 5-HTR6 stimulation activates a non-canonical Gαq/11-RhoA pathway, which modulates nuclear actin and increases histone acetylation and chromatin accessibility. Ablation of this pathway reduces chromatin accessibility in CA1 pyramidal neurons. As a signaling apparatus with proximity to the nucleus, axo-ciliary synapses short circuit neurotransmission to alter the postsynaptic neuron's epigenetic state.
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62
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Roßmann K, Akkaya KC, Poc P, Charbonnier C, Eichhorst J, Gonschior H, Valavalkar A, Wendler N, Cordes T, Dietzek-Ivanšić B, Jones B, Lehmann M, Broichhagen J. N-Methyl deuterated rhodamines for protein labelling in sensitive fluorescence microscopy. Chem Sci 2022; 13:8605-8617. [PMID: 35974762 PMCID: PMC9337740 DOI: 10.1039/d1sc06466e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/02/2022] [Indexed: 11/21/2022] Open
Abstract
Rhodamine fluorophores are setting benchmarks in fluorescence microscopy. Herein, we report the deuterium (d12) congeners of tetramethyl(silicon)rhodamine, obtained by isotopic labelling of the four methyl groups, show improved photophysical parameters (i.e. brightness, lifetimes) and reduced chemical bleaching. We explore this finding for SNAP- and Halo-tag labelling in live cells, and highlight enhanced properties in several applications, such as fluorescence activated cell sorting, fluorescence lifetime microscopy, stimulated emission depletion nanoscopy and single-molecule Förster-resonance energy transfer. We finally extend this idea to other dye families and envision deuteration as a generalizable concept to improve existing and to develop new chemical biology probes.
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Affiliation(s)
- Kilian Roßmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Kerem C Akkaya
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Pascal Poc
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | | | - Jenny Eichhorst
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Hannes Gonschior
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Abha Valavalkar
- Leibniz Institute for Photonic Technology Jena e.V. (Leibniz-IPHT), Research Department Functional Interfaces Jena Germany
| | - Nicolas Wendler
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München Großhaderner Str. 2-4, Planegg-Martinsried 82152 Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München Großhaderner Str. 2-4, Planegg-Martinsried 82152 Germany
| | - Benjamin Dietzek-Ivanšić
- Leibniz Institute for Photonic Technology Jena e.V. (Leibniz-IPHT), Research Department Functional Interfaces Jena Germany
| | - Ben Jones
- Section of Endocrinology and Investigative Medicine, Imperial College London London W12 0NN UK
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie Berlin Germany
- Department of Chemical Biology, Max Planck Institute for Medical Research Heidelberg Germany
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63
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Sun D, Yang S, Ma J, Liu C, Sun J, Li Y, Deng F. A general approach to S-rhodamines from diaryl thioethers and their application in constructing pH probes. Org Biomol Chem 2022; 20:5694-5698. [PMID: 35820176 DOI: 10.1039/d2ob01086k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general strategy for the efficient preparation of S-rhodamines from the condensation of diaryl thioether and 2-carboxybenzaldehydes was reported. We further took a morpholine containing spirolactam structure as an example to illustrate that these S-rhodamine dyes could be utilized to construct fluorescent probes based on the ring-opening process. This work provided a general approach for the synthesis of novel S-rhodamine dyes, thus possibly facilitating the development of fluorescence imaging.
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Affiliation(s)
- Dongsheng Sun
- Department of Basic Medicine, Medical College, Taizhou University, Taizhou, Zhejiang 318000, China
| | - Shixu Yang
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China.
| | - Junxia Ma
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang 318000, China
| | - Can Liu
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China.
| | - Jiabing Sun
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China.
| | - Yulong Li
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China.
| | - Fei Deng
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China.
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64
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Song G, Nong DZ, Li JS, Li G, Zhang W, Cao R, Wang C, Xiao J, Xue D. General Method for the Amination of Aryl Halides with Primary and Secondary Alkyl Amines via Nickel Photocatalysis. J Org Chem 2022; 87:10285-10297. [PMID: 35877165 DOI: 10.1021/acs.joc.2c01284] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Buchwald-Hartwig C-N coupling reaction has been ranked as one of the 20 most frequently used reactions in medicinal chemistry. Owing to its much lower cost and higher reactivity toward less reactive aryl chlorides than palladium, the C-N coupling reaction catalyzed by Ni-based catalysts has received a great deal of attention. However, there appear to be no universal, practical Ni catalytic systems so far that could enable the coupling of electron-rich and electron-poor aryl halides with both primary and secondary alkyl amines. In this study, it is reported that a Ni(II)-bipyridine complex catalyzes efficient C-N coupling of aryl chlorides and bromides with various primary and secondary alkyl amines under direct excitation with light. Intramolecular C-N coupling is also demonstrated. The feasibility and applicability of the protocol in organic synthesis is attested by more than 200 examples.
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Affiliation(s)
- Geyang Song
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Ding-Zhan Nong
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Jing-Sheng Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Gang Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Wei Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Rui Cao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Chao Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Jianliang Xiao
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Dong Xue
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
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65
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Lincoln R, Bossi ML, Remmel M, D'Este E, Butkevich AN, Hell SW. A general design of caging-group-free photoactivatable fluorophores for live-cell nanoscopy. Nat Chem 2022; 14:1013-1020. [PMID: 35864152 PMCID: PMC9417988 DOI: 10.1038/s41557-022-00995-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
The controlled switching of fluorophores between non-fluorescent and fluorescent states is central to every super-resolution fluorescence microscopy (nanoscopy) technique, and the exploration of radically new switching mechanisms remains critical to boosting the performance of established, as well as emerging super-resolution methods. Photoactivatable dyes offer substantial improvements to many of these techniques, but often rely on photolabile protecting groups that limit their applications. Here we describe a general method to transform 3,6-diaminoxanthones into caging-group-free photoactivatable fluorophores. These photoactivatable xanthones (PaX) assemble rapidly and cleanly into highly fluorescent, photo- and chemically stable pyronine dyes upon irradiation with light. The strategy is extendable to carbon- and silicon-bridged xanthone analogues, yielding a family of photoactivatable labels spanning much of the visible spectrum. Our results demonstrate the versatility and utility of PaX dyes in fixed and live-cell labelling for conventional microscopy, as well as the coordinate-stochastic and deterministic nanoscopies STED, PALM and MINFLUX. ![]()
The design of photoactivatable fluorophores—which are required for some super-resolution fluorescence microscopy methods—usually relies on light-sensitive protecting groups imparting lipophilicity and generating reactive by-products. Now, it has been shown that by exploiting a unique intramolecular photocyclization, bright and highly photostable fluorophores can be rapidly generated in situ from appropriately substituted 1-alkenyl-3,6-diaminoxanthone precursors.
