1
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Obloy LM, Jockusch S, Tarnovsky AN. Shortwave infrared polymethine dyes for bioimaging: ultrafast relaxation dynamics and excited-state decay pathways. Phys Chem Chem Phys 2024; 26:24261-24278. [PMID: 38895857 DOI: 10.1039/d4cp01411a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Excited-state relaxation in two prototypical shortwave infrared (SWIR) polymethine dyes developed for bioimaging, heptamethine chromenylium Chrom7 and flavylium Flav7, is studied by means of femtosecond transient absorption with broadband ultraviolet-to-SWIR probing complemented by steady-state and time-resolved fluorescence and phosphorescence measurements. The relaxation processes of the dyes in dichloromethane are resolved with sub-100 fs temporal resolution using SWIR, near-IR, and visible photoexcitation. Different population members of the ground-state inhomogeneous ensemble are found to equilibrate via skeletal deformation changes with time constants of 90 fs and either 230 fs (Chrom7) and 350 fs (Flav7) followed by slower evolution matching the 1-ps timescale of diffusive solvation dynamics. Molecules excited into high-lying singlet electronic states (Sn) by visible excitation repopulate with time constants of 400 fs (Chrom7) and 450 fs (Flav7) the corresponding first excited singlet S1 states, which decay within several hundreds of picoseconds in dichloromethane and chloroform solvents. Vibrational relaxation in S1 for both Chrom7 and Flav7 in dichloromethane occurs with time constants of 350 and 800 fs for excess of vibrational energy of ∼1000 and 10 000 cm-1 deposited by near-IR and visible excitation, respectively. Two competing non-radiative processes are present in S1: temperature-independent internal conversion, and thermally-activated twisting about a carbon-carbon bond of the conjugated chain, which is substantial at room temperature but essentially nonreactive, producing traces of isomer product. Intersystem crossing in S1, and thus the triplet quantum yield, is minor. The importance of absorption bands from the excited S1 state in applications requiring high-intensity excitation conditions is discussed.
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Affiliation(s)
- Laura M Obloy
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
| | - Steffen Jockusch
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
| | - Alexander N Tarnovsky
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
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2
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S V, Nag A, Das AK. A versatile sensor capable of ratiometric fluorescence detection of trace water and turn-on detection of Cu 2+ modulating the binding interaction of a Cu(II) complex with BSA and DNA complemented by docking studies. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5263-5271. [PMID: 39015041 DOI: 10.1039/d4ay00675e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
A fluorescent molecule, pyridine-coupled bis-anthracene (PBA), has been developed for the selective fluorescence turn-on detection of Cu2+. Interestingly, the ligand PBA also exhibited a red-shifted ratiometric fluorescence response in the presence of water. Thus, a ratiometric water sensor has been utilized as a selective fluorescence turn-on sensor for Cu2+, achieving a 10-fold enhancement in the fluorescence and quantum yield at 446 nm, with a lower detection limit of 0.358 μM and a binding constant of 1.3 × 106 M-1. For practical applications, sensor PBA can be used to detect Cu2+ in various types of soils like clay soil, field soil and sand. The interaction of the PBA-Cu(II) complex with transport proteins like bovine serum albumin (BSA) and ct-DNA has been investigated through fluorescence titration experiments. Additionally, the structural optimization of PBA and the PBA-Cu(II) complex has been demonstrated by DFT, and the interaction of the PBA-Cu(II) complex with BSA and ct-DNA has been analyzed using theoretical docking studies.
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Affiliation(s)
- Vishnu S
- Department of Chemistry, Christ University, Hosur Road, Bangalore, Karnataka, 560029, India.
| | - Anish Nag
- Department of Life Science, Christ University, Hosur Road, Bangalore, Karnataka, 560029, India
| | - Avijit Kumar Das
- Department of Chemistry, Christ University, Hosur Road, Bangalore, Karnataka, 560029, India.
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3
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Pati AK, Kilic Z, Martin MI, Terry DS, Borgia A, Bar S, Jockusch S, Kiselev R, Altman RB, Blanchard SC. Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation. Nat Methods 2024; 21:1222-1230. [PMID: 38877317 PMCID: PMC11239528 DOI: 10.1038/s41592-024-02293-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/25/2024] [Indexed: 06/16/2024]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) methods employed to quantify time-dependent compositional and conformational changes within biomolecules require elevated illumination intensities to recover robust photon emission streams from individual fluorophores. Here we show that outside the weak-excitation limit, and in regimes where fluorophores must undergo many rapid cycles of excitation and relaxation, non-fluorescing, excitation-induced triplet states with lifetimes orders of magnitude longer lived than photon-emitting singlet states degrade photon emission streams from both donor and acceptor fluorophores resulting in illumination-intensity-dependent changes in FRET efficiency. These changes are not commonly taken into consideration; therefore, robust strategies to suppress excited state accumulations are required to recover accurate and precise FRET efficiency, and thus distance, estimates. We propose both robust triplet state suppression and data correction strategies that enable the recovery of FRET efficiencies more closely approximating true values, thereby extending the spatial and temporal resolution of smFRET.
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Affiliation(s)
- Avik K Pati
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maxwell I Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alessandro Borgia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sukanta Bar
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Steffen Jockusch
- Center for Photochemical Sciences and Department of Chemistry, Bowling Green State University, Bowling Green, OH, USA
| | - Roman Kiselev
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Roger B Altman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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4
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Kulinich AV, Ishchenko AA. Design and Photonics of Merocyanine Dyes. CHEM REC 2024; 24:e202300262. [PMID: 37850545 DOI: 10.1002/tcr.202300262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/21/2023] [Indexed: 10/19/2023]
Abstract
Merocyanines, thanks to their easily adjustable electronic structure, appear to be the most versatile and promising functional dyes. Their D-π-A framework offers ample opportunities for custom design through variations in both donor/acceptor end-groups and the π-conjugated polymethine chain, and leads to a broad range of practical properties, including noticeable solvatochromism, high polarizability/hyperpolarizabilities, and the ability to sensitize various physicochemical processes. Accordingly, merocyanines are applied and extensively studied in various fields, such as light-converting materials for optoelectronics, nonlinear optics, optical storage, solar cells, fluorescent probes, and antitumor agents in photodynamic therapy. This review encompasses both classical and novel more important publications on the structure-property relationships in merocyanines, with particular emphasis on the results by A. I. Kiprianov and his followers in Institute of Organic Chemistry in Kyiv, Ukraine.
