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Sunny AS, Cleven EC, Kumar P, Venkataramani S, Walls JD, Ramamurthy V. Structure, Dynamics, and Reactivity of Encapsulated Molecules in Restricted Spaces: Arylazoisoxazoles within an Octa Acid Capsule. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:17638-17655. [PMID: 39110852 DOI: 10.1021/acs.langmuir.4c01996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
In this study, a well-defined organic capsule assembled from two octa acid (OA) molecules acting as host and select arylazoisoxazoles (AAIO) acting as guests were employed to demonstrate that confined molecules have restricted freedom that translates into reaction selectivity in both ground and excited states. The behavior of these AAIO guests in confined capsules was found to be different from that found in both crystals, where there is very little freedom, and in isotropic solvents, where there is complete freedom. Through one-dimensional (1D) and two-dimensional (2D) 1H NMR spectroscopic experiments, we have established a relationship between structure, dynamics and reactivity of molecules confined in an OA capsule. Introduction of CF3 and CH3 substitution at the 4-position of the aryl group of AAIO reveals that in addition to space confinement, weak interactions between the guest and the OA capsule control the dynamics and reactivity of guest molecules. 1H NMR studies revealed that there is a temperature-dependence to guest molecules tumbling (180° rotation along the capsular short axis) within an OA capsule. While 1H NMR points to the occurrence of tumbling motion, MD simulations and simulation of the temperature-dependent NMR signals provide an insight into the mechanism of tumbling within OA capsules. Thermal and photochemical isomerization of AAIO were found to occur within an OA capsule just as in organic solvents. The observed selectivity noted during thermal and photo induced isomerization of OA encapsulated AAIOs can be qualitatively understood in terms of the well-known concepts due to Bell-Evans-Polanyi (BEP principle), Hammond and Zimmerman.
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Affiliation(s)
- Amal Sam Sunny
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Elliott C Cleven
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Pravesh Kumar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, Sector 81, Knowledge City, Manauli 140306, Punjab, India
| | - Sugumar Venkataramani
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, Sector 81, Knowledge City, Manauli 140306, Punjab, India
| | - Jamie D Walls
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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2
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Wang B, Lei X, Tian W, Perez-Rathke A, Tseng YY, Liang J. Structure-based pathogenicity relationship identifier for predicting effects of single missense variants and discovery of higher-order cancer susceptibility clusters of mutations. Brief Bioinform 2023; 24:bbad206. [PMID: 37332013 PMCID: PMC10359089 DOI: 10.1093/bib/bbad206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/19/2023] [Accepted: 05/13/2023] [Indexed: 06/20/2023] Open
Abstract
We report the structure-based pathogenicity relationship identifier (SPRI), a novel computational tool for accurate evaluation of pathological effects of missense single mutations and prediction of higher-order spatially organized units of mutational clusters. SPRI can effectively extract properties determining pathogenicity encoded in protein structures, and can identify deleterious missense mutations of germ line origin associated with Mendelian diseases, as well as mutations of somatic origin associated with cancer drivers. It compares favorably to other methods in predicting deleterious mutations. Furthermore, SPRI can discover spatially organized pathogenic higher-order spatial clusters (patHOS) of deleterious mutations, including those of low recurrence, and can be used for discovery of candidate cancer driver genes and driver mutations. We further demonstrate that SPRI can take advantage of AlphaFold2 predicted structures and can be deployed for saturation mutation analysis of the whole human proteome.
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Affiliation(s)
- Boshen Wang
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill, Department of Biomedical Engineering, University of Illinois at Chicago, W103 Suite, 820 S Wood St, 60612 IL, USA
| | - Xue Lei
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill, Department of Biomedical Engineering, University of Illinois at Chicago, W103 Suite, 820 S Wood St, 60612 IL, USA
| | - Wei Tian
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill, Department of Biomedical Engineering, University of Illinois at Chicago, W103 Suite, 820 S Wood St, 60612 IL, USA
| | - Alan Perez-Rathke
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill, Department of Biomedical Engineering, University of Illinois at Chicago, W103 Suite, 820 S Wood St, 60612 IL, USA
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Biochemistry and Molecular Biology Department, School of Medicine, Wayne State University, 540 E. Canfield Avenue, 48201MI, USA
| | - Jie Liang
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill, Department of Biomedical Engineering, University of Illinois at Chicago, W103 Suite, 820 S Wood St, 60612 IL, USA
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3
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Kanagaraj K, Rebek J, Yu Y. Control of reactivity and selectivity in isomerization and rearrangement reactions inside confined spaces. Chem Commun (Camb) 2023. [PMID: 37377149 DOI: 10.1039/d3cc01198d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
In the confined space of supramolecular systems, the substrate can be forced into a reactive conformation and labile intermediates may be stabilized while isolated from the bulk solution. In this highlight, unusual processes mediated by supramolecular hosts are described. These include unfavourable conformational equilibria, unusual product selectivities in bond and ring-chain isomerizations, accelerated rearrangement reactions through labile intermediates, and encapsulated oxidations. In the host, controlled or altered isomerization of the guests can occur via hydrophobic, photochemical and thermal interventions. The inner spaces of the hosts resemble enzyme cavities that stabilize labile intermediates not accessible in the bulk solvent. The effects of confinement and the binding forces involved are discussed and further applications are suggested.
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Affiliation(s)
- Kuppusamy Kanagaraj
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
| | - Julius Rebek
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
- Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yang Yu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China.
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4
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Dalmau D, Crespo O, Matxain JM, Urriolabeitia EP. Fluorescence Amplification of Unsaturated Oxazolones Using Palladium: Photophysical and Computational Studies. Inorg Chem 2023. [PMID: 37315074 DOI: 10.1021/acs.inorgchem.3c00601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Weakly fluorescent (Z)-4-arylidene-5-(4H)-oxazolones (1), ΦPL < 0.1%, containing a variety of conjugated aromatic fragments and/or charged arylidene moieties, have been orthopalladated by reaction with Pd(OAc)2. The resulting dinuclear complexes (2) have the oxazolone ligands bonded as a C^N-chelate, restricting intramolecular motions involving the oxazolone. From 2, a variety of mononuclear derivatives, such as [Pd(C^N-oxazolone)(O2CCF3)(py)] (3), [Pd(C^N-oxazolone)(py)2](ClO4) (4), [Pd(C^N-oxazolone)(Cl)(py)] (5), and [Pd(C^N-oxazolone)(X)(NHC)] (6, 7), have been prepared and fully characterized. Most of complexes 3-6 are strongly fluorescent in solution in the range of wavelengths from green to yellow, with values of ΦPL up to 28% (4h), which are among the highest values of quantum yield ever reported for organometallic Pd complexes with bidentate ligands. This means that the introduction of the Pd in the oxazolone scaffold produces in some cases an amplification of the fluorescence of several orders of magnitude from the free ligand 1 to complexes 3-6. Systematic variations of the substituents of the oxazolones and the ancillary ligands show that the wavelength of emission is tuned by the nature of the oxazolone, while the quantum yield is deeply influenced by the change of ligands. TD-DFT studies of complexes 3-6 show a direct correlation between the participation of the Pd orbitals in the HOMO and the loss of emission through non-radiative pathways. This model allows the understanding of the amplification of the fluorescence and the future rational design of new organopalladium systems with improved properties.