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Affiliation(s)
- Richard Lincoln
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Mariano L Bossi
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Michael Remmel
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Alexey N Butkevich
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany.
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany. .,Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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66
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Mo J, Chen J, Shi Y, Sun J, Wu Y, Liu T, Zhang J, Zheng Y, Li Y, Chen Z. Third‐Generation Covalent TMP‐Tag for Fast Labeling and Multiplexed Imaging of Cellular Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jiaming Mo
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Jingting Chen
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Yabo Shi
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Jingfu Sun
- PKU-Nanjing Institute of translational medicine n/a CHINA
| | - Yunxiang Wu
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Tianyan Liu
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Junwei Zhang
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Yu Zheng
- Peking University School of life science CHINA
| | - Yulong Li
- Peking University School of life science CHINA
| | - Zhixing Chen
- Peking University College of Future Technology 5 Yiheyuan Rd. 100871 Beijing CHINA
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67
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Vinod JK, Koide K. Mono‐
O
‐functionalizations of Pittsburgh Green and Their Applications. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jincy K. Vinod
- Department of Chemistry University of Pittsburgh 219 Parkman Avenue 15260 Pittsburgh Pennsylvania United States
| | - Kazunori Koide
- Department of Chemistry University of Pittsburgh 219 Parkman Avenue 15260 Pittsburgh Pennsylvania United States
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68
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Rao DN, Ji X, Miller SC. Silicon functionalization expands the repertoire of Si-rhodamine fluorescent probes. Chem Sci 2022; 13:6081-6088. [PMID: 35685786 PMCID: PMC9132037 DOI: 10.1039/d2sc01821g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/30/2022] [Indexed: 01/03/2023] Open
Abstract
Fluorescent dyes such as rhodamines are widely used to assay the activity and image the location of otherwise invisible molecules. Si-rhodamines, in which the bridging oxygen of rhodamines is replaced with a dimethyl silyl group, are increasingly the dye scaffold of choice for biological applications, as fluorescence is shifted into the near-infrared while maintaining high brightness. Despite intense interest in Si-rhodamines, there has been no exploration of the scope of silicon functionalization in these dyes, a potential site of modification that does not exist in conventional rhodamines. Here we report a broad range of silyl modifications that enable brighter dyes, further red-shifting, new ways to modulate fluorescence, and the introduction of handles for dye attachment, including fluorogenic labeling agents for nuclear DNA, SNAP-tag and HaloTag labeling. Modifications to the bridging silicon are therefore of broad utility to improve and expand the applications of all Si-dyes. Functionalization of the bridging silicon atom of Si-rhodamine dyes allows tuning of dye performance, the attachment of sensors, and the addition of biomolecular targeting ligands useful for the construction of live cell imaging probes.![]()
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Affiliation(s)
- Desaboini Nageswara Rao
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School Worcester Massachusetts 01605 USA
| | - Xincai Ji
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School Worcester Massachusetts 01605 USA
| | - Stephen C Miller
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School Worcester Massachusetts 01605 USA
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69
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao-Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling. Angew Chem Int Ed Engl 2022; 61:e202112959. [PMID: 35146855 PMCID: PMC9305292 DOI: 10.1002/anie.202112959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.
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Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nadia M Huisjes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Miguel Guirao-Ortiz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hartmann Harz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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70
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Fam KT, Pelletier R, Bouhedda F, Ryckelynck M, Collot M, Klymchenko AS. Rational Design of Self-Quenched Rhodamine Dimers as Fluorogenic Aptamer Probes for Live-Cell RNA Imaging. Anal Chem 2022; 94:6657-6664. [PMID: 35486532 DOI: 10.1021/acs.analchem.1c04556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the growing interest in the understanding of the importance of RNAs in health and disease, detection of RNAs in living cells is of high importance. Fluorogenic dyes that light up specifically selected RNA aptamers constitute an attractive direction in the design of RNA imaging probes. In this work, based on our recently proposed concept of a fluorogenic dimer, we aim to develop a robust molecular tool for intracellular RNA imaging. We rationally designed a fluorogenic self-quenched dimer (orange Gemini, o-Gemini) based on rhodamine and evaluated its capacity to light up its cognate aptamer o-Coral in solution and live cells. We found that the removal of biotin from the dimer slightly improved the fluorogenic response without losing the affinity to the cognate aptamer (o-Coral). On the other hand, replacing sulforhodamine with a carboxyrhodamine produced drastic improvement of the affinity and the turn-on response to o-Coral and, thus, a better limit of detection. In live cells expressing o-Coral-tagged RNAs, the carboxyrhodamine analogue of o-Gemini without a biotin unit displayed a higher signal as well as faster internalization into the cells. We suppose that less hydrophilic carboxyrhodamine compared to sulforhodamine can more readily penetrate through the cell plasma membrane and, together with its higher affinity to o-Coral, provide the observed improvement in the imaging experiments. The promiscuity of the o-Coral RNA aptamer to the fluorogenic dimer allowed us to tune a fluorogen chemical structure and thus drastically improve the fluorescence response of the probe to o-Coral-tagged RNAs.
