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Review of FRET biosensing and its application in biomolecular detection. Am J Transl Res 2023; 15:694-709. [PMID: 36915763 PMCID: PMC10006758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/05/2023] [Indexed: 03/16/2023]
Abstract
Life science research is advancing rapidly in the 21st century. Many innovative technologies and methodologies are being applied in various fields of the life sciences to reveal how macromolecules interact with each other. The technology of using fluorescent molecules in biomedical research has contributed immensely to progress in this field. Fluorescence-based optical biosensors, which show high specificity, exhibit huge potential for clinical diagnosis and treatment of many of the life-changing diseases. Fluorescence resonance energy transfer (FRET), is a technique that has been widely employed in biosensing ever since its discovery. It is a classic fluorescence technique, and an important biosensing research tool extensively utilized in the fields of toxicology, pharmacology, and biomedicine; many biosensor designs are based on FRET. Radiometric imaging of biological molecules, biomolecular interactions, and cellular processes are extensively performed using FRET biosensors. This review focuses on the selection of FRET donors and acceptors used for biosensing, and presents an overview of different FRET technologies. Furthermore, it highlights the progress in the application for FRET in nucleic acid and protein biosensing, and provides a viewpoint for future developmental trends using FRET technology.
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2
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Out-of-Phase Imaging after Optical Modulation (OPIOM) for Multiplexed Fluorescence Imaging Under Adverse Optical Conditions. Methods Mol Biol 2021; 2350:191-227. [PMID: 34331287 DOI: 10.1007/978-1-0716-1593-5_13] [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: 02/07/2023]
Abstract
Fluorescence imaging has become a powerful tool for observations in biology. Yet it has also encountered limitations to overcome optical interferences of ambient light, autofluorescence, and spectrally interfering fluorophores. In this account, we first examine the current approaches which address these limitations. Then we more specifically report on Out-of-Phase Imaging after Optical Modulation (OPIOM), which has proved attractive for highly selective multiplexed fluorescence imaging even under adverse optical conditions. After exposing the OPIOM principle, we detail the protocols for successful OPIOM implementation.
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3
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Protasova EA, Mishin AS, Lukyanov KA, Maksimov EG, Bogdanov AM. Chromophore reduction plus reversible photobleaching: how the mKate2 "photoconversion" works. Photochem Photobiol Sci 2021; 20:791-803. [PMID: 34085171 DOI: 10.1007/s43630-021-00060-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
mKate red-to-green photoconversion is a non-canonical type of phototransformation in fluorescent proteins, with a poorly understood mechanism. We have hypothesized that the daughter mKate2 protein may also be photoconvertible, and that this phenomenon would be connected with mKate(2) chromophore photoreduction. Indeed, upon the intense irradiation of the protein sample supplemented by sodium dithionite, the accumulation of green as well as blue spectral forms is enhanced. The reaction was shown to be reversible upon the reductant's removal. However, an analysis of the fluorescence microscopy data, absorption spectra, kinetics and time-resolved fluorescence spectroscopy revealed that the short-wavelength spectral forms of mKate(2) exist before photoactivation, that their fractions increase light-independently after dithionite addition, and that the conversion is facilitated by the photobleaching of the red chromophore form.
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Affiliation(s)
- Elena A Protasova
- Faculty of Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia
| | | | - Eugene G Maksimov
- Faculty of Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia.
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4
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Peng B, Dikdan R, Hill SE, Patterson-Orazem AC, Lieberman RL, Fahrni CJ, Dickson RM. Optically Modulated and Optically Activated Delayed Fluorescent Proteins through Dark State Engineering. J Phys Chem B 2021; 125:5200-5209. [PMID: 33978414 DOI: 10.1021/acs.jpcb.1c00649] [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
Modulating fluorescent protein emission holds great potential for increasing readout sensitivity for applications in biological imaging and detection. Here, we identify and engineer optically modulated yellow fluorescent proteins (EYFP, originally 10C, but renamed EYFP later, and mVenus) to yield new emitters with distinct modulation profiles and unique, optically gated, delayed fluorescence. The parent YFPs are individually modulatable through secondary illumination, depopulating a long-lived dark state to dynamically increase fluorescence. A single point mutation introduced near the chromophore in each of these YFPs provides access to a second, even longer-lived modulatable dark state, while a different double mutant renders EYFP unmodulatable. The naturally occurring dark state in the parent YFPs yields strong fluorescence modulation upon long-wavelength-induced dark state depopulation, allowing selective detection at the frequency at which the long wavelength secondary laser is intensity modulated. Distinct from photoswitches, however, this near IR secondary coexcitation repumps the emissive S1 level from the long-lived triplet state, resulting in optically activated delayed fluorescence (OADF). This OADF results from secondary laser-induced, reverse intersystem crossing (RISC), producing additional nanosecond-lived, visible fluorescence that is delayed by many microseconds after the primary excitation has turned off. Mutation of the parent chromophore environment opens an additional modulation pathway that avoids the OADF-producing triplet state, resulting in a second, much longer-lived, modulatable dark state. These Optically Modulated and Optically Activated Delayed Fluorescent Proteins (OMFPs and OADFPs) are thus excellent for background- and reference-free, high sensitivity cellular imaging, but time-gated OADF offers a second modality for true background-free detection. Our combined structural and spectroscopic data not only gives additional mechanistic details for designing optically modulated fluorescent proteins but also provides the opportunity to distinguish similarly emitting OMFPs through OADF and through their unique modulation spectra.