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Affiliation(s)
- David Dalmau
- Instituto de Síntesis Química y Catálisis Homogénea, ISQCH (CSIC-Universidad de Zaragoza), Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Olga Crespo
- Instituto de Síntesis Química y Catálisis Homogénea, ISQCH (CSIC-Universidad de Zaragoza), Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Jon M Matxain
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU and Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Euskadi, Spain
| | - Esteban P Urriolabeitia
- Instituto de Síntesis Química y Catálisis Homogénea, ISQCH (CSIC-Universidad de Zaragoza), Pedro Cerbuna 12, 50009 Zaragoza, Spain
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5
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Jones CM, List NH, Martínez TJ. Steric and Electronic Origins of Fluorescence in GFP and GFP-like Proteins. J Am Chem Soc 2022; 144:12732-12746. [PMID: 35786916 DOI: 10.1021/jacs.2c02946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent proteins have become routine tools for biological imaging. However, their nanosecond lifetimes on the excited state present computational hurdles to a full understanding of these photoactive proteins. In this work, we simulate approximately 0.5 nanoseconds of ab initio molecular dynamics to elucidate steric and electronic features responsible for fluorescent protein behavior. Using green fluorescent protein (GFP) and Dronpa2─widely used fluorescent proteins with contrasting functionality─as case studies, we leverage previous findings in the gas phase and solution to explore the deactivation mechanisms available to these proteins. Starting with ground-state analyses, we identify steric (the distribution of empty pockets near the chromophore) and electronic (electric fields exerted on chromophore moieties) factors that offer potential avenues for rational design. Picosecond timescale simulations on the excited state reveal that the chromophore can access twisted structures in Dronpa2, while the chromophore is largely confined to planarity in GFP. We couple ab initio multiple spawning (AIMS) and enhanced sampling simulations to discover and characterize conical intersection seams that facilitate internal conversion, which is a rare event in both systems. Our AIMS simulations correctly capture the relative fluorescence profiles of GFP and Dronpa2 within the first few picoseconds, and we attribute the diminished fluorescence intensity of Dronpa2, relative to GFP, to flexible chromophore intermediates on the excited state. Furthermore, we predict that twisted chromophore intermediates produce red-shifted intensities in the Dronpa2 fluorescence spectrum. If confirmed experimentally, this spectroscopic signature would provide valuable insights when screening and developing novel fluorescent proteins.
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Affiliation(s)
- Chey M Jones
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Nanna H List
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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6
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Zhang J, Li H, Lin B, Luo X, Yin P, Yi T, Xue B, Zhang XL, Zhu H, Nie Z. Development of Near-Infrared Nucleic Acid Mimics of Fluorescent Proteins for In Vivo Imaging of Viral RNA with Turn-On Fluorescence. J Am Chem Soc 2021; 143:19317-19329. [PMID: 34762804 DOI: 10.1021/jacs.1c04577] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
GFP-like fluorescent proteins and their molecular mimics have revolutionized bioimaging research, but their emissions are largely limited in the visible to far-red region, hampering the in vivo applications in intact animals. Herein, we structurally modulate GFP-like chromophores using a donor-acceptor-acceptor (D-A-A') molecular configuration to discover a set of novel fluorogenic derivatives with infrared-shifted spectra. These chromophores can be fluorescently elicited by their specific interaction with G-quadruplex (G4), a unique noncanonical nucleic acid secondary structure, via inhibition of the chromophores' twisted-intramolecular charge transfer. This feature allows us to create, for the first time, FP mimics with tunable emission in the near-infrared (NIR) region (Emmax = 664-705 nm), namely, infrared G-quadruplex mimics of FPs (igMFP). Compared with their FP counterparts, igMFPs exhibit remarkably higher quantum yields, larger Stokes shift, and better photostability. In a proof-of-concept application using pathogen-related G4s as the target, we exploited igMFPs to directly visualize native hepatitis C virus (HCV) RNA genome in living cells via their in situ formation by the chromophore-bound viral G4 structure in the HCV core gene. Furthermore, igMFPs are capable of high contrast HCV RNA imaging in living mice bearing a HCV RNA-presenting mini-organ, providing the first application of FP mimics in whole-animal imaging.
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Affiliation(s)
- Jiaheng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Huiyi Li
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, People's Republic of China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Peng Yin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Ting Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Binbin Xue
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, People's Republic of China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine, Wuhan University, Wuhan 430071, Hubei, People's Republic of China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, People's Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
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7
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Liu MX, Liu XY, Liu JY, Tang JT, Shi K, Mao J, Lu ZL, Qiao HJ, He L. Di[12]aneN 3-Functionalized Green Fluorescent Protein Chromophore for GFP Luminescence Simulation and Efficient Gene Transfection In Vitro and In Vivo. ACS APPLIED BIO MATERIALS 2021; 4:7111-7122. [PMID: 35006943 DOI: 10.1021/acsabm.1c00723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Although a plethora of gene carriers have been developed for potential gene therapy, imageable stimuli-responsive gene vectors with fast access to the nucleus, high biocompatibility, and transfection efficiency are still scarce. Herein, we report the design and synthesis of four dendrite-shaped cationic liposomes, MPA-HBI-R/DOPE (R: n-butyl, 1; n-octyl, 2; n-dodecyl, 3; palmyl, 4), prepared via esterification of 4-alkoxybenzylideneimidazolinone containing aliphatic chains of different lengths (HBI-R), the green fluorescent protein (GFP) chromophore, with a di[12]aneN3 unit. Liposomes were fabricated via the self-assembly of MPA-HBI-R, assisted with 1,2-dioleoyl-sn-glycerol-3-phosphorylethanolamine (DOPE). These liposomes (MPA-HBI-R/DOPE) exhibited efficient DNA condensation, pH-responsive degradation, excellent cellular biocompatibility (up to 150 μM), and high transfection efficiency. Molecular docking experiments were also used to verify the optimal interaction between MPA-HBI-R and DNA, as well as the fluorescence enhancements. In particular, MPA-HBI-2/DOPE delivered DNA into the nucleus in less than an hour, and its luciferase transfection activity was more than 10 times that by Lipo2000, across multiple cell lines. The GFP chromophore conjugation allowed trackable intracellular delivery and release of DNA in real time via fluorescence imaging. Furthermore, efficient red fluorescent protein (RFP) transfection in zebrafish, with an efficiency of more than 6 times that by Lipo2000, was also achieved. The results not only realized, for the first time, the combination of gene delivery and GFP-simulated light emission, allowing fluorescent tracking and highly efficient gene transfection, but also offered valuable insights into the use of biomimetic chromophore for the development of the next-generation nonviral vectors.
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Affiliation(s)
- Ming-Xuan Liu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.,School of Pharmacy, Nantong University, Nantong 226001, China
| | - Xu-Ying Liu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jin-Yu Liu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jin-Tao Tang
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ke Shi
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jie Mao
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zhong-Lin Lu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hai-Jun Qiao
- College of Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Lan He
- China National Institute for Food and Drug Control, Institute of Chemical Drugs, Beijing 100050, China
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8
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Myasnyanko IN, Gavrikov AS, Zaitseva SO, Smirnov AY, Zaitseva ER, Sokolov AI, Malyshevskaya KK, Baleeva NS, Mishin AS, Baranov MS. Color Tuning of Fluorogens for FAST Fluorogen‐Activating Protein. Chemistry 2021; 27:3986-3990. [DOI: 10.1002/chem.202004760] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/16/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Ivan N. Myasnyanko
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexey S. Gavrikov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Snizhana O. Zaitseva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu. Smirnov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Elvira R. Zaitseva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Anatolii I. Sokolov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Kseniya K. Malyshevskaya
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S. Baleeva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander S. Mishin
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University Ostrovitianov 1 Moscow 117997 Russia
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9
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Xiang W, Zhang L, Zhi X, Qian Y. Synthesis, S Atom Promoted Photodynamic Therapy and Two- Photon Fluorescence Imaging of Phenothiazine Fluorescent Protein Chromophore Analogue. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202104040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Wolstenholme CH, Hu H, Ye S, Funk BE, Jain D, Hsiung CH, Ning G, Liu Y, Li X, Zhang X. AggFluor: Fluorogenic Toolbox Enables Direct Visualization of the Multi-Step Protein Aggregation Process in Live Cells. J Am Chem Soc 2020; 142:17515-17523. [PMID: 32915553 DOI: 10.1021/jacs.0c07245] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aberrantly processed or mutant proteins misfold and assemble into a variety of soluble oligomers and insoluble aggregates, a process that is associated with an increasing number of diseases that are not curable or manageable. Herein, we present a chemical toolbox, AggFluor, that allows for live cell imaging and differentiation of complex aggregated conformations in live cells. Based on the chromophore core of green fluorescent proteins, AggFluor is comprised of a series of molecular rotor fluorophores that span a wide range of viscosity sensitivity. As a result, these compounds exhibit differential turn-on fluorescence when incorporated in either soluble oligomers or insoluble aggregates. This feature allows us to develop, for the first time, a dual-color imaging strategy to distinguish unfolded protein oligomers from insoluble aggregates in live cells. Furthermore, we have demonstrated how small molecule proteostasis regulators can drive formation and disassembly of protein aggregates in both conformational states. In summary, AggFluor is the first set of rationally designed molecular rotor fluorophores that evenly cover a wide range of viscosity sensitivities. This set of fluorescent probes not only change the status quo of current imaging methods to visualize protein aggregation in live cells but also can be generally applied to study other biological processes that involve local viscosity changes with temporal and spatial resolutions.
