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Mukherjee S, Douglas N, Jimenez R. Influence of Fluorescence Lifetime Selections and Conformational Flexibility on Brightness of FusionRed Variants. J Phys Chem Lett 2024; 15:1644-1651. [PMID: 38315162 DOI: 10.1021/acs.jpclett.3c02765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Fluorescent proteins (FPs) for bioimaging are typically developed by screening mutant libraries for clones with improved photophysical properties. This approach has resulted in FPs with high brightness, but the mechanistic origins of the improvements are often unclear. We focused on improving the molecular brightness in the FusionRed family of FPs with fluorescence lifetime selections on targeted libraries, with the aim of reducing nonradiative decay rates. Our new variants show fluorescence quantum yields of up to 75% and lifetimes >3.5 ns. We present a comprehensive analysis of these new FPs, including trends in spectral shifts, photophysical data, photostability, and cellular brightness resulting from codon optimization. We also performed all-atom molecular dynamics simulations to investigate the impact of side chain mutations. The trajectories reveal that individual mutations reduce the flexibility of the chromophore and side chains, leading to an overall reduction in nonradiative rates.
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Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado, Boulder, and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Nancy Douglas
- Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado, Boulder, and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
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2
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Sun G, Qu L, Azi F, Liu Y, Li J, Lv X, Du G, Chen J, Chen CH, Liu L. Recent progress in high-throughput droplet screening and sorting for bioanalysis. Biosens Bioelectron 2023; 225:115107. [PMID: 36731396 DOI: 10.1016/j.bios.2023.115107] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/09/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Owing to its ability to isolate single cells and perform high-throughput sorting, droplet sorting has been widely applied in several research fields. Compared with flow cytometry, droplet allows the encapsulation of single cells for cell secretion or lysate analysis. With the rapid development of this technology in the past decade, various droplet sorting devices with high throughput and accuracy have been developed. A droplet sorter with the highest sorting throughput of 30,000 droplets per second was developed in 2015. Since then, increased attention has been paid to expanding the possibilities of droplet sorting technology and strengthening its advantages over flow cytometry. This review aimed to summarize the recent progress in droplet sorting technology from the perspectives of device design, detection signal, actuating force, and applications. Technical details for improving droplet sorting through various approaches are introduced and discussed. Finally, we discuss the current limitations of droplet sorting for single-cell studies along with the existing gap between the laboratory and industry and provide our insights for future development of droplet sorters.
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Affiliation(s)
- Guoyun Sun
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Lisha Qu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Fidelis Azi
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology GTIIT, Shantou, Guangdong, 515063, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Chia-Hung Chen
- Department of Biomedical Engineering, College of Engineering, City University of Hong Kong, Hong Kong, China.
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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3
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Mukherjee S, Manna P, Douglas N, Chapagain PP, Jimenez R. Conformational Dynamics of mCherry Variants: A Link between Side-Chain Motions and Fluorescence Brightness. J Phys Chem B 2023; 127:52-61. [PMID: 36574626 DOI: 10.1021/acs.jpcb.2c05584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The 3-fold higher brightness of the recently developed mCherry-XL red fluorescent protein (FP) compared to its progenitor, mCherry, is due to a significant decrease in the nonradiative decay rate underlying its increased fluorescence quantum yield. To examine the structural and dynamic role of the four mutations that distinguish the two FPs and closely related variants, we employed microsecond time scale, all-atom molecular dynamics simulations. The simulations revealed that the I197R mutation leads to the formation of multiple hydrogen-bonded contacts and increased rigidity of the β-barrel. In particular, mCherryXL showed reduced nanosecond time scale breathing of the gap between the β7 and β10-strands, which was previously shown to be the most flexible region of mCherry. Together with experimental results, the simulations also reveal steric interactions of residue 161 and a network of hydrogen-bonding interactions of the chromophore with residues at positions 59, 143, and 163 that are critical in perturbing the chromophore electronic structure. Finally, we shed light on the conformational dynamics of the conserved residues R95 and S146, which are hydrogen-bonded to the chromophore, and provide physical insights into the observed photophysics. To the best of our knowledge, this is the first study that evaluates the conformational space for a set of closely related FPs generated by directed evolution.