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Affiliation(s)
- Baijie Peng
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Ryan Dikdan
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Shannon E Hill
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Athéna C Patterson-Orazem
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Christoph J Fahrni
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Robert M Dickson
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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5
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Sun T, Li T, Yi K, Gao X. Structure-guided evolution of Green2 toward photostability and quantum yield enhancement by F145Y substitution. Protein Sci 2020; 29:1964-1974. [PMID: 32715541 DOI: 10.1002/pro.3917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 11/10/2022]
Abstract
Quantum yield is a determinant for fluorescent protein (FP) applications and enhancing FP brightness through gene engineering is still a challenge. Green2, our de novo FP synthesized by microfluidic picoarray and cloning, has a significantly lower quantum yield than enhanced green FP, though they have high homology and share the same chromophore. To increase its quantum yield, we introduced an F145Y substitution into Green2 based on rational structural analysis. Y145 significantly increased the quantum yield (0.22 vs. 0.18) and improved the photostability (t1/2 , 73.0 s vs. 46.0 s), but did not affect the excitation and emission spectra. Further structural analysis showed that the F145Y substitution resulted in a significant electrical field change in the immediate environment of the chromophore. The perturbation of electrostatic charge around the chromophore lead to energy barrier changes between the ground and excited states, which resulted in the enhancement of quantum yield and photostability. Our results illustrate a typical example of engineering an FP based solely on fluorescence efficiency optimization and provide novel insights into the rational evolution of FPs.
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Affiliation(s)
- Tingting Sun
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang, Shandong, China
| | - Tianpeng Li
- College of City and Architecture Engineering, Zaozhuang University, Zaozhuang, Shandong, China.,School of Environment, Henan Normal University, Xinxiang, Henan, China.,Shandong Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong, China
| | - Ke Yi
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Xiaolian Gao
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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6
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Chen YC, Sood C, Francis AC, Melikyan GB, Dickson RM. Facile autofluorescence suppression enabling tracking of single viruses in live cells. J Biol Chem 2019; 294:19111-19118. [PMID: 31694918 DOI: 10.1074/jbc.ra119.010268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/01/2019] [Indexed: 11/06/2022] Open
Abstract
Live cell fluorescence imaging is the method of choice for studying dynamic processes, such as nuclear transport, vesicular trafficking, and virus entry and egress. However, endogenous cellular autofluorescence masks a useful fluorescence signal, limiting the ability to reliably visualize low-abundance fluorescent proteins. Here, we employed synchronously amplified fluorescence image recovery (SAFIRe), which optically alters ground versus photophysical dark state populations within fluorescent proteins to modulate and selectively detect their background-free emission. Using a photoswitchable rsFastLime fluorescent protein combined with a simple illumination and image-processing scheme, we demonstrate the utility of this approach for suppressing undesirable, unmodulatable fluorescence background. Significantly, we adapted this technique to different commercial wide-field and spinning-disk confocal microscopes, obtaining >10-fold improvements in signal to background. SAFIRe allowed visualization of rsFastLime targeted to mitochondria by efficiently suppressing endogenous autofluorescence or overexpressed cytosolic unmodulatable EGFP. Suppression of the overlapping EGFP signal provided a means to perform multiplexed imaging of rsFastLime and spectrally overlapping fluorophores. Importantly, we used SAFIRe to reliably visualize and track single rsFastLime-labeled HIV-1 particles in living cells exhibiting high and uneven autofluorescence signals. Time-lapse SAFIRe imaging can be performed for an extended period of time to visualize HIV-1 entry into cells. SAFIRe should be broadly applicable for imaging live cell dynamics with commercial microscopes, even in strongly autofluorescent cells or cells expressing spectrally overlapping fluorescent proteins.
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Affiliation(s)
- Yen-Cheng Chen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400.,Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322
| | - Chetan Sood
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322
| | - Ashwanth C Francis
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322
| | - Gregory B Melikyan
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322 .,Children's Healthcare of Atlanta, Atlanta, Georgia 30332
| | - Robert M Dickson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
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7
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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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8
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Zhou H, Qin C, Chen R, Liu Y, Zhou W, Zhang G, Gao Y, Xiao L, Jia S. Quantum Coherent Modulation-Enhanced Single-Molecule Imaging Microscopy. J Phys Chem Lett 2019; 10:223-228. [PMID: 30599135 DOI: 10.1021/acs.jpclett.8b03606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In fluorescence imaging and detection, undesired fluorescence interference (such as autofluorescence) often hampers the contrast of the image and even prevents the identification of structures of interest. Here, we develop a quantum coherent modulation-enhanced (QCME) single-molecule imaging microscopy (SMIM) to substantially eliminate the strong fluorescence interference, based on manipulation of the excited-state population probability of a single molecule. By periodically modulating the phase difference between the ultrashort pulse pairs and performing a discrete Fourier transform of the arrival time of emitted photons, the decimation of single molecules from strong interference in QCME-SMIM has been clearly determined, where the signal-to-interference ratio is enhanced by more than 2 orders of magnitude. This technique, confirmed to be universal to organic dyes and linked with biomacromolecules, paves the way to high-contrast bioimaging under unfavorable conditions.