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Affiliation(s)
- Kyong Tkhe Fam
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
| | - Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
| | - Farah Bouhedda
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, F-67000 Strasbourg, France
| | - Michael Ryckelynck
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, F-67000 Strasbourg, France
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
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71
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A synergistic strategy to develop photostable and bright dyes with long Stokes shift for nanoscopy. Nat Commun 2022; 13:2264. [PMID: 35477933 PMCID: PMC9046415 DOI: 10.1038/s41467-022-29547-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/11/2022] [Indexed: 11/08/2022] Open
Abstract
The quality and application of super-resolution fluorescence imaging greatly lie in the dyes’ properties, including photostability, brightness, and Stokes shift. Here we report a synergistic strategy to simultaneously improve such properties of regular fluorophores. Introduction of quinoxaline motif with fine-tuned electron density to conventional rhodamines generates new dyes with vibration structure and inhibited twisted-intramolecular-charge-transfer (TICT) formation synchronously, thus increasing the brightness and photostability while enlarging Stokes shift. The new fluorophore YL578 exhibits around twofold greater brightness and Stokes shift than its parental fluorophore, Rhodamine B. Importantly, in Stimulated Emission Depletion (STED) microscopy, YL578 derived probe possesses a superior photostability and thus renders threefold more frames than carbopyronine based probes (CPY-Halo and 580CP-Halo), known as photostable fluorophores for STED imaging. Furthermore, the strategy is well generalized to offer a new class of bright and photostable fluorescent probes with long Stokes shift (up to 136 nm) for bioimaging and biosensing. Super-resolution microscopy is a powerful tool for cellular studies but requires bright and stable fluorescent probes. Here, the authors report on a strategy to introduce quinoxaline motifs to conventional probes to make them brighter, more photostable, larger Stokes shift, and demonstrate the probes for biosensing applications.
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72
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Brøndsted F, Stains CI. Heteroatom-Substituted Xanthene Fluorophores Enter the Shortwave-Infrared Region. Photochem Photobiol 2022; 98:400-403. [PMID: 34953073 PMCID: PMC8930474 DOI: 10.1111/php.13578] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022]
Abstract
This article is a highlight of the paper by Ivanic and Schnermann et al. in this issue of Photochemistry and Photobiology (Daly et al. Photochem. Photobiol. 2022). The collaborative team utilized computational approaches to investigate the influence of electron-withdrawing groups at the 10' position of tetramethylrhodamine (TMR). Leveraging this information, the team was able to extend the emission of the TMR scaffold into the shortwave-infrared region (SWIR, 1000-2500 nm) by incorporation of a ketone functional group at the 10' position (Daly et al. Photochem. Photobiol. 2022). This work provides the first example of a TMR derivative with peak SWIR emission (λabs : 862 nm, λem : 1058 nm). The authors utilize the ketone rhodamine scaffold to generate fluorogenic, pH-responsive reporters. This work demonstrates the potential of the classic xanthene scaffold for use as a SWIR reporter, an important step in the ultimate expansion of the repertoire of small-molecule organic fluorophore scaffolds available for deep-tissue imaging applications.
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Affiliation(s)
- Frederik Brøndsted
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Cliff I. Stains
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA,University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA,Corresponding author: (Cliff I. Stains)
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73
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Kwon J, Elgawish MS, Shim S. Bleaching-Resistant Super-Resolution Fluorescence Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2101817. [PMID: 35088584 PMCID: PMC8948665 DOI: 10.1002/advs.202101817] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 01/07/2022] [Indexed: 05/08/2023]
Abstract
Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.
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Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD21205USA
| | - Mohamed Saleh Elgawish
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
- Medicinal Chemistry DepartmentFaculty of PharmacySuez Canal UniversityIsmailia41522Egypt
| | - Sang‐Hee Shim
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
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74
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Daly HC, Matikonda SS, Steffens HC, Ruehle B, Resch-Genger U, Ivanic J, Schnermann MJ. Ketone Incorporation Extends the Emission Properties of the Xanthene Scaffold Beyond 1000 nm. Photochem Photobiol 2022; 98:325-333. [PMID: 34676539 PMCID: PMC10503429 DOI: 10.1111/php.13544] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022]
Abstract
Imaging in the shortwave-infrared region (SWIR, λ = 1000-2500 nm) has the potential to enable deep tissue imaging with high resolution. Critical to the development of these methods is the identification of low molecular weight, biologically compatible fluorescent probes that emit beyond 1000 nm. Exchanging the bridging oxygen atom on the xanthene scaffold (C10' position) with electron withdrawing groups has been shown to lead to significant redshifts in absorbance and emission. Guided by quantum chemistry computational modeling studies, we investigated the installation of a ketone bridge at the C10' position. This simple modification extends the absorbance maxima to 860 nm and the emission beyond 1000 nm, albeit with reduced photon output. Overall, these studies demonstrate that broadly applied xanthene dyes can be extended into the SWIR range.
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Affiliation(s)
- Harrison C. Daly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Siddharth S. Matikonda
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Helena C. Steffens
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Bastian Ruehle
- Division Biophotonics, Federal Institute of Materials Research and Testing (BAM),Berlin, Germany
| | - Ute Resch-Genger
- Division Biophotonics, Federal Institute of Materials Research and Testing (BAM),Berlin, Germany
| | - Joseph Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD
| | - Martin J. Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
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75
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes N, Guirao M, Narducci A, Smit J, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Bio‐labeling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Zhang
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jens Köhler
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemie GERMANY
| | | | - Nadia Huisjes
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Miguel Guirao
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jochem Smit
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Janko Stoffels
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Hartmann Harz
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Andreas Herrmann
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Thorben Cordes
- Ludwig-Maximilians-Universitat Munchen Faculty of Biology Großhadernerstr. 2-4 82152 Planegg-Martiensried GERMANY
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76
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Lakadamyali M. Single nucleosome tracking to study chromatin plasticity. Curr Opin Cell Biol 2022; 74:23-28. [PMID: 35033775 PMCID: PMC9064914 DOI: 10.1016/j.ceb.2021.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 02/03/2023]
Abstract
The dynamic spatial organization of chromatin within the nucleus is emerging as a key regulator of gene activity and cell phenotype. This review will focus on single molecule tracking as an enabling tool to study chromatin dynamics at the level of individual nucleosomes.