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Affiliation(s)
- Andrii V Kulinich
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Akademika Kukharya St., 02094, Kyiv, Ukraine
| | - Alexander A Ishchenko
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Akademika Kukharya St., 02094, Kyiv, Ukraine
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5
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Sandberg E, Piguet J, Kostiv U, Baryshnikov G, Liu H, Widengren J. Photoisomerization of Heptamethine Cyanine Dyes Results in Red-Emissive Species: Implications for Near-IR, Single-Molecule, and Super-Resolution Fluorescence Spectroscopy and Imaging. J Phys Chem B 2023; 127:3208-3222. [PMID: 37011608 PMCID: PMC10108366 DOI: 10.1021/acs.jpcb.2c08016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Photoisomerization kinetics of the near-infrared (NIR) fluorophore Sulfo-Cyanine7 (SCy7) was studied by a combination of fluorescence correlation spectroscopy (FCS) and transient state (TRAST) excitation modulation spectroscopy. A photoisomerized state with redshifted emission was identified, with kinetics consistent with a three-state photoisomerization model. Combining TRAST excitation modulation with spectrofluorimetry (spectral-TRAST) further confirmed an excitation-induced redshift in the emission spectrum of SCy7. We show how this red-emissive photoisomerized state contributes to the blinking kinetics in different emission bands of NIR cyanine dyes, and how it can influence single-molecule, super-resolution, as well as Förster resonance energy transfer (FRET) and multicolor readouts. Since this state can also be populated at moderate excitation intensities, it can also more broadly influence fluorescence readouts, also readouts not relying on high excitation conditions. However, this additional red-emissive state and its photodynamics, as identified and characterized in this work, can also be used as a strategy to push the emission of NIR cyanine dyes further into the NIR and to enhance photosensitization of nanoparticles with absorption spectra further into the NIR. Finally, we show that the photoisomerization kinetics of SCy7 and the formation of its redshifted photoisomer depend strongly on local environmental conditions, such as viscosity, polarity, and steric constraints, which suggests the use of SCy7 and other NIR cyanine dyes as environmental sensors. Such environmental information can be monitored by TRAST, in the NIR, with low autofluorescence and scattering conditions and on a broad range of samples and experimental conditions.
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Affiliation(s)
- Elin Sandberg
- Experimental Biomolecular Physics, Dept. Applied Physics, Royal Institute of Technology (KTH), Albanova Univ Center, 106 91 Stockholm, Sweden
| | - Joachim Piguet
- Experimental Biomolecular Physics, Dept. Applied Physics, Royal Institute of Technology (KTH), Albanova Univ Center, 106 91 Stockholm, Sweden
| | - Uliana Kostiv
- Experimental Biomolecular Physics, Dept. Applied Physics, Royal Institute of Technology (KTH), Albanova Univ Center, 106 91 Stockholm, Sweden
| | - Glib Baryshnikov
- Dept. Science and Technology, Linköping University, Campus Norrköping, 601 74 Norrköping, Sweden
| | - Haichun Liu
- Experimental Biomolecular Physics, Dept. Applied Physics, Royal Institute of Technology (KTH), Albanova Univ Center, 106 91 Stockholm, Sweden
| | - Jerker Widengren
- Experimental Biomolecular Physics, Dept. Applied Physics, Royal Institute of Technology (KTH), Albanova Univ Center, 106 91 Stockholm, Sweden
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6
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Sandberg E, Piguet J, Liu H, Widengren J. Combined Fluorescence Fluctuation and Spectrofluorometric Measurements Reveal a Red-Shifted, Near-IR Emissive Photo-Isomerized Form of Cyanine 5. Int J Mol Sci 2023; 24:ijms24031990. [PMID: 36768309 PMCID: PMC9916991 DOI: 10.3390/ijms24031990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
Cyanine fluorophores are extensively used in fluorescence spectroscopy and imaging. Upon continuous excitation, especially at excitation conditions used in single-molecule and super-resolution experiments, photo-isomerized states of cyanines easily reach population probabilities of around 50%. Still, effects of photo-isomerization are largely ignored in such experiments. Here, we studied the photo-isomerization of the pentamethine cyanine 5 (Cy5) by two similar, yet complementary means to follow fluorophore blinking dynamics: fluorescence correlation spectroscopy (FCS) and transient-state (TRAST) excitation-modulation spectroscopy. Additionally, we combined TRAST and spectrofluorimetry (spectral-TRAST), whereby the emission spectra of Cy5 were recorded upon different rectangular pulse-train excitations. We also developed a framework for analyzing transitions between multiple emissive states in FCS and TRAST experiments, how the brightness of the different states is weighted, and what initial conditions that apply. Our FCS, TRAST, and spectral-TRAST experiments showed significant differences in dark-state relaxation amplitudes for different spectral detection ranges, which we attribute to an additional red-shifted, emissive photo-isomerized state of Cy5, not previously considered in FCS and single-molecule experiments. The photo-isomerization kinetics of this state indicate that it is formed under moderate excitation conditions, and its population and emission may thus deserve also more general consideration in fluorescence imaging and spectroscopy experiments.