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Affiliation(s)
- Haitao Zhou
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Chengbing Qin
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Ruiyun Chen
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Yaoming Liu
- Scientific Instrument Center , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Wenjin Zhou
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Guofeng Zhang
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Yan Gao
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Liantuan Xiao
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Suotang Jia
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy , Shanxi University , Taiyuan , Shanxi 030006 , China
- Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
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9
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Storti B, Margheritis E, Abbandonato G, Domenichini G, Dreier J, Testa I, Garau G, Nifosì R, Bizzarri R. Role of Gln222 in Photoswitching of Aequorea Fluorescent Proteins: A Twisting and H-Bonding Affair? ACS Chem Biol 2018; 13:2082-2093. [PMID: 29878744 DOI: 10.1021/acschembio.8b00267] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Reversibly photoswitchable fluorescent proteins (RSFPs) admirably combine the genetic encoding of fluorescence with the ability to repeatedly toggle between a bright and dark state, adding a new temporal dimension to the fluorescence signal. Accordingly, in recent years RSFPs have paved the way to novel applications in cell imaging that rely on their reversible photoswitching, including many super-resolution techniques such as F-PALM, RESOLFT, and SOFI that provide nanoscale pictures of the living matter. Yet many RSFPs have been engineered by a rational approach only to a limited extent, in the absence of clear structure-property relationships that in most cases make anecdotic the emergence of the photoswitching. We reported [ Bizzarri et al. J. Am Chem Soc. 2010 , 102 , 85 ] how the E222Q replacement is a single photoswitching mutation, since it restores the intrinsic cis-trans photoisomerization properties of the chromophore in otherwise nonswitchable Aequorea proteins of different color and mutation pattern (Q-RSFPs). We here investigate the subtle role of Q222 on the excited-state photophysics of the two simplest Q-RSFPs by a combined experimental and theoretical approach, using their nonswitchable anacestor EGFP as benchmark. Our findings link indissolubly photoswitching and Q222 presence, by a simple yet elegant scenario: largely twisted chromophore structures around the double bond (including hula-twist configurations) are uniquely stabilized by Q222 via H-bonds. Likely, these H-bonds subtly modulate the electronic properties of the chromophore, enabling the conical intersection that connects the excited cis to ground trans chromophore. Thus, Q222 belongs to a restricted family of single mutations that change dramatically the functional phenotype of a protein. The capability to distinguish quantitatively T65S/E222Q EGFP ("WildQ", wQ) from the spectrally identical EGFP by quantitative Optical Lock-In Detection (qOLID) witnesses the relevance of this mutation for cell imaging.
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Affiliation(s)
- Barbara Storti
- NEST, Scuola Normale Superiore and NANO-CNR, 56127 Pisa, Italy
| | - Eleonora Margheritis
- Center for Nanotechnology Innovation @ NEST, Istituto Italiano di Tecnologia, 56127 Pisa, Italy
| | | | | | - Jes Dreier
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
| | - Gianpiero Garau
- Center for Nanotechnology Innovation @ NEST, Istituto Italiano di Tecnologia, 56127 Pisa, Italy
| | - Riccardo Nifosì
- NEST, Scuola Normale Superiore and NANO-CNR, 56127 Pisa, Italy
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10
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Byrdin M, Duan C, Bourgeois D, Brettel K. A Long-Lived Triplet State Is the Entrance Gateway to Oxidative Photochemistry in Green Fluorescent Proteins. J Am Chem Soc 2018; 140:2897-2905. [PMID: 29394055 DOI: 10.1021/jacs.7b12755] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Though ubiquitously used as selective fluorescence markers in cellular biology, fluorescent proteins (FPs) still have not disclosed all of their surprising properties. One important issue, notably for single-molecule applications, is the nature of the triplet state, suggested to be the starting point for many possible photochemical reactions leading to phenomena such as blinking or bleaching. Here, we applied transient absorption spectroscopy to characterize dark states in the prototypical enhanced green fluorescent protein (EGFP) of hydrozoan origin and, for comparison, in IrisFP, a representative phototransformable FP of anthozoan origin. We identified a long-lived (approximately 5 ms) dark state that is formed with a quantum yield of approximately 1% and has pronounced absorption throughout the visible-NIR range (peak at around 900 nm). Detection of phosphorescence emission with identical kinetics and excitation spectrum allowed unambiguous identification of this state as the first excited triplet state of the deprotonated chromophore. This triplet state was further characterized by determining its phosphorescence emission spectrum, the temperature dependence of its decay kinetics and its reactivity toward oxygen and electron acceptors and donors. It is suggested that it is this triplet state that lies at the origin of oxidative photochemistry in green FPs, leading to phenomena such as so-called "oxidative redding", "primed photoconversion", or, in a manner similar to that previously observed for organic dyes, redox induced blinking control with the reducing and oxidizing system ("ROXS").
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Affiliation(s)
- Martin Byrdin
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS , 38044 Grenoble, France
| | - Chenxi Duan
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS , 38044 Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS , 38044 Grenoble, France
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay , F-91198 Gif-sur-Yvette cedex, France
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11
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Mamontova AV, Grigoryev AP, Tsarkova AS, Lukyanov KA, Bogdanov AM. Struggle for photostability: Bleaching mechanisms of fluorescent proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162017060085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Krause S, Carro-Temboury MR, Cerretani C, Vosch T. Anti-Stokes fluorescence microscopy using direct and indirect dark state formation. Chem Commun (Camb) 2018; 54:4569-4572. [DOI: 10.1039/c8cc01521j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Optically activated delayed fluorescence and upconversion fluorescence allow removing unwanted auto-fluorescence.