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Affiliation(s)
- Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Correspondence should be sent to M.L.:
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77
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Caveat fluorophore: an insiders' guide to small-molecule fluorescent labels. Nat Methods 2022; 19:149-158. [PMID: 34949811 DOI: 10.1038/s41592-021-01338-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 11/01/2021] [Indexed: 01/20/2023]
Abstract
The last three decades have brought a revolution in fluorescence microscopy. The development of new microscopes, fluorescent labels and analysis techniques has pushed the frontiers of biological imaging forward, moving from fixed to live cells, from diffraction-limited to super-resolution imaging and from simple cell culture systems to experiments in vivo. The large and ever-evolving collection of tools can be daunting for biologists, who must invest substantial time and effort in adopting new technologies to answer their specific questions. This is particularly relevant when working with small-molecule fluorescent labels, where users must navigate the jargon, idiosyncrasies and caveats of chemistry. Here, we present an overview of chemical dyes used in biology and provide frank advice from a chemist's perspective.
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78
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Steindel M, Orsine de Almeida I, Strawbridge S, Chernova V, Holcman D, Ponjavic A, Basu S. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol 2022; 2476:209-247. [PMID: 35635707 DOI: 10.1007/978-1-0716-2221-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single-molecule localization microscopy (SMLM) allows the super-resolved imaging of proteins within mammalian nuclei at spatial resolutions comparable to that of a nucleosome itself (~20 nm). The technique is therefore well suited to the study of chromatin structure. Fixed-cell SMLM has already allowed temporal "snapshots" of how proteins are arranged on chromatin within mammalian nuclei. In this chapter, we focus on how recent developments, for example in selective plane illumination, 3D SMLM, and protein labeling, have led to a range of live-cell SMLM studies. We describe how to carry out single-particle tracking (SPT) of single proteins and, by analyzing their diffusion parameters, how to determine whether proteins interact with chromatin, diffuse freely, or do both. We can study the numbers of proteins that interact with chromatin and also determine their residence time on chromatin. We can determine whether these proteins form functional clusters within the nucleus as well as whether they form specific nuclear structures.
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Affiliation(s)
- Maike Steindel
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Stanley Strawbridge
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Valentyna Chernova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Aleks Ponjavic
- School of Physics and Astronomy and School of Food Science and Nutrition, University of Leeds, Leeds, UK.
| | - Srinjan Basu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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79
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Frei MS, Tarnawski M, Roberti MJ, Koch B, Hiblot J, Johnsson K. Engineered HaloTag variants for fluorescence lifetime multiplexing. Nat Methods 2022; 19:65-70. [PMID: 34916672 PMCID: PMC8748199 DOI: 10.1038/s41592-021-01341-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022]
Abstract
Self-labeling protein tags such as HaloTag are powerful tools that can label fusion proteins with synthetic fluorophores for use in fluorescence microscopy. Here we introduce HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines. Combining these HaloTag variants enabled live-cell fluorescence lifetime multiplexing of three cellular targets in one spectral channel using a single fluorophore and the generation of a fluorescence lifetime-based biosensor. Additionally, the brightest HaloTag variant showed up to 40% higher brightness in live-cell imaging applications.
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Affiliation(s)
- Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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80
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Wang N, Hao Y, Feng X, Zhu H, Zhang D, Wang T, Cui X. Silicon-substituted rhodamines for stimulated emission depletion fluorescence nanoscopy. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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81
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Xu S, Pan W, Ren T, Huan S, Yuan L, Zhang X. Molecular Engineering of Novel Fluorophores for
High‐Contrast
Bioimaging. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shuai Xu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
| | - Wenjing Pan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
| | - Tian‐Bing Ren
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
| | - Shuang‐Yan Huan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
| | - Lin Yuan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
| | - Xiao‐Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine Hunan University Changsha 410082 P. R. China
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82
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Chien FC, Lin CY, Abrigo G. Single-Molecule Blinking Fluorescence Enhancement by Surface Plasmon-Coupled Emission-Based Substrates for Single-Molecule Localization Imaging. Anal Chem 2021; 93:15401-15411. [PMID: 34730956 DOI: 10.1021/acs.analchem.1c03206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Surface plasmon-coupled emission (SPCE) substrates to enhance the blinking fluorescence of spontaneously blinking fluorophores in single-molecule localization microscopy (SMLM) were fabricated to reduce the excitation power density requirement and reveal the distribution of fluorophore-labeled proteins on a plasma membrane with nanoscale-level resolution. The systemic investigation of the contribution of local field enhancement, modified quantum yield, and emission coupling yield through glass coverslip substrates coated with metal layers of different thicknesses revealed that the silver-layer substrate with a thickness of 44 nm produces the highest SPCE fluorescence in spontaneously blinking fluorophores, and it has a highly directional SPCE fluorescence, which helps improve the detection efficiency. Moreover, the uniform and surface-enhanced field created on the substrate surface is beneficial for fluorescence background reduction in single fluorophore detection and localization, as well as for revealing the real position of fluorophores. Consequently, compared with a glass coverslip substrate, the presented SPCE substrate demonstrated a fluorescence enhancement of 480% and an increase in blinking events from a single spontaneously blinking fluorophore; moreover, the required excitation power density for SMLM imaging was significantly reduced to 23 W cm-2 for visualizing the distribution of epidermal growth factor receptors (EGFRs) on the basal plasma membrane of A549 lung cancer cells with a localization precision of 19 ± 7 nm. Finally, the fluorophore-labeled EGFRs on the basal plasma membrane in the presence of PIKfyve-specific inhibitor treatment were explored using SPCE-SMLM imaging; the results revealed a distinct reduction in the density of localization events because of a decrease in EGFR abundance at the plasma membranes of the cells.