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7
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Medeiros NG, Braga CA, Câmara VS, Duarte RC, Rodembusch FS. Near‐infrared fluorophores based on heptamethine cyanine dyes: from their synthesis and photophysical properties to recent optical sensing and bioimaging applications. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Natália G Medeiros
- Universidade Federal do Rio Grande do Sul Organic Chemistry Av. Bento Goncalves 9500. Bairro Agronomia 91501-970 Porto Alegre BRAZIL
| | - Cláudia A. Braga
- Universidade Federal do Rio Grande do Sul Organic Chemistry Av. Bento Goncalves 9500. Bairro Agronomia 91501-970 Porto Alegre BRAZIL
| | - Viktor S Câmara
- Universidade Federal do Rio Grande do Sul Organic Chemistry Av. Bento Goncalves 9500. Bairro Agronomia 91501-970 Porto Alegre BRAZIL
| | - Rodrigo C Duarte
- Universidade Federal do Rio Grande do Sul Organic Chemistry Av. Bento Goncalves 9500. Bairro Agronomia 91501-970 Porto Alegre BRAZIL
| | - Fabiano Severo Rodembusch
- Universidade Federal do Rio Grande do Sul Organic Chemistry Av. Bento Gonçalves 9500Bairro Agronomia 91501-970 Porto Alegre BRAZIL
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8
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Matikonda SS, Hammersley G, Kumari N, Grabenhorst L, Glembockyte V, Tinnefeld P, Ivanic J, Levitus M, Schnermann MJ. Impact of Cyanine Conformational Restraint in the Near-Infrared Range. J Org Chem 2020; 85:5907-5915. [PMID: 32275153 PMCID: PMC8459201 DOI: 10.1021/acs.joc.0c00236] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Appending conformationally restraining ring systems to the cyanine chromophore creates exceptionally bright fluorophores in the visible range. Here, we report the application of this strategy in the near-infrared range through the preparation of the first restrained heptamethine indocyanine. Time-resolved absorption spectroscopy and fluorescence correlation spectroscopy verify that, unlike the corresponding parent unrestrained variant, the restrained molecule is not subject to photoisomerization. Notably, however, the room-temperature emission efficiency and the fluorescence lifetime of the restrained cyanine are not extended relative to the parent cyanine, even in viscous solvents. Thus, in contrast to prior reports, the photoisomerization of heptamethine cyanines does not contribute significantly to the excited-state chemistry of these molecules. We also find that the fluorescence lifetime of the restrained heptamethine cyanine is temperature-insensitive and significantly extended at moderately elevated temperatures relative to the parent cyanine. Finally, computational studies have been used to evaluate the impact of the conformational restraint on atomic and orbital structure across the cyanine series. These studies clarify the role of photoisomerization in the heptamethine cyanine scaffold and demonstrate the dramatic effect of restraint on the temperature sensitivity of these dyes.
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Affiliation(s)
- Siddharth S Matikonda
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, Maryland 21702, United States
| | - Gabrielle Hammersley
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, Maryland 21702, United States
| | - Nikita Kumari
- School of Molecular Sciences and The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, United States
| | - Lennart Grabenhorst
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, 81377, Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, 81377, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München, 81377, Germany
| | - Joseph Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Marcia Levitus
- School of Molecular Sciences and The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, United States
| | - Martin J Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, Maryland 21702, United States
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9
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Kumari N, Ciuba MA, Levitus M. Photophysical properties of the hemicyanine Dy-630 and its potential as a single-molecule fluorescent probe for biophysical applications. Methods Appl Fluoresc 2019; 8:015004. [PMID: 31585443 DOI: 10.1088/2050-6120/ab4b0d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Protein-induced fluorescence enhancement (PIFE) is an increasingly used approach to investigate DNA-protein interactions at the single molecule level. The optimal probe for this type of application is highly photostable, has a high absorption extinction coefficient, and has a moderate fluorescence quantum yield that increases significantly when the dye is in close proximity to a large macromolecule such as a protein. So far, the green-absorbing symmetric cyanine known as Cy3 has been the probe of choice in this field because the magnitude of the increase observed upon protein binding (usually 2-4 -fold) is large enough to allow for the analysis of protein dynamics on the inherently noisy single-molecule signals. Here, we report the characterization of the photophysical properties of the red-absorbing hemicyanine dye Dy-630 in the context of its potential application as a single-molecule PIFE probe. The behavior of Dy-630 in solution is similar to that of Cy3; the fluorescence quantum yield and lifetime of Dy-630 increase with increasing viscosity, and decrease with increasing temperature indicating the existence of an activated nonradiative process that depopulates the singlet state of the dye. As in the case of Cy3, the results of transient spectroscopy experiments are consistent with the formation of a photoisomer that reverts to the ground state thermally in the microsecond timescale. Unfortunately, experiments with DNA samples paint a more complex scenario. As in the case of Cy3, the fluorescence quantum yield of Dy-630 increases significantly when the dye interacts with the DNA bases, but in the case of Dy-630 attachment to DNA results in an already long fluorescence lifetime that does not provide a significant window for the protein-induced enhancement observed with Cy3. Although we show that Dy-630 may not be well-suited for PIFE, our results shed light on the optimal design principles for probes for PIFE applications.
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10
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Karlsson JKG, Laude A, Hall MJ, Harriman A. Photo-isomerization of the Cyanine Dye Alexa-Fluor 647 (AF-647) in the Context of dSTORM Super-Resolution Microscopy. Chemistry 2019; 25:14983-14998. [PMID: 31515919 DOI: 10.1002/chem.201904117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Indexed: 02/06/2023]
Abstract
Cyanine dyes, as used in super-resolution fluorescence microscopy, undergo light-induced "blinking", enabling localization of fluorophores with spatial resolution beyond the optical diffraction limit. Despite a plethora of studies, the molecular origins of this blinking are not well understood. Here, we examine the photophysical properties of a bio-conjugate cyanine dye (AF-647), used extensively in dSTORM imaging. In the absence of a potent sacrificial reductant, light-induced electron transfer and intermediates formed via the metastable, triplet excited state are considered unlikely to play a significant role in the blinking events. Instead, it is found that, under conditions appropriate to dSTORM microscopy, AF-647 undergoes reversible photo-induced isomerization to at least two long-lived dark species. These photo-isomers are characterized spectroscopically and their interconversion probed by computational means. The first-formed isomer is light sensitive and transforms to a longer-lived species in modest yield that could be involved in dSTORM related blinking. Permanent photobleaching of AF-647 occurs with very low quantum yield and is partially suppressed by the anaerobic redox buffer.
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Affiliation(s)
- Joshua K G Karlsson
- Molecular Photonics Laboratory, SNES, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alex Laude
- Bio-Imaging Unit, Medical School, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Michael J Hall
- School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Anthony Harriman
- Molecular Photonics Laboratory, SNES, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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11
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Das AK, Ihmels H, Kölsch S. Diphenylaminostyryl-substituted quinolizinium derivatives as fluorescent light-up probes for duplex and quadruplex DNA. Photochem Photobiol Sci 2019; 18:1373-1381. [PMID: 30916703 DOI: 10.1039/c9pp00096h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
(E)-2-[1'-((Diphenylamino)styryl)quinolizinium (3a) and 2,2'-{(phenylimino)-bis[(E)-1'',1'''-styryl]}-bis[quinolizinium] (3b) were synthesized, and their interactions with duplex DNA and quadruplex DNA were investigated with a particular focus on their ability to operate as DNA-sensitive fluorescent probes. Due to the significantly different size and steric demand of these quinolizinium derivatives they exhibit different binding modes. Thus, 3a intercalates into duplex DNA and binds through π stacking to quadruplex DNA, whereas 3b favours groove binding to both DNA forms. The emission intensity of these compounds is very low in aqueous solution, but it increases drastically upon association with duplex DNA by a factor of 11 (3a) and >100 (3b) and with quadruplex DNA by a factor of >100 (3a) and 10 (3b), with emission bands between 600 and 750 nm.