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11
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Bhattacharya B, Roy D, Dey S, Puthuvakkal A, Bhunia S, Mondal S, Chowdhury R, Bhattacharya M, Mandal M, Manoj K, Mandal PK, Reddy CM. Mechanical‐Bending‐Induced Fluorescence Enhancement in Plastically Flexible Crystals of a GFP Chromophore Analogue. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007760] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Biswajit Bhattacharya
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Debjit Roy
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Somnath Dey
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Anisha Puthuvakkal
- Photosciences and Photonics Chemical Sciences and Technology Division CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695019 India
| | - Surojit Bhunia
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
- Centre for Advanced Functional Materials (CAFM) Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Saikat Mondal
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
- Centre for Advanced Functional Materials (CAFM) Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Rituparno Chowdhury
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Manjima Bhattacharya
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Mrinal Mandal
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - Kochunnoonny Manoj
- Photosciences and Photonics Chemical Sciences and Technology Division CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695019 India
| | - Prasun K. Mandal
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
- Centre for Advanced Functional Materials (CAFM) Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
| | - C. Malla Reddy
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
- Centre for Advanced Functional Materials (CAFM) Indian Institute of Science Education and Research (IISER) Kolkata 741246 Nadia, West Bengal India
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12
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Bhattacharya B, Roy D, Dey S, Puthuvakkal A, Bhunia S, Mondal S, Chowdhury R, Bhattacharya M, Mandal M, Manoj K, Mandal PK, Reddy CM. Mechanical-Bending-Induced Fluorescence Enhancement in Plastically Flexible Crystals of a GFP Chromophore Analogue. Angew Chem Int Ed Engl 2020; 59:19878-19883. [PMID: 32667123 DOI: 10.1002/anie.202007760] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Indexed: 01/25/2023]
Abstract
Single crystals of optoelectronic materials that respond to external stimuli, such as mechanical, light, or heat, are immensely attractive for next generation smart materials. Here we report single crystals of a green fluorescent protein (GFP) chromophore analogue with irreversible mechanical bending and associated unusual enhancement of the fluorescence, which is attributed to the strained molecular packing in the perturbed region. Soft crystalline materials with such fluorescence intensity modulations occurring in response to mechanical stimuli under ambient pressure conditions will have potential implications for the design of technologically relevant tunable fluorescent materials.
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Affiliation(s)
- Biswajit Bhattacharya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Debjit Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Somnath Dey
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Anisha Puthuvakkal
- Photosciences and Photonics, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, India
| | - Surojit Bhunia
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India.,Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Saikat Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India.,Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Rituparno Chowdhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Manjima Bhattacharya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Mrinal Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - Kochunnoonny Manoj
- Photosciences and Photonics, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, India
| | - Prasun K Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India.,Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
| | - C Malla Reddy
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India.,Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER), Kolkata, 741246, Nadia, West Bengal, India
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13
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Singh A, Karmakar S, Abraham IM, Rambabu D, Dave D, Manjithaya R, Maji TK. Unraveling the Effect on Luminescent Properties by Postsynthetic Covalent and Noncovalent Grafting of gfp Chromophore Analogues in Nanoscale MOF-808. Inorg Chem 2020; 59:8251-8258. [PMID: 32490672 DOI: 10.1021/acs.inorgchem.0c00625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Here, we demonstrate mimicking of photophysical properties of native green fluorescent protein (gfp) by immobilizing the gfp chromophore analogues in nanoscale MOF-808 and further exploring the bioimaging applications. The two virtually nonfluorescent gfp chromophore analogues carrying different functionalities, BDI-AE (COOH/COOMe) and BDI-EE (COOMe/COOMe) were immobilized in nanosized MOF-808 via postsynthetic modification. An 1H NMR and IR study confirms that BDI-AE was coordinated in NMOF-808, whereas BDI-EE was just noncovalently encapsulated. Interestingly, the extremely weakly fluorescent monomers BDI-AE and BDI-EE (QY = 0.01-0.03%, lifetime = 0.01-0.03 ns) showed a 102-fold increase in quantum efficiency with a significantly longer excited-state lifetime (QY = 1.8-5.6%, lifetime 0.89-1.49 ns) after immobilization in the NMOF-808 scaffold. Moreover, BDI-AE@MOF-808 has 4 times higher quantum efficiency as well as longer excited-state lifetime in comparison to BDI-EE@NMOF-808 due to the rigidity imposed in the chromophore upon coordination with Zr4+ in the former case. Further, a cell viability test performed for BDI-AE@NMOF-808 in HeLa cells confirmed the nontoxic nature of the material and, more importantly, bioimaging applications have also been explored successfully.
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Affiliation(s)
- Ashish Singh
- Molecular Materials Laboratory, Chemistry and Physics of Material Unit (CPMU), School of Advance Material (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Sanchita Karmakar
- Molecular Materials Laboratory, Chemistry and Physics of Material Unit (CPMU), School of Advance Material (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Irine Maria Abraham
- Molecular Biology & Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Darsi Rambabu
- Molecular Materials Laboratory, Chemistry and Physics of Material Unit (CPMU), School of Advance Material (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Dhwanit Dave
- Molecular Materials Laboratory, Chemistry and Physics of Material Unit (CPMU), School of Advance Material (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Ravi Manjithaya
- Molecular Biology & Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Tapas Kumar Maji
- Molecular Materials Laboratory, Chemistry and Physics of Material Unit (CPMU), School of Advance Material (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
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14
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Samanta S, Baldridge A, Tolbert LM, Ramamurthy V. Guest/Host Complexes of Octa Acid and Amphiphilic Benzylidene-3-methylimidazolidinones Exchange Hosts within the NMR Time Scale. ACS OMEGA 2020; 5:8230-8241. [PMID: 32309733 PMCID: PMC7161058 DOI: 10.1021/acsomega.0c00523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/19/2020] [Indexed: 06/11/2023]
Abstract
Cavitand octa acid (OA) is established to form a stable capsular assembly with one or two hydrophobic guest molecules (1:2 or 2:2 guest/host complex). Examples are known in which the guest molecule tumbles within the capsule without disrupting the structure of the capsuleplex. This process makes the two OA molecules that form the capsule magnetically equivalent. In this study, we have examined the dynamics of capsules that host amphiphilic benzylidene-3-methylimidazolidinone molecules as guests. In these capsuleplexes, although the guest does not tumble, the two OA molecules become magnetically equivalent because the two OA molecules that form the capsule exchange their positions in the NMR time scale. This is equivalent to the content of the capsule remaining stationary while the capsule swirls around it. Benzylidene-3-methylimidazolidinones form both 1:1 and 1:2 supramolecular complexes with cavitand OA. Two-dimensional NMR, ROESY, and NOESY data suggest that in a 300 ms time scale, the two halves of the capsule exchange between themselves and with free OA. The conclusion drawn here provides valuable information concerning the stability of the OA capsuleplex and cavitandplex that is used as the well-defined space to control the excited-state chemistry and dynamics of confined guest molecules.