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Affiliation(s)
- Fan-Ching Chien
- Department of Optics and Photonics, National Central University, Taoyuan 32001, Taiwan
| | - Chun-Yu Lin
- College of Photonics, National Yang Ming Chiao Tung University, Tainan 71150, Taiwan
| | - Gerald Abrigo
- Department of Optics and Photonics, National Central University, Taoyuan 32001, Taiwan
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83
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Lardon N, Wang L, Tschanz A, Hoess P, Tran M, D'Este E, Ries J, Johnsson K. Systematic Tuning of Rhodamine Spirocyclization for Super-resolution Microscopy. J Am Chem Soc 2021; 143:14592-14600. [PMID: 34460256 DOI: 10.1021/jacs.1c05004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Rhodamines are the most important class of fluorophores for applications in live-cell fluorescence microscopy. This is mainly because rhodamines exist in a dynamic equilibrium between a fluorescent zwitterion and a nonfluorescent but cell-permeable spirocyclic form. Different imaging applications require different positions of this dynamic equilibrium, and an adjustment of the equilibrium poses a challenge for the design of suitable probes. We describe here how the conversion of the ortho-carboxy moiety of a given rhodamine into substituted acyl benzenesulfonamides and alkylamides permits the systematic tuning of the equilibrium of spirocyclization with unprecedented accuracy and over a large range. This allows one to transform the same rhodamine into either a highly fluorogenic and cell-permeable probe for live-cell-stimulated emission depletion (STED) microscopy or a spontaneously blinking dye for single-molecule localization microscopy (SMLM). We used this approach to generate differently colored probes optimized for different labeling systems and imaging applications.
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Affiliation(s)
- Nicolas Lardon
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Faculty of Chemistry and Earth Sciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Lu Wang
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Zhangheng Road 826, 201203 Shanghai, China
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | - Philipp Hoess
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | - Mai Tran
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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84
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Nguyen VQ, Ranjan A, Liu S, Tang X, Ling YH, Wisniewski J, Mizuguchi G, Li KY, Jou V, Zheng Q, Lavis LD, Lionnet T, Wu C. Spatiotemporal coordination of transcription preinitiation complex assembly in live cells. Mol Cell 2021; 81:3560-3575.e6. [PMID: 34375585 PMCID: PMC8420877 DOI: 10.1016/j.molcel.2021.07.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/18/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
Transcription initiation by RNA polymerase II (RNA Pol II) requires preinitiation complex (PIC) assembly at gene promoters. In the dynamic nucleus, where thousands of promoters are broadly distributed in chromatin, it is unclear how multiple individual components converge on any target to establish the PIC. Here we use live-cell, single-molecule tracking in S. cerevisiae to visualize constrained exploration of the nucleoplasm by PIC components and Mediator's key role in guiding this process. On chromatin, TFIID/TATA-binding protein (TBP), Mediator, and RNA Pol II instruct assembly of a short-lived PIC, which occurs infrequently but efficiently within a few seconds on average. Moreover, PIC exclusion by nucleosome encroachment underscores regulated promoter accessibility by chromatin remodeling. Thus, coordinated nuclear exploration and recruitment to accessible targets underlies dynamic PIC establishment in yeast. Our study provides a global spatiotemporal model for transcription initiation in live cells.
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Affiliation(s)
- Vu Q Nguyen
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Anand Ranjan
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sheng Liu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xiaona Tang
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yick Hin Ling
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jan Wisniewski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Experimental Immunology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Gaku Mizuguchi
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kai Yu Li
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vivian Jou
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Timothée Lionnet
- Institute of Systems Genetics, Langone Medical Center, New York University, New York, NY 10016, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
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85
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Tyson J, Hu K, Zheng S, Kidd P, Dadina N, Chu L, Toomre D, Bewersdorf J, Schepartz A. Extremely Bright, Near-IR Emitting Spontaneously Blinking Fluorophores Enable Ratiometric Multicolor Nanoscopy in Live Cells. ACS CENTRAL SCIENCE 2021; 7:1419-1426. [PMID: 34471685 PMCID: PMC8393207 DOI: 10.1021/acscentsci.1c00670] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 05/16/2023]
Abstract
New bright, photostable, emission-orthogonal fluorophores that blink without toxic additives are needed to enable multicolor, live-cell, single-molecule localization microscopy (SMLM). Here we report the design, synthesis, and biological evaluation of Yale676sb, a photostable, near-IR-emitting fluorophore that achieves these goals in the context of an exceptional quantum yield (0.59). When used alongside HMSiR, Yale676sb enables simultaneous, live-cell, two-color SMLM of two intracellular organelles (ER + mitochondria) with only a single laser and no chemical additives.
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Affiliation(s)
- Jonathan Tyson
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Kevin Hu
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Department
of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Shuai Zheng
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Phylicia Kidd
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
| | - Neville Dadina
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ling Chu
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Derek Toomre
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Nanobiology
Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Joerg Bewersdorf
- Department
of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Department
of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
- Kavli
Institute for Neuroscience, Yale School
of Medicine, New Haven, Connecticut 06510, United States
- Nanobiology
Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Alanna Schepartz
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States
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86
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Jeronimo C, Angel A, Nguyen VQ, Kim JM, Poitras C, Lambert E, Collin P, Mellor J, Wu C, Robert F. FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner. Mol Cell 2021; 81:3542-3559.e11. [PMID: 34380014 DOI: 10.1016/j.molcel.2021.07.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 05/25/2021] [Accepted: 07/12/2021] [Indexed: 12/29/2022]
Abstract
The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Andrew Angel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Vu Q Nguyen
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jee Min Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Christian Poitras
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Elie Lambert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Pierre Collin
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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87
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Kim JM, Visanpattanasin P, Jou V, Liu S, Tang X, Zheng Q, Li KY, Snedeker J, Lavis LD, Lionnet T, Wu C. Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin. eLife 2021; 10:e69387. [PMID: 34313223 PMCID: PMC8352589 DOI: 10.7554/elife.69387] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending 'tug-of-war' that controls a temporally shifting window of accessibility for the transcription initiation machinery.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | | | - Vivian Jou
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Sheng Liu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xiaona Tang
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Kai Yu Li
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Jonathan Snedeker
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Timothee Lionnet
- Institute of Systems Genetics, Langone Medical Center, New York UniversityNew YorkUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins School of MedicineBaltimoreUnited States
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88
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Hoboth P, Šebesta O, Hozák P. How Single-Molecule Localization Microscopy Expanded Our Mechanistic Understanding of RNA Polymerase II Transcription. Int J Mol Sci 2021; 22:6694. [PMID: 34206594 PMCID: PMC8269275 DOI: 10.3390/ijms22136694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 11/16/2022] Open
Abstract
Classical models of gene expression were built using genetics and biochemistry. Although these approaches are powerful, they have very limited consideration of the spatial and temporal organization of gene expression. Although the spatial organization and dynamics of RNA polymerase II (RNAPII) transcription machinery have fundamental functional consequences for gene expression, its detailed studies have been abrogated by the limits of classical light microscopy for a long time. The advent of super-resolution microscopy (SRM) techniques allowed for the visualization of the RNAPII transcription machinery with nanometer resolution and millisecond precision. In this review, we summarize the recent methodological advances in SRM, focus on its application for studies of the nanoscale organization in space and time of RNAPII transcription, and discuss its consequences for the mechanistic understanding of gene expression.