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Affiliation(s)
- Avijit Kumar Das
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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12
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Mahoney DP, Demissie AA, Dickson RM. Optically Activated Delayed Fluorescence through Control of Cyanine Dye Photophysics. J Phys Chem A 2019; 123:3599-3606. [PMID: 30908044 DOI: 10.1021/acs.jpca.9b01333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Merocyanine 540 fluorescence can be enhanced by optically depopulating dark photoisomer states to regenerate the fluorescence-generating manifold of the all-trans isomer. Here, we utilize a competing modulation route, long-wavelength coexcitation of the trans triplet population to not only modulate fluorescence through enhanced ground-state recovery but also generate optically activated delayed fluorescence (OADF) with longer-wavelength co-illumination. Such OADF (∼580 nm) is directly observed with pulsed fluorescence excitation at 532 nm, followed by long-wavelength (637 nm) continuous wave depopulation of the photogenerated triplet by repopulating the emissive S1 state. Such reverse intersystem crossing (RISC) results in ns-lived fluorescence delayed by several microseconds after the initial primary excitation pulse and the prompt 1 ns-lived fluorescence that it induces. The dark state from which OADF is generated decays more rapidly with increased secondary laser intensity, as the optically induced RISC rate increases. This first OADF from organic dyes is observed, as the red secondary laser excites ∼580 nm, <1 ns-lived fluorescence from the previously optically prepared ∼1 μs-lived triplet state. This sequential two-photon, repumped fluorescence yields background-free collection with potential for new high-sensitivity fluorescence imaging schemes.
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Affiliation(s)
- Daniel P Mahoney
- School of Chemistry & Biochemistry and Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Aida A Demissie
- School of Chemistry & Biochemistry and Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Robert M Dickson
- School of Chemistry & Biochemistry and Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
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13
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Kulinich AV, Ishchenko AA, Bondarev SL, Knyukshto VN. Low-Temperature Effect on the Electronic Structure and Spectral-Fluorescent Properties of Highly Dipolar Merocyanines. J Phys Chem A 2018; 122:9645-9652. [PMID: 30452263 DOI: 10.1021/acs.jpca.8b09522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Absorption and fluorescence spectra of a vinylogous series of reversely solvatochromic merocyanines based on benzimidazole and malononitrile have been studied in frozen ethanol solutions at 77 K. It is found that they possess negative thermochromism-in contrast to both positively solvatochromic merocyanines and negatively solvatochromic symmetrical ionic polymethines-and even stronger negative thermofluorochromism. It has been deduced from the spectral data that at low temperature their electronic structure becomes more dipolar, deviating substantially from the virtual ideal polymethine in both the ground and the excited states. At that, owing probably to the high polarity and ordering of frozen ethanol, the dipolarity of the studied merocyanines increases with the polymethine chain lengthening-the tendency not observed for them in common solvents. The conclusions, based on the spectral data analysis, have been verified by the (TD)DFT-PCM simulations of the dyes within the four-level scheme of electronic transitions.
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Affiliation(s)
- Andrii V Kulinich
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine , Murmanska Street 5 , Kyiv 02660 , Ukraine
| | - Alexander A Ishchenko
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine , Murmanska Street 5 , Kyiv 02660 , Ukraine
| | - Stanislav L Bondarev
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus , Nezalezhnasti Avenue 68-2 , Minsk 220072 , Republic of Belarus
| | - Valery N Knyukshto
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus , Nezalezhnasti Avenue 68-2 , Minsk 220072 , Republic of Belarus
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14
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Ihmels H, Mahmoud MM, Patrick BO. Optical differentiation between quadruplex DNA and duplex DNA with a [2.2.2]heptamethinecyanine dye. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Heiko Ihmels
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Mohamed M.A. Mahmoud
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Brian O. Patrick
- Department of Chemistry; University of British Columbia; Vancouver Canada
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15
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Ngo JT, Adams SR, Deerinck TJ, Boassa D, Rodriguez-Rivera F, Palida SF, Bertozzi CR, Ellisman MH, Tsien RY. Click-EM for imaging metabolically tagged nonprotein biomolecules. Nat Chem Biol 2016; 12:459-65. [PMID: 27110681 PMCID: PMC4871776 DOI: 10.1038/nchembio.2076] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 03/08/2016] [Indexed: 12/14/2022]
Abstract
EM has long been the main technique for imaging cell structures with nanometer resolution but has lagged behind light microscopy in the crucial ability to make specific molecules stand out. Here we introduce click-EM, a labeling technique for correlative light microscopy and EM imaging of nonprotein biomolecules. In this approach, metabolic labeling substrates containing bioorthogonal functional groups are provided to cells for incorporation into biopolymers by endogenous biosynthetic machinery. The unique chemical functionality of these analogs is exploited for selective attachment of singlet oxygen-generating fluorescent dyes via bioorthogonal 'click chemistry' ligations. Illumination of dye-labeled structures generates singlet oxygen to locally catalyze the polymerization of diaminobenzidine into an osmiophilic reaction product that is readily imaged by EM. We describe the application of click-EM in imaging metabolically tagged DNA, RNA and lipids in cultured cells and neurons and highlight its use in tracking peptidoglycan synthesis in the Gram-positive bacterium Listeria monocytogenes.