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Affiliation(s)
- Stefan Krause
- Nanoscience Center and Department of Chemistry
- University of Copenhagen
- Copenhagen 2100
- Denmark
| | | | - Cecilia Cerretani
- Nanoscience Center and Department of Chemistry
- University of Copenhagen
- Copenhagen 2100
- Denmark
| | - Tom Vosch
- Nanoscience Center and Department of Chemistry
- University of Copenhagen
- Copenhagen 2100
- Denmark
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13
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Abstract
We harness the photophysics of few-atom silver nanoclusters to create the first fluorophores capable of optically activated delayed fluorescence (OADF). In analogy with thermally activated delayed fluorescence, often resulting from oxygen- or collision-activated reverse intersystem crossing from triplet levels, this optically controllable/reactivated visible emission occurs with the same 2.2 ns fluorescence lifetime as that produced with primary excitation alone but is excited with near-infrared light from either of two distinct, long-lived photopopulated dark states. In addition to faster ground-state recovery under long-wavelength co-illumination, this "repumped" visible fluorescence occurs many microsceconds after visible excitation and only when gated by secondary near-IR excitation of ∼1-100 μs-lived dark excited states. By deciphering the Ag nanocluster photophysics, we demonstrate that OADF improves upon previous optical modulation schemes for near-complete background rejection in fluorescence detection. Likely extensible to other fluorophores with photopopulatable excited dark states, OADF holds potential for drastically improving fluorescence signal recovery from high backgrounds.
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Affiliation(s)
- Blake C. Fleischer
- School of Chemistry and Biochemistry and Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, GA 30332-0400
| | | | - Jung-Cheng Hsiang
- School of Chemistry and Biochemistry and Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, GA 30332-0400
| | - Robert M. Dickson
- School of Chemistry and Biochemistry and Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, GA 30332-0400
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14
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Chen YC, Dickson RM. Improved Fluorescent Protein Contrast and Discrimination by Optically Controlling Dark State Lifetimes. J Phys Chem Lett 2017; 8:733-736. [PMID: 28125231 PMCID: PMC5313373 DOI: 10.1021/acs.jpclett.6b02816] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Modulation and optical control of photoswitchable fluorescent protein (PS-FP) dark state lifetimes drastically improves sensitivity and selectivity in fluorescence imaging. The dark state population of PS-FPs generates an out-of-phase fluorescence component relative to the sinusoidally modulated 488 nm laser excitation. Because this apparent phase advanced emission results from slow recovery to the fluorescent manifold, we hasten recovery and, therefore, modulation frequency by varying coillumination intensity at 405 nm. As 405 nm illumination regenerates the fluorescent ground state more rapidly than via thermal recovery, we experimentally demonstrate that secondary illumination can control PS-FPs dark state lifetime to act as an additional dimension for discriminating spatially and spectrally overlapping emitters. This experimental combination of out of phase imaging after optical modulation (OPIOM) and synchronously amplified fluorescence image recovery (SAFIRe) optically controls the fluorescent protein dark state lifetimes for improved time resolution, with the resulting modulation-based selective signal recovery being quantitatively modeled. The combined experimental results and quantitative numerical simulations further demonstrate the potential of SAFIRe-OPIOM for wide-field biological imaging with improved speed, sensitivity, and optical resolution over other modulation-based fluorescence microscopies.
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15
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Ma C, Liu Y, Li C, Yang Y. The fluorescence quenching phenomenon in newly synthesized blue fluorescence protein molecule caused by anchoring group substitution: a DFT and TD-DFT study. RSC Adv 2017. [DOI: 10.1039/c6ra26470k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The newly synthesized blue fluorescence protein (BFP) molecule combined with its derivatives were fully investigated using DFT and TD-DFT methods.
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Affiliation(s)
- Chi Ma
- College of Physics and Material Science
- Henan Normal University
- Xinxiang 453007
- China
| | - Yufang Liu
- College of Physics and Material Science
- Henan Normal University
- Xinxiang 453007
- China
| | - Chaozheng Li
- College of Physics and Material Science
- Henan Normal University
- Xinxiang 453007
- China
| | - Yonggang Yang
- College of Physics and Material Science
- Henan Normal University
- Xinxiang 453007
- China
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16
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Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
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Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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17
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Qiu Z, Shu J, He Y, Lin Z, Zhang K, Lv S, Tang D. CdTe/CdSe quantum dot-based fluorescent aptasensor with hemin/G-quadruplex DNzyme for sensitive detection of lysozyme using rolling circle amplification and strand hybridization. Biosens Bioelectron 2016; 87:18-24. [PMID: 27504793 DOI: 10.1016/j.bios.2016.08.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 07/29/2016] [Accepted: 08/02/2016] [Indexed: 12/12/2022]
Abstract
Lysozyme with a small monomeric globular enzymatic protein is part of the innate immune system, and its deficiency can cause the increased incidence of disease. Herein, we devise a new signal-enhanced fluorescence aptasensing platform for quantitative screening of lysozyme by coupling with rolling circle amplification (RCA) and strand hybridization reaction, accompanying the assembly of CdTe/CdSe quantum dots (QDs) and hemin/G-quadruplex DNzyme. Initially, target-triggered release of the primer was carried out from DNA duplex via the reaction of the aptamer with the analyte, and the released primer could be then utilized as the template to produce numerous repeated oligonucleotide sequences by the RCA reaction. Following that, the formed long-stranded DNA simultaneously hybridized with the CdTe/CdSe QD-labeled probe and hemin/G-quadruplex DNzyme strand in the system, thereby resulting in the quenching of QD fluorescent signal through the proximity hemin/G-quadruplex DNzyme on the basis of transferring photoexcited conduction band electrons of quantum dots to Fe(III)/Fe(II)-protoporphyrin IX (hemin) complex. Under optimal conditions, the fluorescent signal decreased with the increasing target lysozyme within the dynamic range from 5.0 to 500nM with a detection limit (LOD) of 2.6nM at the 3sblank criterion. Intra-assay and interassay coefficients of variation (CVs) were below 8.5% and 11.5%, respectively. Finally, the system was applied to analyze spiked human serum samples, and the recoveries in all cases were 85-111.9%.