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Affiliation(s)
- Shampa
R. Samanta
- Department
of Chemistry, University of Miami, Coral Gables, Miami, Florida 33146, United States
| | - Anthony Baldridge
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United
States
| | - Laren M. Tolbert
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United
States
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15
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Dolgopolova EA, Berseneva AA, Faillace MS, Ejegbavwo OA, Leith GA, Choi SW, Gregory HN, Rice AM, Smith MD, Chruszcz M, Garashchuk S, Mythreye K, Shustova NB. Confinement-Driven Photophysics in Cages, Covalent−Organic Frameworks, Metal–Organic Frameworks, and DNA. J Am Chem Soc 2020; 142:4769-4783. [DOI: 10.1021/jacs.9b13505] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ekaterina A. Dolgopolova
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Anna A. Berseneva
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Martín S. Faillace
- INFIQC-UNC, CONICET, Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - Otega A. Ejegbavwo
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Gabrielle A. Leith
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Seok W. Choi
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Haley N. Gregory
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Allison M. Rice
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Sophya Garashchuk
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Karthikeyan Mythreye
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Natalia B. Shustova
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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16
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Deng H, Yu C, Yan D, Zhu X. Dual-Self-Restricted GFP Chromophore Analogues with Significantly Enhanced Emission. J Phys Chem B 2020; 124:871-880. [PMID: 31928005 DOI: 10.1021/acs.jpcb.9b11329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The tremendous gap of fluorescence emission of synthetic green fluorescent protein (GFP) chromophore to the protein itself makes it impossible to use for applications in molecular and cellular imaging. Here, we developed an efficient methodology to enhance the photoluminescence response of synthetic GFP chromophore analogues by constructing dual-self-restricted chromophores. Single self-restricted chromophores were first generated with 2,5-dimethoxy substitution on the aromatic ring, which were further modified with phenyl or 2,5-dimethoxy phenyl to form dual-self-restricted chromophores. These two chromophores showed an obvious solvatofluorochromic color palette across blue to yellow with a maximum emission Stokes shift of 95 nm and dramatically enhanced fluorescence emission in various aprotic solvents, especially in hexane, where the QY reached around 0.6. Importantly, in acetonitrile and dimethyl sulfoxide, the fluorescence QYs of both chromophores were over 0.22, which were the highest reported so far in high polar organic solvents. Meanwhile, the fluorescence lifetimes also improved obviously with the maximum of around 4.5 ns. Theoretical calculations revealed a more favorable Mülliken atomic charge translocation over the double-bond bridge and illustrated much higher energy barriers for the Z/E photoisomerization together with larger bond orders compared with the GFP core chromophore, p-HBDI. Our work significantly improved the fluorescence emission of synthetic GFP chromophore analogues in polar solvents while reserved the multicolor emitting function, providing a solid molecular motif for engineering high-performance fluorescent probes.
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Affiliation(s)
- Hongping Deng
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
| | - Chunyang Yu
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
| | - Deyue Yan
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory of Electrical Insulation and Thermal Aging, State Key Laboratory of Metal Matrix Composites , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , People's Republic of China
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17
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Singh A, Gupta R, Siddiqui N, Kumar Iyer SS, Ramanathan G. Tuning Thin Film Properties by Structural Modulations in Red Fluorescent Protein Chromophore Analogues. ChemistrySelect 2019. [DOI: 10.1002/slct.201903024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ashish Singh
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
| | - Raghav Gupta
- Department of Electrical EngineeringIndian Institute of Technology Kanpur Kanpur 208016 India
- Samtel Centre for Display TechnologiesIndian Institute of Technology Kanpur Kanpur 208016 India
| | - Nazia Siddiqui
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
| | - S. Sundar Kumar Iyer
- Department of Electrical EngineeringIndian Institute of Technology Kanpur Kanpur 208016 India
- Samtel Centre for Display TechnologiesIndian Institute of Technology Kanpur Kanpur 208016 India
| | - Gurunath Ramanathan
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
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18
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Povarova NV, Zaitseva SO, Baleeva NS, Smirnov AY, Myasnyanko IN, Zagudaylova MB, Bozhanova NG, Gorbachev DA, Malyshevskaya KK, Gavrikov AS, Mishin AS, Baranov MS. Red-Shifted Substrates for FAST Fluorogen-Activating Protein Based on the GFP-Like Chromophores. Chemistry 2019; 25:9592-9596. [PMID: 31111975 DOI: 10.1002/chem.201901151] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/14/2019] [Indexed: 11/10/2022]
Abstract
A genetically encoded fluorescent tag for live cell microscopy is presented. This tag is composed of previously published fluorogen-activating protein FAST and a novel fluorogenic derivative of green fluorescent protein (GFP)-like chromophore with red fluorescence. The reversible binding of the novel fluorogen and FAST is accompanied by three orders of magnitude increase in red fluorescence (580-650 nm). The proposed dye instantly stains target cellular proteins fused with FAST, washes out in a minute timescale, and exhibits higher photostability of the fluorescence signal in confocal and widefield microscopy, in contrast with previously published fluorogen:FAST complexes.
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Affiliation(s)
- Natalia V Povarova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Snizhana O Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Marina B Zagudaylova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Nina G Bozhanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Blvd 30, Moscow, 121205, Russia
| | - Kseniya K Malyshevskaya
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Blvd 30, Moscow, 121205, Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
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19
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Yan X, Wei P, Liu Y, Wang M, Chen C, Zhao J, Li G, Saha ML, Zhou Z, An Z, Li X, Stang PJ. Endo- and Exo-Functionalized Tetraphenylethylene M 12L 24 Nanospheres: Fluorescence Emission inside a Confined Space. J Am Chem Soc 2019; 141:9673-9679. [PMID: 31125220 PMCID: PMC6689230 DOI: 10.1021/jacs.9b03885] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The intrinsic relationship between the properties of green fluorescent protein (GFP) and its encapsulated small molecular light machine has spurred many biomimicking studies, aiming at revealing the detailed mechanism and further promoting its wide applications in different disciplines. However, how to build a similar confined microenvironment to mimic the cavity of a β-barrel and the fluorescence turn-on process is a fundamental challenge for both chemists and biologists. Herein, two distinct exo- and endo-functionalized tetraphenylethylene (TPE)-based M12L24 nanospheres with precise distribution of anchored TPE moieties and unique photophysical properties were constructed by means of a coordination-driven self-assembly strategy. Under dilute conditions, the nanospheres fluoresce more strongly than the corresponding TPE subcomponents. Meanwhile, the endo-functionalized sphere is able to induce a higher local concentration and more restrained motion of the enclosed 24 TPE units compared with exo-functionalized counterpart and thus induces much stronger emission due to the restriction of the rotation of the pendant TPE units. The biomimetic methodology developed here represents a promising way to understand and construct artificial GFP materials on the platforms of supramolecular coordination complexes.