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Affiliation(s)
- John T. Ngo
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093
| | - Stephen R. Adams
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093
| | - Thomas J. Deerinck
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093
| | - Daniela Boassa
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093
| | | | - Sakina F. Palida
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093
| | - Carolyn R. Bertozzi
- Howard Hughes Medical Institute
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Mark H. Ellisman
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093
| | - Roger Y. Tsien
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093
- Howard Hughes Medical Institute
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16
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Zakharova GV, Avakyan VG, Markelov VP, Svyatoslavskii NL, Svyatoslavskaya TA, Chibisov AK. Effect of cucurbituril on the primary photoprocesses in indocarbocyanine dyes in water. HIGH ENERGY CHEMISTRY 2015. [DOI: 10.1134/s001814391506017x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Mahoney DP, Owens EA, Fan C, Hsiang JC, Henary MM, Dickson RM. Tailoring cyanine dark states for improved optically modulated fluorescence recovery. J Phys Chem B 2015; 119:4637-43. [PMID: 25763888 DOI: 10.1021/acs.jpcb.5b00777] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cyanine dyes are well-known for their bright fluorescence and utility in biological imaging. However, cyanines also readily photoisomerize to produce nonemissive dark states. Co-illumination with a secondary, red-shifted light source on-resonance with the longer wavelength absorbing dark state reverses the photoisomerization and returns the cyanine dye to the fluorescent manifold, increasing steady-state fluorescence intensity. Modulation of this secondary light source dynamically alters emission intensity, drastically improving detection sensitivity and facilitating fluorescence signals to be recovered from an otherwise overwhelming background. Red and near-IR emitting cyanine derivatives have been synthesized with varying alkyl chain lengths and halogen substituents to alter dual-laser fluorescence enhancement. Photophysical properties and enhancement with dual laser modulation were coupled with density functional calculations to characterize substituent effects on dark state photophysics, potentially improving detection in high background biological environments.
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Affiliation(s)
| | - Eric A Owens
- ‡Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | | | | | - Maged M Henary
- ‡Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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18
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Wu X, Liu F, Wells KL, Tan SLJ, Webster RD, Tan H, Zhang D, Xing B, Yeow EKL. Interplay of Hole Transfer and Host–Guest Interaction in a Molecular Dyad and Triad: Ensemble and Single‐Molecule Spectroscopy and Sensing Applications. Chemistry 2014; 21:3387-98. [DOI: 10.1002/chem.201404360] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Xiangyang Wu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Fax: (+65) 6791‐1961
| | - Fang Liu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Fax: (+65) 6791‐1961
| | - Kym L. Wells
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Fax: (+65) 6791‐1961
| | - Serena L. J. Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Fax: (+65) 6791‐1961
| | - Richard D. Webster
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Fax: (+65) 6791‐1961
| | - Howe‐Siang Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Fax: (+65) 6791‐1961
| | - Dawei Zhang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Fax: (+65) 6791‐1961
| | - Bengang Xing
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Fax: (+65) 6791‐1961
| | - Edwin K. L. Yeow
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Fax: (+65) 6791‐1961
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19
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Wang TY, Friedman LJ, Gelles J, Min W, Hoskins AA, Cornish VW. The covalent trimethoprim chemical tag facilitates single molecule imaging with organic fluorophores. Biophys J 2014; 106:272-8. [PMID: 24411259 DOI: 10.1016/j.bpj.2013.11.4488] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/05/2013] [Accepted: 11/25/2013] [Indexed: 11/24/2022] Open
Abstract
Chemical tags can be used to selectively label proteins with fluorophores that have high photon outputs. By permitting straightforward single molecule (SM) detection and imaging with organic fluorophores, chemical tags have the potential to advance SM imaging as a routine experimental tool for studying biological mechanism. However, there has been little characterization of the photophysical consequences of using chemical tags with organic fluorophores. Here, we examine the effect the covalent trimethoprim chemical tag (A-TMP-tag) has on the SM imaging performance of the fluorophores, Atto655 and Alexa647, by evaluating the photophysical properties of these fluorophores and their A-TMP-tag conjugates. We measure SM photon flux, survival lifetime, and total photon output under conditions that mimic the live cell environment and demonstrate that the A-TMP-tag complements the advantageous SM imaging properties of Atto655 and Alexa647. We also measure the ensemble properties of quantum yield and photostability lifetime, revealing a correlation between SM and ensemble properties. Taken together, these findings establish a systematic method for evaluating the impact chemical tags have on fluorophores for SM imaging and demonstrate that the A-TMP-tag with Atto655 and Alexa647 are promising reagents for biological imaging.
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Affiliation(s)
- Tracy Y Wang
- Department of Chemistry, Columbia University, New York, New York
| | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts
| | - Wei Min
- Department of Chemistry, Columbia University, New York, New York
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin
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20
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Zheng Q, Juette MF, Jockusch S, Wasserman MR, Zhou Z, Altman RB, Blanchard SC. Ultra-stable organic fluorophores for single-molecule research. Chem Soc Rev 2014; 43:1044-56. [PMID: 24177677 PMCID: PMC3946787 DOI: 10.1039/c3cs60237k] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fluorescence provides a mechanism for achieving contrast in biological imaging that enables investigations of molecular structure, dynamics, and function at high spatial and temporal resolution. Small-molecule organic fluorophores have proven essential for such efforts and are widely used in advanced applications such as single-molecule and super-resolution microscopy. Yet, organic fluorophores, like all fluorescent species, exhibit instabilities in their emission characteristics, including blinking and photobleaching that limit their utility and performance. Here, we review the photophysics and photochemistry of organic fluorophores as they pertain to mitigating such instabilities, with a specific focus on the development of stabilized fluorophores through derivatization. Self-healing organic fluorophores, wherein the triplet state is intramolecularly quenched by a covalently attached protective agent, exhibit markedly improved photostabilities. We discuss the potential for further enhancements towards the goal of developing "ultra-stable" fluorophores spanning the visible spectrum and how such fluorophores are likely to impact the future of single-molecule research.
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Affiliation(s)
- Qinsi Zheng
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, USA.