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Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Premashis Manna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nancy Douglas
- Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Prem P Chapagain
- Department of Physics, Florida International University, 11200 SW Eighth Street, CP204, Miami, Florida 33199, United States
| | - Ralph Jimenez
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
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4
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Optimization of Ultrahigh-Throughput Screening Assay for Protein Engineering of d-Allulose 3-Epimerase. Biomolecules 2022; 12:biom12111547. [DOI: 10.3390/biom12111547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
d-Allulose is the corresponding epimer of d-fructose at the C-3 position, which exhibits a similar taste and sweetness to sucrose. As a low-calorie sweetener, d-allulose has broad application prospects in the fields of medicine, food, and so on. Currently, the production method of d-allulose is mainly the enzymatic conversion of d-fructose by d-allulose 3-epimerase (DAEase). However, the limited specific activity and thermal stability of DAEase restrict its industrial application. Herein, an ultrahigh-throughput screening assay based on the transcription factor PsiR was extensively optimized from the aspects of culture medium components, screening plasmid, and expression host, which enhanced the correction between the fluorescent readout and the enzyme activity. Then, the error-prone PCR (epPCR) library of Clostridium cellulolyticum H10 DAEase (CcDAEase) was screened through the above optimized method, and the variant I228V with improved specific activity and thermal stability was obtained. Moreover, after combining two beneficial substitutions, D281G and C289R, which were previously obtained by this optimized assay, the specific activity of the triple-mutation variant I228V/D281G/C289R reached up to 1.42-fold of the wild type (WT), while its half-life (T1/2) at 60 °C was prolonged by 62.97-fold. The results confirmed the feasibility of the optimized screening assay as a powerful tool for the directed evolution of DAEase.
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Mukherjee S, Manna P, Hung ST, Vietmeyer F, Friis P, Palmer AE, Jimenez R. Directed Evolution of a Bright Variant of mCherry: Suppression of Nonradiative Decay by Fluorescence Lifetime Selections. J Phys Chem B 2022; 126:4659-4668. [PMID: 35709514 DOI: 10.1021/acs.jpcb.2c01956] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The approximately linear scaling of fluorescence quantum yield (ϕ) with fluorescence lifetime (τ) in fluorescent proteins (FPs) has inspired engineering of brighter fluorophores based on screening for increased lifetimes. Several recently developed FPs such as mTurquoise2, mScarlet, and FusionRed-MQV which have become useful for live cell imaging are products of lifetime selection strategies. However, the underlying photophysical basis of the improved brightness has not been scrutinized. In this study, we focused on understanding the outcome of lifetime-based directed evolution of mCherry, which is a popular red-FP (RFP). We identified four positions (W143, I161, Q163, and I197) near the FP chromophore that can be mutated to create mCherry-XL (eXtended Lifetime: ϕ = 0.70; τ = 3.9 ns). The 3-fold higher quantum yield of mCherry-XL is on par with that of the brightest RFP to date, mScarlet. We examined selected variants within the evolution trajectory and found a near-linear scaling of lifetime with quantum yield and consistent blue-shifts of the absorption and emission spectra. We find that the improvement in brightness is primarily due to a decrease in the nonradiative decay of the excited state. In addition, our analysis revealed the decrease in nonradiative rate is not limited to the blue-shift of the energy gap and changes in the excited state reorganization energy. Our findings suggest that nonradiative mechanisms beyond the scope of energy-gap models such the Englman-Jortner model are suppressed in this lifetime evolution trajectory.