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Affiliation(s)
- Xuzhou Yan
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Peifa Wei
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Yuhang Liu
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ming Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, P. R. China
| | - Chuanshuang Chen
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jun Zhao
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Guangfeng Li
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Manik Lal Saha
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Zhixuan Zhou
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Zhe An
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Peter J. Stang
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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20
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Jung KH, Fares M, Grainger LS, Wolstenholme CH, Hou A, Liu Y, Zhang X. A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede. Org Biomol Chem 2019; 17:1906-1915. [PMID: 30265264 DOI: 10.1039/c8ob01483c] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Self-labelling protein tags with fluorogenic probes serve as great fluorescence imaging tools to understand key questions of protein dynamics and functions in living cells. In the present study, we report a SNAP-tag fluorogenic probe 4c mimicking the chromophore of the red fluorescent protein Kaede. The molecular rotor properties of 4c were utilized as a fluorogenic probe for SNAP-tag, such that conjugation with SNAPf protein leads to inhibition of twisted intramolecular charge transfer, triggering fluorogenecity. Upon conjugation with SNAPf, 4c exhibited approximately a 90-fold enhancement in fluorescence intensity with fast labelling kinetics (k2 = 15 000 M-1 s-1). Biochemical and spectroscopic studies confirmed that fluorescence requires formation of folded SNAPf·4c covalent conjugate between Cys 145 and 4c. Confocal microscopy and flow cytometry showed that 4c is capable of detecting SNAPf proteins or SNAPf fused with a protein of interest in living cells. This work provides a framework to develop the large family of FP chromophores into fluorogenic probes for self-labelling protein tags.
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Affiliation(s)
- Kwan Ho Jung
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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21
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Affiliation(s)
- Alice Henley
- Department of Chemistry, University College London, London, UK
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22
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Zaitseva SO, Farkhutdinova DA, Baleeva NS, Smirnov AY, Zagudaylova MB, Shakhov AM, Astafiev AA, Baranov MS, Bochenkova AV. Excited-state locked amino analogues of the green fluorescent protein chromophore with a giant Stokes shift. RSC Adv 2019; 9:38730-38734. [PMID: 35540244 PMCID: PMC9076007 DOI: 10.1039/c9ra08808c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 11/18/2019] [Indexed: 11/21/2022] Open
Abstract
We design a new class of excited-state locked GFP chromophores which intrinsically exhibit a very large Stokes shift.
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Affiliation(s)
| | | | - Nadezhda S. Baleeva
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- 117997 Moscow
- Russia
| | | | | | | | - Artyom A. Astafiev
- Semenov Institute of Chemical Physics of RAS
- Moscow
- Russia
- Department of Chemistry
- Lomonosov Moscow State University
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- 117997 Moscow
- Russia
- Pirogov Russian National Research Medical University
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23
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Hu H, Wolstenholme CH, Zhang X, Li X. Inverted solvatochromic Stokes shift in GFP-like chromophores with extended conjugation. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1806160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hang Hu
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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24
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Liu Y, Wolstenholme CH, Carter GC, Liu H, Hu H, Grainger LS, Miao K, Fares M, Hoelzel CA, Yennawar HP, Ning G, Du M, Bai L, Li X, Zhang X. Modulation of Fluorescent Protein Chromophores To Detect Protein Aggregation with Turn-On Fluorescence. J Am Chem Soc 2018; 140:7381-7384. [PMID: 29883112 PMCID: PMC6258209 DOI: 10.1021/jacs.8b02176] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a fluorogenic method to visualize misfolding and aggregation of a specific protein-of-interest in live cells using structurally modulated fluorescent protein chromophores. Combining photophysical analysis, X-ray crystallography, and theoretical calculation, we show that fluorescence is triggered by inhibition of twisted-intramolecular charge transfer of these fluorophores in the rigid microenvironment of viscous solvent or protein aggregates. Bioorthogonal conjugation of the fluorophore to Halo-tag fused protein-of-interests allows for fluorogenic detection of both misfolded and aggregated species in live cells. Unlike other methods, our method is capable of detecting previously invisible misfolded soluble proteins. This work provides the first application of fluorescent protein chromophores to detect protein conformational collapse in live cells.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Charles H. Wolstenholme
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Gregory C. Carter
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Hongbin Liu
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Hang Hu
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Leeann S. Grainger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kun Miao
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Matthew Fares
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Conner A. Hoelzel
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Hemant P. Yennawar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Gang Ning
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Manyu Du
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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25
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Ermakova YG, Sen T, Bogdanova YA, Smirnov AY, Baleeva NS, Krylov AI, Baranov MS. Pyridinium Analogues of Green Fluorescent Protein Chromophore: Fluorogenic Dyes with Large Solvent-Dependent Stokes Shift. J Phys Chem Lett 2018; 9:1958-1963. [PMID: 29589942 DOI: 10.1021/acs.jpclett.8b00512] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Novel fluorogenic dyes based on the GFP chromophore are developed. The compounds contain a pyridinium ring instead of phenolate and feature large Stokes shifts and solvent-dependent variations in the fluorescence quantum yield. Electronic structure calculations explain the trends in solvatochromic behavior in terms of the increase of the dipole moment upon excited-state relaxation in polar solvents associated with the changes in bonding pattern in the excited state. A unique combination of such optical characteristics and lipophilic properties enables using one of the new dyes for imaging the membrane structure of endoplasmic reticulum. An extremely high photostability (due to a dynamic exchange between the free and absorbed states) and selectivity make this compound a promising label for this type of cellular organelles.
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Affiliation(s)
- Yulia G Ermakova
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1 , 117997 Moscow , Russia
- European Molecular Biology Laboratory , 69117 Heidelberg , Germany
| | - Tirthendu Sen
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
| | - Anna I Krylov
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1 , 117997 Moscow , Russia
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26
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Mohan Raj A, Ramamurthy V. Volume Conserving Geometric Isomerization of Encapsulated Azobenzenes in Ground and Excited States and as Radical Ion. Org Lett 2017; 19:6116-6119. [PMID: 29083193 DOI: 10.1021/acs.orglett.7b02963] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To probe the role of the supramolecular steric effects and free volume on photoreactions, geometric isomerization of neutral azobenzenes (ABs) and their radical ions, generated by electron transfer with gold nanoparticles, included within an octa acid capsule, was investigated. A comparison of the isomerization of ABs that proceed by volume conserving pyramidalization and stilbene analogues that proceed by volume demanding one bond flip has indicated the differing influence of 4-alkyl groups on these two processes.
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Affiliation(s)
- A Mohan Raj
- Department of Chemistry, University of Miami , Coral Gables, Florida 33124, United States
| | - V Ramamurthy
- Department of Chemistry, University of Miami , Coral Gables, Florida 33124, United States
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27
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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28
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Feng G, Luo C, Yi H, Yuan L, Lin B, Luo X, Hu X, Wang H, Lei C, Nie Z, Yao S. DNA mimics of red fluorescent proteins (RFP) based on G-quadruplex-confined synthetic RFP chromophores. Nucleic Acids Res 2017; 45:10380-10392. [PMID: 28981852 PMCID: PMC5737560 DOI: 10.1093/nar/gkx803] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/26/2017] [Accepted: 08/31/2017] [Indexed: 12/29/2022] Open
Abstract
Red fluorescent proteins (RFPs) have emerged as valuable biological markers for biomolecule imaging in living systems. Developing artificial fluorogenic systems that mimic RFPs remains an unmet challenge. Here, we describe the design and synthesis of six new chromophores analogous to the chromophores in RFPs. We demonstrate, for the first time, that encapsulating RFP chromophore analogues in canonical DNA G-quadruplexes (G4) can activate bright fluorescence spanning red and far-red spectral regions (Em = 583-668 nm) that nearly match the entire RFP palette. Theoretical calculations and molecular dynamics simulations reveal that DNA G4 greatly restricts radiationless deactivation of chromophores induced by a twisted intramolecular charge transfer (TICT). These DNA mimics of RFP exhibit attractive photophysical properties comparable or superior to natural RFPs, including high quantum yield, large Stokes shifts, excellent anti-photobleaching properties, and two-photon fluorescence. Moreover, these RFP chromophore analogues are a novel and distinctive type of topology-selective G4 probe specific to parallel G4 conformation. The DNA mimics of RFP have been further exploited for imaging of target proteins. Using cancer-specific cell membrane biomarkers as targets, long-term real-time monitoring in single live cell and two-photon fluorescence imaging in tissue sections have been achieved without the need for genetic coding.