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21
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Kulinich AV, Ishchenko AA, Chibisov AK, Zakharova GV. Effect of electronic asymmetry and the polymethine chain length on photoprocesses in merocyanine dyes. J Photochem Photobiol A Chem 2014. [DOI: 10.1016/j.jphotochem.2013.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Cao J, Hu C, Sun W, Xu Q, Fan J, Song F, Sun S, Peng X. The mechanism of different sensitivity of meso-substituted and unsubstituted cyanine dyes in rotation-restricted environments for biomedical imaging applications. RSC Adv 2014. [DOI: 10.1039/c3ra46612d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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23
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Stennett EMS, Ciuba MA, Levitus M. Photophysical processes in single molecule organic fluorescent probes. Chem Soc Rev 2014; 43:1057-75. [DOI: 10.1039/c3cs60211g] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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24
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25
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Ciuba MA, Levitus M. Manganese-Induced Triplet Blinking and Photobleaching of Single Molecule Cyanine Dyes. Chemphyschem 2013; 14:3495-502. [DOI: 10.1002/cphc.201300634] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 07/24/2013] [Indexed: 11/09/2022]
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26
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Photophysical studies of a new water soluble indocarbocyanine dye adsorbed onto microcrystalline cellulose and β-cyclodextrin. Molecules 2013; 18:5648-68. [PMID: 23676472 PMCID: PMC6269746 DOI: 10.3390/molecules18055648] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 04/26/2013] [Accepted: 05/09/2013] [Indexed: 11/16/2022] Open
Abstract
A water-soluble indocarbocyanine dye was synthesized and its photophysics were studied for the first time on two solid hosts, microcrystalline cellulose and b-cyclodextrin, as well as in homogeneous media. The inclusion of the indocarbocyanine moiety onto microcrystalline cellulose increased the dye aggregation with both H and J aggregates being formed. Adsorption on b-cyclodextrin enhanced aggregation in a similar way. The fluorescence quantum yields were determined for the powdered samples of the cyanine dye on the two hosts and a significant increase was observed relative to homogeneous solution. A remarkable concentration dependence was also detected in both cases. A lifetime distribution analysis has shown that the indocarbocyanine dye mainly occupies the amorphous part of cellulose and is not entrapped in the crystalline part of this host. In the b-CD case, the adsorption occurs outside the host cavity. In both hosts a strong concentration quenching effect is observed and only monomers emit. Both adsorptions may be explained by stereochemical constraints imposed by the two long sulphoethyl tails linked to nitrogen atoms of the indocarbocyanine dye.
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27
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Zheng Q, Jockusch S, Zhou Z, Altman RB, Warren JD, Turro NJ, Blanchard SC. On the Mechanisms of Cyanine Fluorophore Photostabilization. J Phys Chem Lett 2012; 3:2200-2203. [PMID: 22984636 PMCID: PMC3439216 DOI: 10.1021/jz300670p] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Cyanine fluorophores exhibit greatly improved photostability when covalently linked to stabilizers, such as cyclooctatetraene (COT), nitrobenzyl alcohol (NBA) or Trolox. However, the mechanism by which photostabilization is mediated has yet to be determined. Here we present spectroscopic evidence that COT, when covalently linked to Cy5, substantially reduces the lifetime of the Cy5 triplet state, and that the degree of triplet state quenching correlates with enhancements in photostability observed in single-molecule fluorescence measurements. By contrast, NBA and Trolox did not quench the Cy5 triplet state under our conditions suggesting that their mechanism of photostabilization is different from COT and does not target the fluorophore triplet state directly. These findings provide insights into the mechanisms of fluorophore photostabilization that may lead to improved fluorophore designs for biological imaging applications.
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Affiliation(s)
- Qinsi Zheng
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, United States
- Tri-Institutional Training Program in Chemical Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, United States
| | - Steffen Jockusch
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Zhou Zhou
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, United States
| | - Roger B. Altman
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, United States
| | - J. David Warren
- Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, United States
| | - Nicholas J. Turro
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Scott C. Blanchard
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, United States
- Tri-Institutional Training Program in Chemical Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, United States
- Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, United States
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28
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Hall LM, Gerowska M, Brown T. A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5 and Cy3B monomers. Nucleic Acids Res 2012; 40:e108. [PMID: 22495935 PMCID: PMC3413114 DOI: 10.1093/nar/gks303] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Cy3B is an extremely bright and stable fluorescent dye, which is only available for coupling to nucleic acids post-synthetically. This severely limits its use in the fields of genomics, biology and nanotechnology. We have optimized the synthesis of Cy3B, and for the first time produced a diverse range of Cy3B monomers for use in solid-phase oligonucleotide synthesis. This molecular toolkit includes phosphoramidite monomers with Cy3B linked to deoxyribose, to the 5-position of thymine, and to a hexynyl linker, in addition to an oligonucleotide synthesis resin in which Cy3B is linked to deoxyribose. These monomers have been used to incorporate single and multiple Cy3B units into oligonucleotides internally and at both termini. Cy3B Taqman probes, Scorpions and HyBeacons have been synthesized and used successfully in mutation detection, and a dual Cy3B Molecular Beacon was synthesized and found to be superior to the corresponding Cy3B/DABCYL Beacon. Attachment of Cy3, Cy3B and Cy5 to the 5-position of thymidine by an ethynyl linker enabled the synthesis of an oligonucleotide FRET system. The rigid linker between the dye and nucleobase minimizes dye–dye and dye–DNA interactions and reduces fluorescence quenching. These reagents open up new future applications of Cy3B, including more sensitive single-molecule and cell-imaging studies.
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Affiliation(s)
- Lucy M Hall
- School of Chemistry, University of Southampton, SO17 1BJ, UK
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29
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Matichak JD, Hales JM, Barlow S, Perry JW, Marder SR. Dioxaborine- and Indole-Terminated Polymethines: Effects of Bridge Substitution on Absorption Spectra and Third-Order Polarizabilities. J Phys Chem A 2011; 115:2160-8. [DOI: 10.1021/jp110425r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan D. Matichak
- School of Chemistry and Biochemistry and Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Joel M. Hales
- School of Chemistry and Biochemistry and Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Stephen Barlow
- School of Chemistry and Biochemistry and Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Joseph W. Perry
- School of Chemistry and Biochemistry and Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Seth R. Marder
- School of Chemistry and Biochemistry and Center for Organic Photonics and Electronics, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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30
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Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments. Q Rev Biophys 2010; 44:123-51. [DOI: 10.1017/s0033583510000247] [Citation(s) in RCA: 294] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThe breakthroughs in single molecule spectroscopy of the last decade and the recent advances in super resolution microscopy have boosted the popularity of cyanine dyes in biophysical research. These applications have motivated the investigation of the reactions and relaxation processes that cyanines undergo in their electronically excited states. Studies show that the triplet state is a key intermediate in the photochemical reactions that limit the photostability of cyanine dyes. The removal of oxygen greatly reduces photobleaching, but induces rapid intensity fluctuations (blinking). The existence of non-fluorescent states lasting from milliseconds to seconds was early identified as a limitation in single-molecule spectroscopy and a potential source of artifacts. Recent studies demonstrate that a combination of oxidizing and reducing agents is the most efficient way of guaranteeing that the ground state is recovered rapidly and efficiently. Thiol-containing reducing agents have been identified as the source of long-lived dark states in some cyanines that can be photochemically switched back to the emissive state. The mechanism of this process is the reversible addition of the thiol-containing compound to a double bond in the polymethine chain resulting in a non-fluorescent molecule. This process can be reverted by irradiation at shorter wavelengths. Another mechanism that leads to non-fluorescent states in cyanine dyes is cis–trans isomerization from the singlet-excited state. This process, which competes with fluorescence, involves the rotation of one-half of the molecule with respect to the other with an efficiency that depends strongly on steric effects. The efficiency of fluorescence of most cyanine dyes has been shown to depend dramatically on their molecular environment within the biomolecule. For example, the fluorescence quantum yield of Cy3 linked covalently to DNA depends on the type of linkage used for attachment, DNA sequence and secondary structure. Cyanines linked to the DNA termini have been shown to be mostly stacked at the end of the helix, while cyanines linked to the DNA internally are believed to partially bind to the minor or major grooves. These interactions not only affect the photophysical properties of the probes but also create a large uncertainty in their orientation.