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Affiliation(s)
- Peter Hoboth
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic;
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic;
| | - Ondřej Šebesta
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic;
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic;
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
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89
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Fan M, An H, Wang C, Huo S, Wang T, Cui X, Zhang D. STED Imaging the Dynamics of Lysosomes by Dually Fluorogenic Si-Rhodamine. Chemistry 2021; 27:9620-9626. [PMID: 33899976 DOI: 10.1002/chem.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Indexed: 11/07/2022]
Abstract
Super-resolution microscopy (SRM) imaging of the finite subcellular structures and subtle bioactivities inside organelles delivers abundant cellular information with high fidelity to unravel the intricate biological processes. An ideal fluorescent probe with precise control of fluorescence is critical in SRM technique like stimulated emission depletion (STED). Si-rhodamine was decorated with both targeting group and H+ -receptor, affording the dually fluorogenic Si-rhodamine in which the NIR fluorescence was efficiently controlled by the coalescent of spirolactone-zwitterion equilibrium and PeT mechanism. The dually fluorogenic characters of the probe offer a perfect mutual enhancement in sensitivity, specificity and spatial resolution. Strong fluorescence only released in the existence of targeting protein at acidic lysosomal pH, ensured precisely tracking the dynamic of lysosomal structure and pH in living cells by STED.
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Affiliation(s)
- Mengting Fan
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Haiyan An
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai, 200433, P. R. China
| | - Chuanfeng Wang
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Shuhui Huo
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Ting Wang
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai, 200433, P. R. China
| | - Xiaoyan Cui
- Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China
| | - Dazhi Zhang
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai, 200433, P. R. China
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90
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Ogasawara H, Tanaka Y, Taki M, Yamaguchi S. Late-stage functionalisation of alkyne-modified phospha-xanthene dyes: lysosomal imaging using an off-on-off type of pH probe. Chem Sci 2021; 12:7902-7907. [PMID: 34168843 PMCID: PMC8188471 DOI: 10.1039/d1sc01705e] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
Near-infrared (NIR) fluorescent molecules are of great importance for the visualisation of biological processes. Among the most promising dye scaffolds for this purpose are P[double bond, length as m-dash]O-substituted phospha-xanthene (POX) dyes, which show NIR emission with high photostability. Their practical utility for in vitro and in vivo imaging has recently been demonstrated. Although classical modification methods have been used to produce POX-based fluorescent probes, it is still a challenge to introduce additional functional groups to control the localisation of the probe in cells. Herein, we report on the development of POXs that bear a 4-ethynylphenyl group on the phosphorus atom. These dyes can subsequently be functionalised with azide-tagged biomolecules via a late-stage Cu-catalysed azide/alkyne cycloaddition (CuAAC) reaction, thus achieving target-selective labelling. To demonstrate the practical utility of the functionalised POXs, we designed a sophisticated NIR probe that exhibits a bell-shaped off-on-off pH-response and is able to assess the degree of endosomal maturation.
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Affiliation(s)
- Hiroaki Ogasawara
- Department of Chemistry, Graduate School of Science, Integrated Research Consortium on Chemical Sciences (IRCCS), Nagoya University Furo, Chikusa Nagoya 464-8602 Japan
| | - Yoshiki Tanaka
- Department of Chemistry, Graduate School of Science, Integrated Research Consortium on Chemical Sciences (IRCCS), Nagoya University Furo, Chikusa Nagoya 464-8602 Japan
| | - Masayasu Taki
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University Furo, Chikusa Nagoya 464-8601 Japan
| | - Shigehiro Yamaguchi
- Department of Chemistry, Graduate School of Science, Integrated Research Consortium on Chemical Sciences (IRCCS), Nagoya University Furo, Chikusa Nagoya 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University Furo, Chikusa Nagoya 464-8601 Japan
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91
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Turnbull JL, Benlian BR, Golden RP, Miller EW. Phosphonofluoresceins: Synthesis, Spectroscopy, and Applications. J Am Chem Soc 2021; 143:6194-6201. [PMID: 33797899 DOI: 10.1021/jacs.1c01139] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Xanthene fluorophores, like fluorescein, have been versatile molecules across diverse fields of chemistry and life sciences. Despite the ubiquity of 3-carboxy and 3-sulfonofluorescein for the last 150 years, to date, no reports of 3-phosphonofluorescein exist. Here, we report the synthesis, spectroscopic characterization, and applications of 3-phosphonofluoresceins. The absorption and emission of 3-phosphonofluoresceins remain relatively unaltered from the parent 3-carboxyfluorescein. 3-Phosphonofluoresceins show enhanced water solubility compared to 3-carboxyfluorescein and persist in an open, visible light-absorbing state even at low pH and in low dielectric media while 3-carboxyfluoresceins tend to lactonize. In contrast, the spirocyclization tendency of 3-phosphonofluoresceins can be modulated by esterification of the phosphonic acid. The bis-acetoxymethyl ester of 3-phosphonofluorescein readily enters living cells, showing excellent accumulation (>6x) and retention (>11x), resulting in a nearly 70-fold improvement in cellular brightness compared to 3-carboxyfluorescein. In a complementary fashion, the free acid form of 3-phosphonofluorescein does not cross cellular membranes, making it ideally suited for incorporation into a voltage-sensing scaffold. We develop a new synthetic route to functionalized 3-phosphonofluoresceins to enable the synthesis of phosphono-voltage sensitive fluorophores, or phosVF2.1.Cl. Phosphono-VF2.1.Cl shows excellent membrane localization, cellular brightness, and voltage sensitivity (26% ΔF/F per 100 mV), rivaling that of sulfono-based VF dyes. In summary, we develop the first synthesis of 3-phosphonofluoresceins, characterize the spectroscopic properties of this new class of xanthene dyes, and utilize these insights to show the utility of 3-phosphonofluoresceins in intracellular imaging and membrane potential sensing.