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Affiliation(s)
- Guangfu Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Chao Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Haibo Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Xingyu Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaoxiao Hu
- Molecular Science and Biomedicine laboratory, Hunan University, Changsha 410082, PR China
| | - Honghui Wang
- College of Biology, Hunan University, Changsha 410082, PR China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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29
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Shinde DN, Trivedi R, Vamsi Krishna N, Giribabu L, Sridhar B, Rathod B, Prakasham R. Facile synthesis, characterisation and anti‐inflammatory activities of ferrocenyl ester derivatives of 4‐arylidene‐5‐imidazolinones. Appl Organomet Chem 2017. [DOI: 10.1002/aoc.4021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Dilip N. Shinde
- Inorganic and Physical Chemistry DivisionCSIR‐Indian Institute of Chemical Technology Hyderabad 500007 India
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐IICT Campus Hyderabad 500007 India
| | - Rajiv Trivedi
- Inorganic and Physical Chemistry DivisionCSIR‐Indian Institute of Chemical Technology Hyderabad 500007 India
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐IICT Campus Hyderabad 500007 India
| | - N. Vamsi Krishna
- Inorganic and Physical Chemistry DivisionCSIR‐Indian Institute of Chemical Technology Hyderabad 500007 India
| | - L. Giribabu
- Inorganic and Physical Chemistry DivisionCSIR‐Indian Institute of Chemical Technology Hyderabad 500007 India
- Academy of Scientific and Innovative Research (AcSIR)CSIR‐IICT Campus Hyderabad 500007 India
| | - B. Sridhar
- Center for X‐ray CrystallographyCSIR‐Indian Institute of Chemical Technology Hyderabad 500007 India
| | - B.B. Rathod
- Medicinal Chemistry and Biotechnology DivisionCSIR‐Indian Institute of Chemical Technology Hyderabad 500007 India
| | - R.S. Prakasham
- Medicinal Chemistry and Biotechnology DivisionCSIR‐Indian Institute of Chemical Technology Hyderabad 500007 India
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30
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Bochenkova AV, Mooney CRS, Parkes MA, Woodhouse JL, Zhang L, Lewin R, Ward JM, Hailes HC, Andersen LH, Fielding HH. Mechanism of resonant electron emission from the deprotonated GFP chromophore and its biomimetics. Chem Sci 2017; 8:3154-3163. [PMID: 28507691 PMCID: PMC5413970 DOI: 10.1039/c6sc05529j] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 02/04/2017] [Indexed: 11/29/2022] Open
Abstract
The Green Fluorescent Protein (GFP), which is widely used in bioimaging, is known to undergo light-induced redox transformations. Electron transfer is thought to occur resonantly through excited states of its chromophore; however, a detailed understanding of the electron gateway states of the chromophore is still missing. Here, we use photoelectron spectroscopy and high-level quantum chemistry calculations to show that following UV excitation, the ultrafast electron dynamics in the chromophore anion proceeds via an excited shape resonance strongly coupled to the open continuum. The impact of this state is found across the entire 355-315 nm excitation range, from above the first bound-bound transition to below the opening of higher-lying continua. By disentangling the electron dynamics in the photodetachment channels, we provide an important reference for the adiabatic position of the electron gateway state, which is located at 348 nm, and discover the source of the curiously large widths of the photoelectron spectra that have been reported in the literature. By introducing chemical modifications to the GFP chromophore, we show that the detachment threshold and the position of the gateway state, and hence the underlying excited-state dynamics, can be changed systematically. This enables a fine tuning of the intrinsic electron emission properties of the GFP chromophore and has significant implications for its function, suggesting that the biomimetic GFP chromophores are more stable to photooxidation.
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Affiliation(s)
| | - Ciarán R S Mooney
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Michael A Parkes
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Joanne L Woodhouse
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Lijuan Zhang
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Ross Lewin
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - John M Ward
- Department of Biochemical Engineering , UCL , Bernard Katz Building, Gordon Street , London , WC1E 0AH , UK
| | - Helen C Hailes
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Lars H Andersen
- Department of Physics and Astronomy , Aarhus University , DK-8000 Aarhus C , Denmark
| | - Helen H Fielding
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
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31
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McLaughlin C, Assmann M, Parkes MA, Woodhouse JL, Lewin R, Hailes HC, Worth GA, Fielding HH. ortho and para chromophores of green fluorescent protein: controlling electron emission and internal conversion. Chem Sci 2017; 8:1621-1630. [PMID: 29780449 PMCID: PMC5933426 DOI: 10.1039/c6sc03833f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/05/2016] [Indexed: 12/22/2022] Open
Abstract
Green fluorescent protein (GFP) continues to play an important role in the biological and biochemical sciences as an efficient fluorescent probe and is also known to undergo light-induced redox transformations. Here, we employ photoelectron spectroscopy and quantum chemistry calculations to investigate how the phenoxide moiety controls the competition between electron emission and internal conversion in the isolated GFP chromophore anion, following photoexcitation with ultraviolet light in the range 400-230 nm. We find that moving the phenoxide group from the para position to the ortho position enhances internal conversion back to the ground electronic state but that adding an additional OH group to the para chromophore, at the ortho position, impedes internal conversion. Guided by quantum chemistry calculations, we interpret these observations in terms of torsions around the C-C-C bridge being enhanced by electrostatic repulsions or impeded by the formation of a hydrogen-bonded seven-membered ring. We also find that moving the phenoxide group from the para position to the ortho position reduces the energy required for detachment processes, whereas adding an additional OH group to the para chromophore at the ortho position increases the energy required for detachment processes. These results have potential applications in tuning light-induced redox processes of this biologically and technologically important fluorescent protein.
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Affiliation(s)
- Conor McLaughlin
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Mariana Assmann
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Michael A Parkes
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Joanne L Woodhouse
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Ross Lewin
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Helen C Hailes
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Graham A Worth
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
| | - Helen H Fielding
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , UK .
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32
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Huang S, Li F, Liao C, Zheng B, Du J, Xiao D. A selective and sensitive fluorescent probe for the determination of HSA and trypsin. Talanta 2017; 170:562-568. [PMID: 28501212 DOI: 10.1016/j.talanta.2017.01.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 01/26/2023]
Abstract
A simple fluorescent probe HBI-GR based on the combination of the fluorophore (p-HBI) in green fluorescent protein (GFP) and Guanine riboside (GR) for HSA was successfully synthesized. HBI-GR showed an obvious fluorescence enhancement toward HSA without interference from other proteins, amino acids, anions and commonly existing metal ions. HBI-GR exhibited high sensitivity towards HSA with a good linear relationship between the fluorescence intensity of HBI-GR and HSA concentration from 0 to 0.06mgmL-1. The limit of detection, based on a signal-to-noise ratio of 3, was 15.09ngmL-1, which was much lower than that of most other reported probes. HBI-GR was almost non-fluorescent because of the bond twisting in the exited state of chromophore HBI. After binding to the hydrophobic pocket of HSA, it showed an obvious fluorescence enhancement due to the rigidifying of the flexible chromophore HBI by the hydrophobic environment. The resulting HBI-GR/HSA system also showed a satisfactory sensing ability toward trypsin through decreased fluorescence intensity with the detection limit of 0.0282ngmL-1. The fluorescence decreasing process was occurred as the lysine and arginine amino acids residues of HSA were cleaved by trypsin, which led to further exposure of HBI-GR to the PBS buffer phase and a concomitant decrease of the HBI-GR fluorescence intensity. Moreover, the probe HBI-GR was successfully used to detect HSA in healthy human urine and human blood serum samples. The practical application of the HBI-GR/HSA system for trypsin detection in healthy human urine also achieved satisfactory result.