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Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Premashis Manna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sheng-Ting Hung
- Department of Physics, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Felix Vietmeyer
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Pia Friis
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Amy E Palmer
- Department of Biochemistry, University of Colorado at Boulder, 596 UCB, Boulder, Colorado 80309, United States.,BioFrontiers Institute, University of Colorado, Boulder, 596 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
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6
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7
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Mukherjee S, Jimenez R. Photophysical Engineering of Fluorescent Proteins: Accomplishments and Challenges of Physical Chemistry Strategies. J Phys Chem B 2022; 126:735-750. [DOI: 10.1021/acs.jpcb.1c05629] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
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8
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Two-photon fluorescence lifetime for label-free microfluidic droplet sorting. Anal Bioanal Chem 2021; 414:721-730. [PMID: 34792636 PMCID: PMC8748334 DOI: 10.1007/s00216-021-03745-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 12/19/2022]
Abstract
Microfluidic droplet sorting systems facilitate automated selective micromanipulation of compartmentalized micro- and nano-entities in a fluidic stream. Current state-of-the-art droplet sorting systems mainly rely on fluorescence detection in the visible range with the drawback that pre-labeling steps are required. This limits the application range significantly, and there is a high demand for alternative, label-free methods. Therefore, we introduce time-resolved two-photon excitation (TPE) fluorescence detection with excitation at 532 nm as a detection technique in droplet microfluidics. This enables label-free in-droplet detection of small aromatic compounds that only absorb in a deep-UV spectral region. Applying time-correlated single-photon counting, compounds with similar emission spectra can be distinguished due to their fluorescence lifetimes. This information is then used to trigger downstream dielectrophoretic droplet sorting. In this proof-of-concept study, we developed a polydimethylsiloxane-fused silica (FS) hybrid chip that simultaneously provides a very high optical transparency in the deep-UV range and suitable surface properties for droplet microfluidics. The herein developed system incorporating a 532-nm picosecond laser, time-correlated single-photon counting (TCSPC), and a chip-integrated dielectrophoretic pulsed actuator was exemplarily applied to sort droplets containing serotonin or propranolol. Furthermore, yeast cells were screened using the presented platform to show its applicability to study cells based on their protein autofluorescence via TPE fluorescence lifetime at 532 nm.
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Bitton A, Sambrano J, Valentino S, Houston JP. A Review of New High-Throughput Methods Designed for Fluorescence Lifetime Sensing From Cells and Tissues. FRONTIERS IN PHYSICS 2021; 9:648553. [PMID: 34007839 PMCID: PMC8127321 DOI: 10.3389/fphy.2021.648553] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Though much of the interest in fluorescence in the past has been on measuring spectral qualities such as wavelength and intensity, there are two other highly useful intrinsic properties of fluorescence: lifetime (or decay) and anisotropy (or polarization). Each has its own set of unique advantages, limitations, and challenges in detection when it comes to use in biological studies. This review will focus on the property of fluorescence lifetime, providing a brief background on instrumentation and theory, and examine the recent advancements and applications of measuring lifetime in the fields of high-throughput fluorescence lifetime imaging microscopy (HT-FLIM) and time-resolved flow cytometry (TRFC). In addition, the crossover of these two methods and their outlooks will be discussed.
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10
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Pärnamets K, Pardy T, Koel A, Rang T, Scheler O, Le Moullec Y, Afrin F. Optical Detection Methods for High-Throughput Fluorescent Droplet Microflow Cytometry. MICROMACHINES 2021; 12:mi12030345. [PMID: 33807031 PMCID: PMC8004903 DOI: 10.3390/mi12030345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
High-throughput microflow cytometry has become a focal point of research in recent years. In particular, droplet microflow cytometry (DMFC) enables the analysis of cells reacting to different stimuli in chemical isolation due to each droplet acting as an isolated microreactor. Furthermore, at high flow rates, the droplets allow massive parallelization, further increasing the throughput of droplets. However, this novel methodology poses unique challenges related to commonly used fluorometry and fluorescent microscopy techniques. We review the optical sensor technology and light sources applicable to DMFC, as well as analyze the challenges and advantages of each option, primarily focusing on electronics. An analysis of low-cost and/or sufficiently compact systems that can be incorporated into portable devices is also presented.
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Affiliation(s)
- Kaiser Pärnamets
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia; (A.K.); (T.R.); (Y.L.M.); (F.A.)
- Correspondence:
| | - Tamas Pardy
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 19086 Tallinn, Estonia; (T.P.); (O.S.)
| | - Ants Koel
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia; (A.K.); (T.R.); (Y.L.M.); (F.A.)
| | - Toomas Rang
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia; (A.K.); (T.R.); (Y.L.M.); (F.A.)
| | - Ott Scheler
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 19086 Tallinn, Estonia; (T.P.); (O.S.)
| | - Yannick Le Moullec
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia; (A.K.); (T.R.); (Y.L.M.); (F.A.)
| | - Fariha Afrin
- Thomas Johann Seebeck Department of Electronics, Tallinn University of Technology, 19086 Tallinn, Estonia; (A.K.); (T.R.); (Y.L.M.); (F.A.)