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92
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The HaloTag as a general scaffold for far-red tunable chemigenetic indicators. Nat Chem Biol 2021; 17:718-723. [PMID: 33795886 DOI: 10.1038/s41589-021-00775-w] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/19/2021] [Indexed: 12/16/2022]
Abstract
Functional imaging using fluorescent indicators has revolutionized biology, but additional sensor scaffolds are needed to access properties such as bright, far-red emission. Here, we introduce a new platform for 'chemigenetic' fluorescent indicators, utilizing the self-labeling HaloTag protein conjugated to environmentally sensitive synthetic fluorophores. We solve a crystal structure of HaloTag bound to a rhodamine dye ligand to guide engineering efforts to modulate the dye environment. We show that fusion of HaloTag with protein sensor domains that undergo conformational changes near the bound dye results in large and rapid changes in fluorescence output. This generalizable approach affords bright, far-red calcium and voltage sensors with highly tunable photophysical and chemical properties, which can reliably detect single action potentials in cultured neurons.
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93
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Choquet D, Sainlos M, Sibarita JB. Advanced imaging and labelling methods to decipher brain cell organization and function. Nat Rev Neurosci 2021; 22:237-255. [PMID: 33712727 DOI: 10.1038/s41583-021-00441-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2021] [Indexed: 01/31/2023]
Abstract
The brain is arguably the most complex organ. The branched and extended morphology of nerve cells, their subcellular complexity, the multiplicity of brain cell types as well as their intricate connectivity and the scattering properties of brain tissue present formidable challenges to the understanding of brain function. Neuroscientists have often been at the forefront of technological and methodological developments to overcome these hurdles to visualize, quantify and modify cell and network properties. Over the last few decades, the development of advanced imaging methods has revolutionized our approach to explore the brain. Super-resolution microscopy and tissue imaging approaches have recently exploded. These instrumentation-based innovations have occurred in parallel with the development of new molecular approaches to label protein targets, to evolve new biosensors and to target them to appropriate cell types or subcellular compartments. We review the latest developments for labelling and functionalizing proteins with small localization and functionalized reporters. We present how these molecular tools are combined with the development of a wide variety of imaging methods that break either the diffraction barrier or the tissue penetration depth limits. We put these developments in perspective to emphasize how they will enable step changes in our understanding of the brain.
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Affiliation(s)
- Daniel Choquet
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France. .,University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, Bordeaux, France.
| | - Matthieu Sainlos
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.
| | - Jean-Baptiste Sibarita
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.
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94
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Touizer E, Sieben C, Henriques R, Marsh M, Laine RF. Application of Super-Resolution and Advanced Quantitative Microscopy to the Spatio-Temporal Analysis of Influenza Virus Replication. Viruses 2021; 13:233. [PMID: 33540739 PMCID: PMC7912985 DOI: 10.3390/v13020233] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023] Open
Abstract
With an estimated three to five million human cases annually and the potential to infect domestic and wild animal populations, influenza viruses are one of the greatest health and economic burdens to our society, and pose an ongoing threat of large-scale pandemics. Despite our knowledge of many important aspects of influenza virus biology, there is still much to learn about how influenza viruses replicate in infected cells, for instance, how they use entry receptors or exploit host cell trafficking pathways. These gaps in our knowledge are due, in part, to the difficulty of directly observing viruses in living cells. In recent years, advances in light microscopy, including super-resolution microscopy and single-molecule imaging, have enabled many viral replication steps to be visualised dynamically in living cells. In particular, the ability to track single virions and their components, in real time, now allows specific pathways to be interrogated, providing new insights to various aspects of the virus-host cell interaction. In this review, we discuss how state-of-the-art imaging technologies, notably quantitative live-cell and super-resolution microscopy, are providing new nanoscale and molecular insights into influenza virus replication and revealing new opportunities for developing antiviral strategies.
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Affiliation(s)
- Emma Touizer
- Division of Infection and Immunity, University College London, London WC1E 6AE, UK;
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Christian Sieben
- Department of Cell Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
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95
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G. Keller S, Kamiya M, Urano Y. Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes. Molecules 2020; 25:E5964. [PMID: 33339370 PMCID: PMC7766215 DOI: 10.3390/molecules25245964] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10'. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure-behavior relationship including novel computational approaches.
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Affiliation(s)
- Sascha G. Keller
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (S.G.K.); (M.K.)
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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96
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Lesiak L, Zhou X, Fang Y, Zhao J, Beck JR, Stains CI. Imaging GPCR internalization using near-infrared Nebraska red-based reagents. Org Biomol Chem 2020; 18:2459-2467. [PMID: 32167123 DOI: 10.1039/d0ob00043d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Internalization of G protein-coupled receptor (GPCRs) represents a nearly universal pathway for receptor downregulation. Imaging this process provides a means for the identification of pharmaceutical agents as well as potential ligands for orphan receptors. However, there is a need for the further development of near-infrared (NIR) probes capable of monitoring internalization in order to enable multiplexing with existing green fluorescent GPCR activity assays. Our laboratory has recently described a series of near-infrared (NIR) fluorophores in which a phosphinate functionality is inserted at the bridging position of the xanthene scaffold. These fluorophores, termed Nebraska Red (NR) dyes, provide attractive reagents for imaging protein localization. Herein, we disclose the development of NR-based HaloTag ligands for imaging membrane proteins on living cells. These new probes are utilized to image membrane pools of the human orexin type 2 receptor, an established target for the treatment of insomnia. We demonstrate the ability of fetal bovine serum (FBS) to noncovalently associate with a spirolactonized NR probe, enabling no-wash imaging with a 45-fold enhancement of fluorescence. Furthermore, we characterize the utility of NR-based HaloTag ligands for real-time monitoring of receptor internalization upon agonist stimulation. These new reagents enable potential multiplexing with existing GPCR activity assays in order to identify new modulators of GPCR activity as well as ligands for orphan receptors.