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Affiliation(s)
- Zhenli Qiu
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 People's Republic of China
| | - Jian Shu
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 People's Republic of China
| | - Yu He
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 People's Republic of China.
| | - Zhenzhen Lin
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 People's Republic of China
| | - Kangyao Zhang
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 People's Republic of China
| | - Shuzhen Lv
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 People's Republic of China
| | - Dianping Tang
- Key Laboratory of Analysis and Detection for Food Safety (MOE & Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 People's Republic of China.
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18
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Hsiang JC, Fleischer BC, Dickson RM. Dark State-Modulated Fluorescence Correlation Spectroscopy for Quantitative Signal Recovery. J Phys Chem Lett 2016; 7:2496-501. [PMID: 27299945 PMCID: PMC5218585 DOI: 10.1021/acs.jpclett.6b00940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Excitation of few-atom Ag cluster fluorescence produces significant steady-state dark state populations that can be dynamically optically depopulated with long wavelength coillumination. Modulating this secondary illumination dynamically repopulates the ground state, thereby directly modulating nanodot fluorescence without modulating background. Both fast and slow modulation enable unmodulated background to be quantitatively removed in fluorescence correlation spectroscopy (FCS) through simple correlation-based averaging. Such modulated dual-laser FCS enables recovery of pure Ag nanodot fluorescence correlations even in the presence of strong, spectrally overlapping background emission. Fluorescence recovery is linear with Fourier amplitude of the modulated fluorescence, providing a complementary approach to background-free quantitation of modulatable emitter concentration in high background environments. Using the expanding range of modulatable fluorophores, such methodologies should facilitate biologically relevant studies in both complex autofluorescent environments and multiplexed assays.
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Affiliation(s)
- Jung-Cheng Hsiang
- School of Chemistry & Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Blake C Fleischer
- School of Chemistry & Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Robert M Dickson
- School of Chemistry & Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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19
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Wu D, Guo WW, Liu XY, Cui G. Excited-State Intramolecular Proton Transfer in a Blue Fluorescence Chromophore Induces Dual Emission. Chemphyschem 2016; 17:2340-7. [DOI: 10.1002/cphc.201600386] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Dan Wu
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Wei-Wei Guo
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Xiang-Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry; Ministry of Education; College of Chemistry; Beijing Normal University; Beijing 100875 China
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20
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Quérard J, Le Saux T, Gautier A, Alcor D, Croquette V, Lemarchand A, Gosse C, Jullien L. Kinetics of Reactive Modules Adds Discriminative Dimensions for Selective Cell Imaging. Chemphyschem 2016; 17:1396-413. [PMID: 26833808 DOI: 10.1002/cphc.201500987] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 11/07/2022]
Abstract
Living cells are chemical mixtures of exceptional interest and significance, whose investigation requires the development of powerful analytical tools fulfilling the demanding constraints resulting from their singular features. In particular, multiplexed observation of a large number of molecular targets with high spatiotemporal resolution appears highly desirable. One attractive road to address this analytical challenge relies on engaging the targets in reactions and exploiting the rich kinetic signature of the resulting reactive module, which originates from its topology and its rate constants. This review explores the various facets of this promising strategy. We first emphasize the singularity of the content of a living cell as a chemical mixture and suggest that its multiplexed observation is significant and timely. Then, we show that exploiting the kinetics of analytical processes is relevant to selectively detect a given analyte: upon perturbing the system, the kinetic window associated to response read-out has to be matched with that of the targeted reactive module. Eventually, we introduce the state-of-the-art of cell imaging exploiting protocols based on reaction kinetics and draw some promising perspectives.