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Affiliation(s)
- Shanshan Huang
- College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, PR China
| | - Fangfang Li
- College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, PR China; College of Chemical Engineering, Sichuan University, 29 Wangjiang Road, Chengdu 610065, PR China
| | - Caiyun Liao
- College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, PR China
| | - Baozhan Zheng
- College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, PR China; College of Chemical Engineering, Sichuan University, 29 Wangjiang Road, Chengdu 610065, PR China
| | - Juan Du
- College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, PR China.
| | - Dan Xiao
- College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu 610064, PR China; College of Chemical Engineering, Sichuan University, 29 Wangjiang Road, Chengdu 610065, PR China.
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33
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Dolgopolova EA, Moore TM, Ejegbavwo OA, Pellechia PJ, Smith MD, Shustova NB. A metal–organic framework as a flask: photophysics of confined chromophores with a benzylidene imidazolinone core. Chem Commun (Camb) 2017; 53:7361-7364. [DOI: 10.1039/c7cc02253k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Photophysics and dynamics of chromophores with a benzylidene imidazolinone core, responsible for emission of green fluorescent protein variants, were studied as a function of host topology by three approaches.
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Affiliation(s)
| | - Thomas M. Moore
- Department of Chemistry and Biochemistry
- University of South Carolina
- Columbia
- USA
| | - Otega A. Ejegbavwo
- Department of Chemistry and Biochemistry
- University of South Carolina
- Columbia
- USA
| | - Perry J. Pellechia
- Department of Chemistry and Biochemistry
- University of South Carolina
- Columbia
- USA
| | - Mark D. Smith
- Department of Chemistry and Biochemistry
- University of South Carolina
- Columbia
- USA
| | - Natalia B. Shustova
- Department of Chemistry and Biochemistry
- University of South Carolina
- Columbia
- USA
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34
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Santos FS, Ramasamy E, Ramamurthy V, Rodembusch FS. Photoinduced electron transfer across an organic molecular wall: octa acid encapsulated ESIPT dyes as electron donors. Photochem Photobiol Sci 2017; 16:840-844. [DOI: 10.1039/c7pp00065k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Efficient photoinduced electron transfer from proton transfer dyes encapsulated within water soluble supramolecular host octa acid to electron acceptors present outside the capsule was observed in aqueous solution.
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Affiliation(s)
- Fabiano S. Santos
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
- Grupo de Pesquisa em Fotoquímica Orgânica Aplicada
| | | | - V. Ramamurthy
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Fabiano S. Rodembusch
- Grupo de Pesquisa em Fotoquímica Orgânica Aplicada
- Instituto de Química
- Universidade Federal do Rio Grande do Sul
- Porto Alegre
- Brazil
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35
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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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36
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Deng H, Yu C, Gong L, Zhu X. Self-Restricted Green Fluorescent Protein Chromophore Analogues: Dramatic Emission Enhancement and Remarkable Solvatofluorochromism. J Phys Chem Lett 2016; 7:2935-2944. [PMID: 27404318 DOI: 10.1021/acs.jpclett.6b01251] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The confinement effect of the β-barrel defines the emission profiles of the chromophores of the green fluorescent protein (GFP) family. Here, we describe the design strategy and mimicking of confinement effects via the chromophore itself, termed the self-restricted effect. By systematically tailoring the GFP core, a family of 2,5-dialkoxy-substituted GFP chromophore analogues is found to be highly emissive and show remarkable solvatofluorochromism in fluid solvents. Fluorescence quantum yield (QY) and lifetime measurements, in combination with theoretical calculations, illustrate the mechanism relying on inhibition of torsional rotation around the exocyclic CC bond. Meanwhile, theoretical calculations further reveal that the electrostatic interaction between the solvent and the imidazolinone oxygen can contribute to suppress the radiationless decay channel around the exocyclic C═C double bond. Our findings put forward a universal approach toward unlocked highly emissive GFPc analogues, potentially promoting the understanding of the photophysics and biochemical application of GFP chromophore analogues.
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Affiliation(s)
- Hongping Deng
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Chunyang Yu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Lidong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University , 850 Huanghe Road, Dalian 116029, People's Republic of China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University , 800 Dongchuan Road, Shanghai 200240, People's Republic of China
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37
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Mosca S, Yu Y, Rebek J. Preparative scale and convenient synthesis of a water-soluble, deep cavitand. Nat Protoc 2016; 11:1371-87. [PMID: 27388554 DOI: 10.1038/nprot.2016.078] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cavitands are established tools of supramolecular chemistry and molecular recognition, and they are finding increasing application in sensing and sequestration of physiologically relevant molecules in aqueous solution. The synthesis of a water-soluble, deep cavitand is described. The route comprises six (linear) steps from commercially available precursors, and it relies on the fourfold oligomeric cyclization reaction of resorcinol with 2,3-dihydrofuran that leads to the formation of a shallow resorcinarene framework; condensation with aromatic panels, which deepens the hydrophobic binding cavity; construction of rigid urea functionalities on the upper rim; and the introduction of the water-solubilizing methylimidazolium groups on the lower rim. Late intermediates of the synthesis can be used in the preparation of congener cavitands with different properties and applications, and a sample of such a synthetic procedure is included in this protocol. Emphasis is placed on scaled-up reactions and on purification procedures that afford materials in high yield and avoid chromatographic purification. This protocol provides improvements over previously described procedures, and it enables the preparation of sizable amounts of deep cavitands: 7 g of a water-soluble cavitand can be prepared from resorcinol in 13 working days.
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Affiliation(s)
- Simone Mosca
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Yang Yu
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
| | - Julius Rebek
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Department of Chemistry, Fudan University, Shanghai, China
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38
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Singh A, Ramanathan G. Rational Design of Heterogeneous Silver Catalysts by Exploitation of Counteranion-Induced Coordination Geometry. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ashish Singh
- Department of Chemistry; Indian Institute of Technology; Kanpur 208016 India
| | - Gurunath Ramanathan
- Department of Chemistry; Indian Institute of Technology; Kanpur 208016 India
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39
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Chatterjee T, Mandal M, Das A, Bhattacharyya K, Datta A, Mandal PK. Dual Fluorescence in GFP Chromophore Analogues: Chemical Modulation of Charge Transfer and Proton Transfer Bands. J Phys Chem B 2016; 120:3503-10. [PMID: 26998908 DOI: 10.1021/acs.jpcb.6b01993] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tanmay Chatterjee
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West-Bengal 741246, India
| | - Mrinal Mandal
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West-Bengal 741246, India
| | - Ananya Das
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West-Bengal 741246, India
| | - Kalishankar Bhattacharyya
- Department
of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Ayan Datta
- Department
of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Prasun K. Mandal
- Department
of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West-Bengal 741246, India
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40
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Liu BQ, Chen YT, Chen YW, Chung KY, Tsai YH, Li YJ, Chao CM, Liu KM, Tseng HW, Chou PT. Ethylene glycol modified 2-(2′-aminophenyl)benzothiazoles at the amino site: the excited-state N-H proton transfer reactions in aqueous solution, micelles and potential application in live-cell imaging. Methods Appl Fluoresc 2016. [DOI: 10.1088/2050-6120/4/1/014004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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41
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Dolgopolova EA, Moore TM, Fellows WB, Smith MD, Shustova NB. Photophysics of GFP-related chromophores imposed by a scaffold design. Dalton Trans 2016; 45:9884-91. [DOI: 10.1039/c5dt05063d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In this paper, a rigid scaffold imposes the photophysics of chromophores with a benzylidene imidazolidinone core by mimicking the β-barrel structure of the green fluorescent protein (GFP) and its analogs.