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Gaa R, Menang-Ndi E, Pratapa S, Nguyen C, Kumar S, Doerner A. Versatile and rapid microfluidics-assisted antibody discovery. MAbs 2021; 13:1978130. [PMID: 34586015 PMCID: PMC8489958 DOI: 10.1080/19420862.2021.1978130] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Recent years have seen unparalleled development of microfluidic applications for antibody discovery in both academic and pharmaceutical research. Microfluidics can support native chain-paired library generation as well as direct screening of antibody secreting cells obtained by rodent immunization or from the human peripheral blood. While broad diversities of neutralizing antibodies against infectious diseases such as HIV, Ebola, or COVID-19 have been identified from convalescent individuals, microfluidics can expedite therapeutic antibody discovery for cancer or immunological disease indications. In this study, a commercially available microfluidic device, Cyto-Mine, was used for the rapid identification of natively paired antibodies from rodents or human donors screened for specific binding to recombinant antigens, for direct screening with cells expressing the target of interest, and, to our knowledge for the first time, for direct broad functional IgG antibody screening in droplets. The process time from cell preparation to confirmed recombinant antibodies was four weeks. Application of this or similar microfluidic devices and methodologies can accelerate and enhance pharmaceutical antibody hit discovery.
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Affiliation(s)
- Ramona Gaa
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Emmanuel Menang-Ndi
- Institute for Molecular Biotechnology, University of Bodenkultur, Vienna, Austria
| | - Shruti Pratapa
- Protein Engineering and Antibody Technologies, EMD Serono, Billerica, MA, USA
| | - Christine Nguyen
- Protein Engineering and Antibody Technologies, EMD Serono, Billerica, MA, USA
| | - Satyendra Kumar
- Protein Engineering and Antibody Technologies, EMD Serono, Billerica, MA, USA
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
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12
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Berlanda SF, Breitfeld M, Dietsche CL, Dittrich PS. Recent Advances in Microfluidic Technology for Bioanalysis and Diagnostics. Anal Chem 2020; 93:311-331. [DOI: 10.1021/acs.analchem.0c04366] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Simon F. Berlanda
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Maximilian Breitfeld
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Claudius L. Dietsche
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
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13
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Mukherjee S, Hung ST, Douglas N, Manna P, Thomas C, Ekrem A, Palmer AE, Jimenez R. Engineering of a Brighter Variant of the FusionRed Fluorescent Protein Using Lifetime Flow Cytometry and Structure-Guided Mutations. Biochemistry 2020; 59:3669-3682. [PMID: 32914619 DOI: 10.1021/acs.biochem.0c00484] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of fluorescent proteins (FPs) has revolutionized biological imaging. FusionRed, a monomeric red FP (RFP), is known for its low cytotoxicity and correct localization of target fusion proteins in mammalian cells but is limited in application by low fluorescence brightness. We report a brighter variant of FusionRed, "FR-MQV," which exhibits an extended fluorescence lifetime (2.8 ns), enhanced quantum yield (0.53), higher extinction coefficient (∼140 000 M-1 cm-1), increased radiative rate constant, and reduced nonradiative rate constant with respect to its precursor. The properties of FR-MQV derive from three mutations-M42Q, C159V, and the previously identified L175M. A structure-guided approach was used to identify and mutate candidate residues around the para-hydroxyphenyl and the acylimine sites of the chromophore. The C159V mutation was identified via lifetime-based flow cytometry screening of a library in which multiple residues adjacent to the para-hydroxyphenyl site of the chromophore were mutated. The M42Q mutation is located near the acylimine moiety of the chromophore and was discovered using site-directed mutagenesis guided by X-ray crystal structures. FR-MQV exhibits a 3.4-fold higher molecular brightness and a 5-fold increase in the cellular brightness in HeLa cells [based on fluorescence-activated cell sorting (FACS)] compared to FusionRed. It also retains the low cytotoxicity and high-fidelity localization of FusionRed, as demonstrated through assays in mammalian cells. These properties make FR-MQV a promising template for further engineering into a new family of RFPs.
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Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Sheng-Ting Hung
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Nancy Douglas
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Premashis Manna
- Department of Chemistry, MIT, 77 Massachusetts Avenue, 18-084, Cambridge, Massachusetts 02139, United States
| | - Connor Thomas
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Annika Ekrem
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Amy E Palmer
- Department of Biochemistry, University of Colorado at Boulder, 596 UCB, Boulder, Colorado 80309, United States
- BioFrontiers Institute, University of Colorado, Boulder, 596 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
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