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Affiliation(s)
- Jérôme Quérard
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
| | - Thomas Le Saux
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
| | - Arnaud Gautier
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
| | - Damien Alcor
- INSERM U1065, C3M; 151 route Saint Antoine de Ginestière, BP 2 3194 F-06204 Nice Cedex 3 France
| | - Vincent Croquette
- Ecole Normale Supérieure; Département de Physique and Département de Biologie, Laboratoire de Physique Statistique UMR CNRS-ENS 8550; 24 rue Lhomond F-75005 Paris France
| | - Annie Lemarchand
- Sorbonne Universités; UPMC Univ Paris 06, Laboratoire de Physique Théorique de la Matière Condensée; 4 place Jussieu, case courrier 121 75252 Paris cedex 05 France
- CNRS, UMR 7600 LPTMC; 75005 Paris France
| | - Charlie Gosse
- Laboratoire de Photonique et de Nanostructures, LPN-CNRS; route de Nozay 91460 Marcoussis France
| | - Ludovic Jullien
- Ecole Normale Supérieure-PSL Research University; Département de Chimie; 24, rue Lhomond F-75005 Paris France
- Sorbonne Universités; UPMC Univ Paris 06, PASTEUR; F-75005 Paris France
- CNRS, UMR 8640 PASTEUR; F-75005 Paris France
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21
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Zhang Y, Zhang K, Wang J, Tian Z, Li ADQ. Photoswitchable fluorescent nanoparticles and their emerging applications. NANOSCALE 2015; 7:19342-19357. [PMID: 26445313 DOI: 10.1039/c5nr05436b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Although fluorescence offers ultrasensitivity, real-world applications of fluorescence techniques encounter many practical problems. As a noninvasive means to investigate biomolecular mechanisms, pathways, and regulations in living cells, the intrinsic heterogeneity and inherent complexity of biological samples always generates optical interferences such as autofluorescence. Therefore, innovative fluorescence technologies are needed to enhance measurement reliability while not compromising sensitivity. In this review, we present current strategies that use photoswitchable nanoparticles to address these real-world challenges. The unique feature in these photoswitchable nanoparticles is that fundamental molecular photoswitches are playing the critical role of fluorescence modulation rather than traditional methods like modulating the light source. As a result, new innovative technologies that have recently emerged include super-resolution imaging, frequency-domain imaging, antiphase dual-color correlation, etc. Some of these methods improve imaging resolution down to the nanometer level, while others boost the detection sensitivity by orders of magnitude and confirm the nanoparticle probes unambiguously. These enhancements, which are not possible with non-photoswitching molecular probes, are the central topics of this review.
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Affiliation(s)
- Yuanlin Zhang
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China.
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22
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Liu Z, Zhang G, Zhang D. Molecular Materials That Can Both Emit Light and Conduct Charges: Strategies and Perspectives. Chemistry 2015; 22:462-71. [DOI: 10.1002/chem.201503038] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Indexed: 12/12/2022]
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23
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Chen YC, Jablonski AE, Issaeva I, Bourassa D, Hsiang JC, Fahrni CJ, Dickson RM. Optically Modulated Photoswitchable Fluorescent Proteins Yield Improved Biological Imaging Sensitivity. J Am Chem Soc 2015; 137:12764-7. [PMID: 26402244 DOI: 10.1021/jacs.5b07871] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Photoswitchable fluorescent proteins (PS-FPs) open grand new opportunities in biological imaging. Through optical manipulation of FP emission, we demonstrate that dual-laser modulated synchronously amplified fluorescence image recovery (DM-SAFIRe) improves signal contrast in high background through unambiguous demodulation and is linear in relative fluorophore abundance at different points in the cell. The unique bright-to-dark state interconversion rates of each PS-FP not only enables discrimination of different, yet spectrally indistinguishable FPs, but also allows signal rejection of diffusing relative to bound forms of the same PS-FP, rsFastLime. Adding to the sensitivity gains realized from rejecting non-modulatable background, the selective signal recovery of immobilized vs diffusing intracellular rsFastLime suggests that DM-SAFIRe can detect weak protein-protein interactions that are normally obscured by large fractions of unbound FPs.
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Affiliation(s)
- Yen-Cheng Chen
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Amy E Jablonski
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Irina Issaeva
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Daisy Bourassa
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Jung-Cheng Hsiang
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Christoph J Fahrni
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Robert M Dickson
- School of Chemistry and Biochemistry and Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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24
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Mishin AS, Belousov VV, Solntsev KM, Lukyanov KA. Novel uses of fluorescent proteins. Curr Opin Chem Biol 2015; 27:1-9. [PMID: 26022943 DOI: 10.1016/j.cbpa.2015.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/07/2015] [Indexed: 11/28/2022]
Abstract
The field of genetically encoded fluorescent probes is developing rapidly. New chromophore structures were characterized in proteins of green fluorescent protein (GFP) family. A number of red fluorescent sensors, for example, for pH, Ca(2+) and H2O2, were engineered for multiparameter imaging. Progress in development of microscopy hardware and software together with specially designed FPs pushed superresolution fluorescence microscopy towards fast live-cell imaging. Deeper understanding of FPs structure and photophysics led to further development of imaging techniques. In addition to commonly used GFP-like proteins, unrelated types of FPs on the base of flavin-binding domains, bilirubin-binding domains or biliverdin-binding domains were designed. Their distinct biochemical and photophysical properties opened previously unexplored niches of FP uses such as labeling under anaerobic conditions, deep tissue imaging and even patients' blood analysis.
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Affiliation(s)
- Alexander S Mishin
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Vsevolod V Belousov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA 30332-0400, United States
| | - Konstantin A Lukyanov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia.