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31
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Chmyrov A, Sandén T, Widengren J. Recovery of Photoinduced Reversible Dark States Utilized for Molecular Diffusion Measurements. Anal Chem 2010; 82:9998-10005. [DOI: 10.1021/ac1014047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andriy Chmyrov
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Tor Sandén
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Jerker Widengren
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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32
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Pandey RK, James N, Chen Y, Dobhal MP. Cyanine Dye-Based Compounds for Tumor Imaging With and Without Photodynamic Therapy. TOPICS IN HETEROCYCLIC CHEMISTRY 2008. [DOI: 10.1007/7081_2008_113] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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33
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Tani K, Ito C, Hanawa Y, Uchida M, Otaguro K, Horiuchi H, Hiratsuka H. Photophysical property and photostability of J-aggregate thin films of thiacyanine dyes prepared by the spin-coating method. J Phys Chem B 2008; 112:836-44. [PMID: 18171049 DOI: 10.1021/jp077088o] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By use of electrostatic interactions of dye molecules and poly(diallyldimethylammonium chloride) (PDDA), the spin-coating technique has been successfully applied to the preparation of stable J-aggregate thin films of thiacarbocyanine dyes on a polycarbonate or quartz plate. The J-aggregate thin films were prepared by the spin-coating of PDDA aqueous solution on dye thin films prepared on a substrate by the spin-coating of 2,2,3,3-tetrafluoro-1-propanol solution of dyes. Photophysical properties of the dye thin films and J-aggregate thin films were studied by measuring the fluorescence spectra, quantum yields, and lifetimes. Coherent size of the J-aggregates was estimated to be 3-12 by means of the absorption bandwidth (full width at half maximum) or radiative lifetime. Photostability of the J-aggregate thin films was also studied in terms of photodegradation efficiency under argon and oxygen in comparison with the dye thin films, and J-aggregate thin films were found to be more stable than the corresponding dye thin films.
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Affiliation(s)
- Katsuhiko Tani
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University, Kiryu, Gunma 376-8515, Japan
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34
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Sanborn ME, Connolly BK, Gurunathan K, Levitus M. Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA. J Phys Chem B 2007; 111:11064-74. [PMID: 17718469 DOI: 10.1021/jp072912u] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sulfoindocyanine Cy3 is one of the most commonly used fluorescent dyes in the investigation of the structure and dynamics of nucleic acids by means of fluorescence methods. In this work, we report the fluorescence and photophysical properties of Cy3 attached covalently to single-stranded and duplex DNA. Steady-state and time-resolved fluorescence techniques were used to determine fluorescence quantum yields, emission lifetimes, and fluorescence anisotropy decays. The existence of a transient photoisomer was investigated by means of transient absorption techniques. The fluorescence quantum yield of Cy3 is highest when attached to the 5' terminus of single-stranded DNA (Cy3-5' ssDNA), and decreases by a factor of 2.4 when the complementary strand is annealed to form duplex DNA (Cy3-5' dsDNA). Substantial differences were also observed between the 5'-modified strands and strands modified through an internal amino-modified deoxy uridine. The fluorescence decay of Cy3 became multiexponential upon conjugation to DNA. The longest lifetime was observed for Cy3-5' ssDNA, where about 50% of the decay is dominated by a 2.0-ns lifetime. This value is more than 10 times larger than the fluorescence lifetime of the free dye in solution. These observations are interpreted in terms of a model where the molecule undergoes a trans-cis isomerization reaction from the first excited state. We observed that the activation energy for photoisomerization depends strongly on the microenvironment in which the dye is located. The unusually high activation energy measured for Cy3-5' ssDNA is an indication of dye-ssDNA interactions. In fact, the time-resolved fluorescence anisotropy decay of this sample is dominated by a 2.5-ns rotational correlation time, which evidences the lack of rotational freedom of the dye around the linker that separates it from the terminal 5' phosphate. The remarkable variations in the photophysical properties of Cy3-DNA constructs demonstrate that caution should be used when Cy3 is used in studies employing DNA conjugates.
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Affiliation(s)
- Matthew E Sanborn
- Department of Chemistry and Biochemistry, Department of Physics and The Biodesign Institute, Arizona State University, Tempe, Arizona 85287-5601, USA
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35
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Improta R, Santoro F. A Theoretical Study on the Factors Influencing Cyanine Photoisomerization: The Case of Thiacyanine in Gas Phase and in Methanol. J Chem Theory Comput 2005; 1:215-29. [DOI: 10.1021/ct049899r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Köhn F, Hofkens J, Gronheid R, Cotlet M, Müllen K, Van der Auweraer M, De Schryver FC. Excitation energy transfer in dendritic host-guest donor-acceptor systems. Chemphyschem 2002; 3:1005-13. [PMID: 12516210 DOI: 10.1002/cphc.200290001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We report on a study of a physically formed host-guest system, which was designed to be investigated by fluorescence energy transfer. All donor and acceptor molecules used were cyanine dyes. Investigation was performed at the ensemble level as well as at the single-molecule level. The ensemble measurements revealed a distribution of binding sites as well for the donor as for the acceptor. Accordingly, we found a distribution of the energy transfer efficiency. At the single-molecule level, these distributions are still present. We could discriminate entities that show very efficient energy transfer, some that do not show any energy transfer and systems whose energy transfer efficiency is only about 50%. The latter allowed the time-resolved detection of energy transfer of single entities through the acceptor decay. Finally, we discuss the observation that the energy transfer efficiency fluctuates as a function of time.