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Affiliation(s)
- Lauren Lesiak
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
| | - Yuan Fang
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, USA. and Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Jia Zhao
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
| | - Jon R Beck
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588, USA. and Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA and Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA and Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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97
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Hira J, Uddin MJ, Haugland MM, Lentz CS. From Differential Stains to Next Generation Physiology: Chemical Probes to Visualize Bacterial Cell Structure and Physiology. Molecules 2020; 25:E4949. [PMID: 33114655 PMCID: PMC7663024 DOI: 10.3390/molecules25214949] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022] Open
Abstract
Chemical probes have been instrumental in microbiology since its birth as a discipline in the 19th century when chemical dyes were used to visualize structural features of bacterial cells for the first time. In this review article we will illustrate the evolving design of chemical probes in modern chemical biology and their diverse applications in bacterial imaging and phenotypic analysis. We will introduce and discuss a variety of different probe types including fluorogenic substrates and activity-based probes that visualize metabolic and specific enzyme activities, metabolic labeling strategies to visualize structural features of bacterial cells, antibiotic-based probes as well as fluorescent conjugates to probe biomolecular uptake pathways.
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Affiliation(s)
- Jonathan Hira
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Md. Jalal Uddin
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
| | - Marius M. Haugland
- Department of Chemistry and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway;
| | - Christian S. Lentz
- Research Group for Host-Microbe Interactions, Department of Medical Biology and Centre for New Antibacterial Strategies (CANS), UiT—The Arctic University of Norway, 9019 Tromsø, Norway; (J.H.); (M.J.U.)
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98
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Guthrie DA, Klein Herenbrink C, Lycas MD, Ku T, Bonifazi A, DeVree BT, Mathiasen S, Javitch JA, Grimm JB, Lavis L, Gether U, Newman AH. Novel Fluorescent Ligands Enable Single-Molecule Localization Microscopy of the Dopamine Transporter. ACS Chem Neurosci 2020; 11:3288-3300. [PMID: 32926777 DOI: 10.1021/acschemneuro.0c00397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The dopamine transporter (DAT) is critical for spatiotemporal control of dopaminergic neurotransmission and is the target for therapeutic agents, including ADHD medications, and abused substances, such as cocaine. Here, we develop new fluorescently labeled ligands that bind DAT with high affinity and enable single-molecule detection of the transporter. The cocaine analogue MFZ2-12 (1) was conjugated to novel rhodamine-based Janelia Fluorophores (JF549 and JF646). High affinity binding of the resulting ligands to DAT was demonstrated by potent inhibition of [3H]dopamine uptake in DAT transfected CAD cells and by competition radioligand binding experiments on rat striatal membranes. Visualization of binding was substantiated by confocal or TIRF microscopy revealing selective binding of the analogues to DAT transfected CAD cells. Single particle tracking experiments were performed with JF549-conjugated DG3-80 (3) and JF646-conjugated DG4-91 (4) on DAT transfected CAD cells enabling quantification and categorization of the dynamic behavior of DAT into four distinct motion classes (immobile, confined, Brownian, and directed). Finally, we show that the ligands can be used in direct stochastic optical reconstruction microscopy (dSTORM) experiments permitting further analyses of DAT distribution on the nanoscale. In summary, these novel fluorescent ligands are promising new tools for studying DAT localization and regulation with single-molecule resolution.
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Affiliation(s)
- Daryl A. Guthrie
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States,
| | - Carmen Klein Herenbrink
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Matthew Domenic Lycas
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Therese Ku
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States,
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States,
| | - Brian T. DeVree
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Signe Mathiasen
- Department of Psychiatry, Columbia University Vagelos College of Physicians & Surgeon and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032, United States
| | - Jonathan A. Javitch
- Department of Psychiatry, Columbia University Vagelos College of Physicians & Surgeon and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032, United States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Luke Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Ulrik Gether
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States,
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99
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Möckl L, Moerner WE. Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges. J Am Chem Soc 2020; 142:17828-17844. [PMID: 33034452 PMCID: PMC7582613 DOI: 10.1021/jacs.0c08178] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 12/31/2022]
Abstract
Single-molecule super-resolution microscopy has developed from a specialized technique into one of the most versatile and powerful imaging methods of the nanoscale over the past two decades. In this perspective, we provide a brief overview of the historical development of the field, the fundamental concepts, the methodology required to obtain maximum quantitative information, and the current state of the art. Then, we will discuss emerging perspectives and areas where innovation and further improvement are needed. Despite the tremendous progress, the full potential of single-molecule super-resolution microscopy is yet to be realized, which will be enabled by the research ahead of us.
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Affiliation(s)
- Leonhard Möckl
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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100
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Deng F, Liu L, Huang W, Huang C, Qiao Q, Xu Z. Systematic study of synthesizing various heteroatom-substituted rhodamines from diaryl ether analogues. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 240:118466. [PMID: 32521444 DOI: 10.1016/j.saa.2020.118466] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 06/11/2023]
Abstract
The dye rhodamine, as the most popular scaffold to construct fluorescent labels and probes, has been explored extensively on its structure-fluorescence relationships. Particularly, the replacement of the oxygen atom in the 10th position with heteroatoms obtained various new rhodamines with improved photophysical properties, such as brightness, photostability, red-shifted emission and fluorogenicity. However, the applications of heteroatom-substituted rhodamines have been hindered by difficult synthetic routes. Herein, we explored the condensation strategy of diaryl ether analogues and o-tolualdehyde to synthesize various heteroatom-substituted rhodamines. We found that the electron property and steric effect in the rhodamine 10th position determined the synthetic yield. It's concluded that this condensation method was more suitable for the synthesis of heteroatom-substituted rhodamines with small or electron-donating groups like rhodamine, S-rhodamine and Si-rhodamine. We hope these results will benefit the design and synthesis of heteroatom-substituted rhodamines.
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Affiliation(s)
- Fei Deng
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Limin Liu
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China.
| | - Wei Huang
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China
| | - Chunfang Huang
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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