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25
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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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26
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Wan W, Zhu MQ, Tian Z, Li ADQ. Antiphase dual-color correlation in a reactant-product pair imparts ultrasensitivity in reaction-linked double-photoswitching fluorescence imaging. J Am Chem Soc 2015; 137:4312-5. [PMID: 25774573 DOI: 10.1021/jacs.5b01007] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A pair of reversible photochemical reactions correlates their reactant and product specifically, and such a correlation uniquely distinguishes their correlated signal from others that are not linked by this reversible reaction. Here a nanoparticle-shielded fluorophore is photodriven to undergo structural dynamics, alternating between a green-fluorescence state and a red-fluorescence state. As time elapses, the fluorophore can be in either state but not both at the same time. Thus, the red fluorescence is maximized while the green fluorescence is minimized and vice versa. Such an antiphase dual-color (AD) corelationship between the red and green fluorescence maxima as well as between their minima can be exploited to greatly improve the signal-to-noise ratio, thus enhancing the ultimate detection limit. Potential benefits of this correlation include elimination of all interferences originating from single-color dyes and signal amplification of AD photoswitching molecules by orders of magnitude.
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Affiliation(s)
- Wei Wan
- †Department of Chemistry and Center for Materials Research, Washington State University, Pullman, Washington 99164, United States
| | - Ming-Qiang Zhu
- ‡Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Zhiyuan Tian
- §School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Alexander D Q Li
- †Department of Chemistry and Center for Materials Research, Washington State University, Pullman, Washington 99164, United States
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27
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Querard J, Gautier A, Le Saux T, Jullien L. Expanding discriminative dimensions for analysis and imaging. Chem Sci 2015; 6:2968-2978. [PMID: 28706678 PMCID: PMC5490003 DOI: 10.1039/c4sc03955f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/18/2015] [Indexed: 01/01/2023] Open
Abstract
OPTIMAL can discriminate – without any separation or washing step – a targeted photoswitchable probe used as labelling or titration contrast agent among various interfering compounds, photoswitchable or not.
Eliminating the contribution of interfering compounds is a key step in chemical analysis. In complex media, one possible approach is to perform a preliminary separation. However purification is often demanding, long, and costly; it may also considerably alter the properties of interacting components of the mixture (e.g. in a living cell). Hence there is a strong interest for developing separation-free non-invasive analytical protocols. Using photoswitchable probes as labelling and titration contrast agents, we demonstrate that the association of a modulated monochromatic light excitation with a kinetic filtering of the overall observable is much more attractive than constant excitation to read-out the contribution from a target probe under adverse conditions. An extensive theoretical framework enabled us to optimize the out-of-phase concentration first-order response of a photoswitchable probe to modulated illumination by appropriately matching the average light intensity and the radial frequency of the light modulation to the probe dynamics. Thus, we can selectively and quantitatively extract from an overall signal the contribution from a target photoswitchable probe within a mixture of species, photoswitchable or not. This simple titration strategy is more specifically developed in the context of fluorescence imaging, which offers promising perspectives.
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Affiliation(s)
- Jérôme Querard
- Ecole Normale Supérieure-PSL Research University , Département de Chimie , 24, rue Lhomond , F-75005 Paris , France . ; ; ; Tel: +33 4432 3333.,Sorbonne Universités , UPMC Univ Paris 06 , PASTEUR , F-75005 , Paris , France.,CNRS , UMR 8640 PASTEUR , F-75005 , Paris , France
| | - Arnaud Gautier
- Ecole Normale Supérieure-PSL Research University , Département de Chimie , 24, rue Lhomond , F-75005 Paris , France . ; ; ; Tel: +33 4432 3333.,Sorbonne Universités , UPMC Univ Paris 06 , PASTEUR , F-75005 , Paris , France.,CNRS , UMR 8640 PASTEUR , F-75005 , Paris , France
| | - Thomas Le Saux
- Ecole Normale Supérieure-PSL Research University , Département de Chimie , 24, rue Lhomond , F-75005 Paris , France . ; ; ; Tel: +33 4432 3333.,Sorbonne Universités , UPMC Univ Paris 06 , PASTEUR , F-75005 , Paris , France.,CNRS , UMR 8640 PASTEUR , F-75005 , Paris , France
| | - Ludovic Jullien
- Ecole Normale Supérieure-PSL Research University , Département de Chimie , 24, rue Lhomond , F-75005 Paris , France . ; ; ; Tel: +33 4432 3333.,Sorbonne Universités , UPMC Univ Paris 06 , PASTEUR , F-75005 , Paris , France.,CNRS , UMR 8640 PASTEUR , F-75005 , Paris , France
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28
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Vegh RB, Bloch DA, Bommarius AS, Verkhovsky M, Pletnev S, Iwaï H, Bochenkova AV, Solntsev KM. Hidden photoinduced reactivity of the blue fluorescent protein mKalama1. Phys Chem Chem Phys 2015; 17:12472-85. [DOI: 10.1039/c5cp00887e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report a complete photocycle of the blue fluorescent protein exhibiting two delayed branches coupled to hidden proton transfer events.