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Affiliation(s)
- Fabian Köhn
- Department of Chemistry, Laboratory for Photochemistry and Spectroscopy, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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Slavnova TD, Chibisov AK, Görner H. Photoprocesses of Thiacarbocyanine Monomers, Dimers, and Aggregates Bound to Polyanions. J Phys Chem A 2002. [DOI: 10.1021/jp020210t] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tatyana D. Slavnova
- Max-Planck-Institut für Strahlenchemie, D-45413 Mülheim an der Ruhr, Germany
| | | | - Helmut Görner
- Max-Planck-Institut für Strahlenchemie, D-45413 Mülheim an der Ruhr, Germany
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38
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Chibisov AK, Görner H. Photophysics of aggregated 9-methylthiacarbocyanine bound to polyanions. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)00531-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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39
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Köhn F, Hofkens J, Gronheid R, Van der Auweraer M, De Schryver FC. Parameters Influencing the On- and Off-Times in the Fluorescence Intensity Traces of Single Cyanine Dye Molecules. J Phys Chem A 2002. [DOI: 10.1021/jp012959u] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabian Köhn
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200 F, 3001 Leuven, Belgium
| | - Johan Hofkens
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200 F, 3001 Leuven, Belgium
| | - Roel Gronheid
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200 F, 3001 Leuven, Belgium
| | - Mark Van der Auweraer
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200 F, 3001 Leuven, Belgium
| | - Frans C. De Schryver
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200 F, 3001 Leuven, Belgium
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40
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Abd El-Aal RM. Synthesis and absorption spectra of new polymethine cyanine dyes. DYES AND PIGMENTS 2002; 52:129-136. [DOI: 10.1016/s0143-7208(01)00088-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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41
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Palit DK, Singh AK, Bhasikuttan AC, Mittal JP. Relaxation Dynamics in the Excited States of LDS-821 in Solution. J Phys Chem A 2001. [DOI: 10.1021/jp004142r] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dipak K. Palit
- Radiation Chemistry and Chemical Dynamics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Ajay K. Singh
- Radiation Chemistry and Chemical Dynamics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - A. C. Bhasikuttan
- Radiation Chemistry and Chemical Dynamics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Jai P. Mittal
- Radiation Chemistry and Chemical Dynamics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
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42
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Chibisov AK, Shvedov SV, Görner H. Photosensitized processes in dicarbocyanine dyes induced by energy transfer: delayed fluorescence, trans→cis isomerization and electron transfer. J Photochem Photobiol A Chem 2001. [DOI: 10.1016/s1010-6030(01)00426-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Tatikolov AS, Costa SM. Photophysical and aggregation properties of a long-chain squarylium indocyanine dye. J Photochem Photobiol A Chem 2001. [DOI: 10.1016/s1010-6030(01)00405-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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44
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Widengren J, Schwille P. Characterization of Photoinduced Isomerization and Back-Isomerization of the Cyanine Dye Cy5 by Fluorescence Correlation Spectroscopy. J Phys Chem A 2000. [DOI: 10.1021/jp000059s] [Citation(s) in RCA: 301] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jerker Widengren
- Department of Spectroscopy and Photochemical Kinetics, and Department of Experimental Biophysics, Max-Planck Institute for Biophysical Chemistry, 370 77 Göttingen, Germany
| | - Petra Schwille
- Department of Spectroscopy and Photochemical Kinetics, and Department of Experimental Biophysics, Max-Planck Institute for Biophysical Chemistry, 370 77 Göttingen, Germany
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45
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Mishra A, Behera RK, Behera PK, Mishra BK, Behera GB. Cyanines during the 1990s: A Review. Chem Rev 2000; 100:1973-2012. [PMID: 11749281 DOI: 10.1021/cr990402t] [Citation(s) in RCA: 959] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A Mishra
- Centre of Studies in Surface Science and Technology, Department of Chemistry, Sambalpur University, Jyoti Vihar 768 019, Orissa, India
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46
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Sanchez-Galvez A, Hunt P, Robb MA, Olivucci M, Vreven T, Schlegel HB. Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines. J Am Chem Soc 2000. [DOI: 10.1021/ja993985x] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adelaida Sanchez-Galvez
- Contribution from the Department of Chemistry, King's College London, Strand, London WC2R 2LS, U.K., Istituto di Chimica Organica, Universitá degli Studi di Siena, via Aldo Moro, I-53100 Siena, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Patricia Hunt
- Contribution from the Department of Chemistry, King's College London, Strand, London WC2R 2LS, U.K., Istituto di Chimica Organica, Universitá degli Studi di Siena, via Aldo Moro, I-53100 Siena, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Michael A. Robb
- Contribution from the Department of Chemistry, King's College London, Strand, London WC2R 2LS, U.K., Istituto di Chimica Organica, Universitá degli Studi di Siena, via Aldo Moro, I-53100 Siena, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Massimo Olivucci
- Contribution from the Department of Chemistry, King's College London, Strand, London WC2R 2LS, U.K., Istituto di Chimica Organica, Universitá degli Studi di Siena, via Aldo Moro, I-53100 Siena, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Thom Vreven
- Contribution from the Department of Chemistry, King's College London, Strand, London WC2R 2LS, U.K., Istituto di Chimica Organica, Universitá degli Studi di Siena, via Aldo Moro, I-53100 Siena, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - H. Bernhard Schlegel
- Contribution from the Department of Chemistry, King's College London, Strand, London WC2R 2LS, U.K., Istituto di Chimica Organica, Universitá degli Studi di Siena, via Aldo Moro, I-53100 Siena, Italy, and Department of Chemistry, Wayne State University, Detroit, Michigan 48202
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47
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Khimenko V, Chibisov AK, Görner H. Effects of Alkyl Substituents in the Polymethine Chain on the Photoprocesses in Thiacarbocyanine Dyes. J Phys Chem A 1997. [DOI: 10.1021/jp971472b] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vitalii Khimenko
- Center of Photochemistry, Russian Academy of Sciences, 117421 Moscow, Russia
| | | | - Helmut Görner
- Max-Planck-Institut für Strahlenchemie, D-45413 Mülheim an der Ruhr, Germany
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48
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Chibisov AK, Görner H. Singlet versus triplet photoprocesses in indodicarbocyanine dyes and spiropyran-derived merocyanines. J Photochem Photobiol A Chem 1997. [DOI: 10.1016/s1010-6030(96)04604-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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