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Affiliation(s)
- Russell B. Vegh
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- Petit Institute of Bioengineering and Bioscience
| | - Dmitry A. Bloch
- Research Program in Structural Biology and Biophysics
- Institute of Biotechnology
- University of Helsinki
- Helsinki 00014
- Finland
| | - Andreas S. Bommarius
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- Petit Institute of Bioengineering and Bioscience
| | - Michael Verkhovsky
- Research Program in Structural Biology and Biophysics
- Institute of Biotechnology
- University of Helsinki
- Helsinki 00014
- Finland
| | - Sergei Pletnev
- Synchrotron Radiation Research Section
- Macromolecular Crystallography Laboratory
- National Cancer Institute
- Argonne
- USA
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics
- Institute of Biotechnology
- University of Helsinki
- Helsinki 00014
- Finland
| | | | - Kyril M. Solntsev
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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29
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Adam V, Berardozzi R, Byrdin M, Bourgeois D. Phototransformable fluorescent proteins: Future challenges. Curr Opin Chem Biol 2014; 20:92-102. [DOI: 10.1016/j.cbpa.2014.05.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/19/2014] [Accepted: 05/22/2014] [Indexed: 01/28/2023]
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30
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Hsiang JC, Jablonski AE, Dickson RM. Optically modulated fluorescence bioimaging: visualizing obscured fluorophores in high background. Acc Chem Res 2014; 47:1545-54. [PMID: 24725021 PMCID: PMC4033652 DOI: 10.1021/ar400325y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Fluorescence
microscopy and detection have become indispensible
for understanding organization and dynamics in biological systems.
Novel fluorophores with improved brightness, photostability, and biocompatibility
continue to fuel further advances but often rely on having minimal
background. The visualization of interactions in very high biological
background, especially for proteins or bound complexes at very low
copy numbers, remains a primary challenge. Instead of focusing on
molecular brightness of fluorophores, we have adapted the principles
of high-sensitivity absorption spectroscopy to improve the sensitivity
and signal discrimination in fluorescence bioimaging. Utilizing
very long wavelength transient absorptions of kinetically
trapped dark states, we employ molecular modulation schemes that do
not simultaneously modulate the background fluorescence. This improves
the sensitivity and ease of implementation over high-energy photoswitch-based
recovery schemes, as no internal dye reference or nanoparticle-based
fluorophores are needed to separate the desired signals from background. In this Account, we describe the selection process for and identification
of fluorophores that enable optically modulated fluorescence to decrease
obscuring background. Differing from thermally stable photoswitches
using higher-energy secondary lasers, coillumination at very low energies
depopulates transient dark states, dynamically altering the fluorescence
and giving characteristic modulation time scales for each modulatable
emitter. This process is termed synchronously amplified fluorescence
image recovery (SAFIRe) microscopy. By understanding and optically
controlling the dye photophysics, we selectively modulate desired
fluorophore signals independent of all autofluorescent background.
This shifts the fluorescence of interest to unique detection frequencies
with nearly shot-noise-limited detection, as no background signals
are collected. Although the fluorescence brightness is improved
slightly, SAFIRe
yields up to 100-fold improved signal visibility by essentially removing
obscuring, unmodulated background (RichardsC. I.; 2009, 131, 461919284790). While SAFIRe exhibits a wide,
linear dynamic range, we have demonstrated single-molecule signal
recovery buried within 200 nM obscuring dye. In addition to enabling
signal recovery through background reduction, each dye exhibits a
characteristic modulation frequency indicative of its photophysical
dynamics. Thus, these characteristic time scales offer opportunities
not only to expand the dimensionality of fluorescence imaging by using
dark-state lifetimes but also to distinguish the dynamics of subpopulations
on the basis of photophysical versus diffusional time scales, even
within modulatable populations. The continued development of modulation
for signal recovery and observation of biological dynamics holds great
promise for studying a range of transient biological phenomena in
natural environments. Through the development of a wide range of fluorescent
proteins, organic dyes, and inorganic emitters that exhibit significant
dark-state populations under steady-state illumination, we can drastically
expand the applicability of fluorescence imaging to probe lower-abundance
complexes and their dynamics.
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Affiliation(s)
- Jung-Cheng Hsiang
- School of Physics, ‡School of Chemistry & Biochemistry, and §Petit Institute of Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Amy E. Jablonski
- School of Physics, ‡School of Chemistry & Biochemistry, and §Petit Institute of Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Robert M. Dickson
- School of Physics, ‡School of Chemistry & Biochemistry, and §Petit Institute of Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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31
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Xiao H, Peters FB, Yang PY, Reed S, Chittuluru JR, Schultz PG. Genetic incorporation of histidine derivatives using an engineered pyrrolysyl-tRNA synthetase. ACS Chem Biol 2014; 9:1092-6. [PMID: 24506189 PMCID: PMC4033645 DOI: 10.1021/cb500032c] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
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A polyspecific
amber suppressor aminoacyl-tRNA synthetase/tRNA
pair was evolved that genetically encodes a series of histidine analogues
in both Escherichia coli and mammalian cells. In
combination with tRNACUAPyl, a pyrrolysyl-tRNA
synthetase mutant was able to site-specifically incorporate 3-methyl-histidine,
3-pyridyl-alanine, 2-furyl-alanine, and 3-(2-thienyl)-alanine into
proteins in response to an amber codon. Substitution of His66 in the
blue fluorescent protein (BFP) with these histidine analogues created
mutant proteins with distinct spectral properties. This work further
expands the structural and chemical diversity of unnatural amino acids
(UAAs) that can be genetically encoded in prokaryotic and eukaryotic
organisms and affords new probes of protein structure and function.
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Affiliation(s)
- Han Xiao
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Francis B. Peters
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peng-Yu Yang
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sean Reed
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Johnathan R. Chittuluru
- High Tech High Chula Vista, 1945 Discovery Falls Drive, Chula Vista, California 91915, United States
| | - Peter G. Schultz
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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