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Affiliation(s)
- E. A. Dolgopolova
- Department of Chemistry and Biochemistry
- University of South Carolina
- Columbia
- USA
| | - T. M. Moore
- Department of Chemistry and Biochemistry
- University of South Carolina
- Columbia
- USA
| | - W. B. Fellows
- Department of Chemistry and Biochemistry
- University of South Carolina
- Columbia
- USA
| | - M. D. Smith
- Department of Chemistry and Biochemistry
- University of South Carolina
- Columbia
- USA
| | - N. B. Shustova
- Department of Chemistry and Biochemistry
- University of South Carolina
- Columbia
- USA
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42
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Abstract
Photochemistry along with life as we know it originated on earth billions of years ago. Supramolecular Photochemistry had its beginning when plants that sustain life began transforming water into oxygen by carrying out light initiated reactions within highly organized assemblies. Prompted by the efforts of J. Priestly (photosynthesis), F. Sestini, S. Cannizaro, and C. Liebermann (solid-state photochemistry of santonin, quinones, and cinnamic acid), orderly scientific investigations of the link between light absorption by matter and molecules and the chemical and physical consequences began in the mid-1700s. By 1970 when Molecular Photochemistry had matured, it was clear that controlling photochemical reactions by conventional methods of varying reaction parameters like temperature and pressure would be futile due to the photoreactions' very low activation energies and enthalpies. During the last 50 years, the excited state behavior of molecules has been successfully manipulated with the use of confining media and weak interactions between the medium and the reactant molecule. In this context, with our knowledge from experimentation with micelles, cyclodextrins (CD), cucurbitruils (CB), calixarenes (CA), Pd nanocage, crystals, and zeolites as media, we began about a decade ago to explore the use of a new water-soluble synthetic organic cavitand, octa acid (OA) as a reaction container. The uniqueness of OA as an organic cavitand lies in that two OA molecules form a closed hydrophobic capsule to encapsulate water-insoluble guest molecule(s). The ability to include a large number of guest molecules in OA has provided an opportunity to examine the excited state chemistry of organic molecules in a hydrophobic, confined environment. OA distinguishes itself from the well-known cavitands CD and CB by its active reaction cavity absorbing UV-radiation between 200 and 300 nm and serving as energy, electron, and hydrogen donor. The freedom of guest molecules in OA, between that in crystals and isotropic solution can be transformed into photoproducts selectivity. The results of our photochemical investigations elaborated in this Account demonstrate that OA with a medium sized cavity exerts better control on excited state processes than the more common and familiar organic hosts such as CD, CB, CA, and micelles. By examining the photochemistry of a number of molecules (olefins, carbonyls, aromatics and singlet oxygen) that undergo varied reactions (cleavage, cycloaddition, cis-trans isomerization, oxidation and cyclization) within OA capsule, we have demonstrated that the free space within the container, the capsule influenced conformation and preorientation of guest molecules, supramolecular steric control, and capsular dynamics contribute to the altered excited state behavior. In this Account, we have shown that photochemistry based on concepts of physical organic and supramolecular chemistry continues to be a discipline with unlimited potential. The future of supramolecular photochemistry lies in synthetic, materials, medicinal, and biological chemistries. Success in these areas depends on synthesizing well-designed water-soluble hosts that can emulate complex biological assemblies, organizing and examining the behavior of supramolecular assemblies on solid surfaces, rendering the photoreactions catalytic, and delivering encapsulated drugs in a targeted fashion.
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43
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Walker CL, Lukyanov KA, Yampolsky IV, Mishin AS, Bommarius AS, Duraj-Thatte AM, Azizi B, Tolbert LM, Solntsev KM. Fluorescence imaging using synthetic GFP chromophores. Curr Opin Chem Biol 2015; 27:64-74. [DOI: 10.1016/j.cbpa.2015.06.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/21/2015] [Accepted: 06/05/2015] [Indexed: 01/22/2023]
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44
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Abstract
This review focuses on molecular containers formed by assembly processes driven by the hydrophobic effect, and summarizes the progress made in the field over the last ten years. This small but growing facet of supramolecular chemistry discusses three classes of molecules used by researchers to investigate how self-assembly can be applied to form discrete, mono-dispersed, and structurally well-defined supramolecular entities. The approaches demonstrate the importance of preorganization of arrays of rigid moieties to define a specific form predisposed to bind, fold, or assemble. As the examples demonstrate, studying these systems and their properties is teaching us how to control supramolecular chemistry in water, shedding light on aspects of aqueous solutions chemistry, and illustrating novel applications that harness the unique properties of the hydrophobic effect.
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Affiliation(s)
- Jacobs H Jordan
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
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45
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Gaffarogullari EC, Greulich P, Kobitski AY, Nierth A, Nienhaus GU, Jäschke A. Unravelling RNA-substrate interactions in a ribozyme-catalysed reaction using fluorescent turn-on probes. Chemistry 2015; 21:5864-71. [PMID: 25753253 DOI: 10.1002/chem.201406512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 11/07/2022]
Abstract
The Diels-Alder reaction is one of the most important C-C bond-forming reactions in organic chemistry, and much effort has been devoted to controlling its enantio- and diastereoselectivity. The Diels-Alderase ribozyme (DAse) catalyses the reaction between anthracene dienes and maleimide dienophiles with multiple-turnover, stereoselectivity, and up to 1100-fold rate acceleration. Here, a new generation of anthracene-BODIPY-based fluorescent probes was developed to monitor catalysis by the DAse. The brightness of these probes increases up to 93-fold upon reaction with N-pentylmaleimide (NPM), making these useful tools for investigating the stereochemistry of the ribozyme-catalysed reaction. With these probes, we observed that the DAse catalyses the reaction with >91% de and >99% ee. The stereochemistry of the major product was determined unambiguously by rotating-frame nuclear Overhauser NMR spectroscopy (ROESY-NMR) and is in agreement with crystallographic structure information. The pronounced fluorescence change of the probes furthermore allowed a complete kinetic analysis, which revealed an ordered bi uni type reaction mechanism, with the dienophile binding first.
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Affiliation(s)
- Ece Cazibe Gaffarogullari
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany), Fax: (+49) 6221-54-6430
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46
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Williams DE, Dolgopolova EA, Pellechia PJ, Palukoshka A, Wilson TJ, Tan R, Maier JM, Greytak AB, Smith MD, Krause JA, Shustova NB. Mimic of the Green Fluorescent Protein β-Barrel: Photophysics and Dynamics of Confined Chromophores Defined by a Rigid Porous Scaffold. J Am Chem Soc 2015; 137:2223-6. [DOI: 10.1021/ja5131269] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Derek E. Williams
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ekaterina A. Dolgopolova
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Andrei Palukoshka
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Thomas J. Wilson
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Rui Tan
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Josef M. Maier
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Andrew B. Greytak
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jeanette A. Krause
- Department
of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Natalia B. Shustova
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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47
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Zhou Q, Wu F, Wu M, Tian Y, Niu Z. Confined chromophores in tobacco mosaic virus to mimic green fluorescent protein. Chem Commun (Camb) 2015; 51:15122-4. [DOI: 10.1039/c5cc05751e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Grafting green fluorescent protein-like chromophores in the 4 nm channel of tobacco mosaic virus greatly enhances its fluorescence emission.
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Affiliation(s)
- Quan Zhou
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Fengchi Wu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Man Wu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Ye Tian
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Zhongwei Niu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
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48
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Olsen S. Locally-Excited (LE) versus Charge-Transfer (CT) Excited State Competition in a Series of Para-Substituted Neutral Green Fluorescent Protein (GFP) Chromophore Models. J Phys Chem B 2014; 119:2566-75. [DOI: 10.1021/jp508723d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Seth Olsen
- School of Mathematics and
Physics, The University of Queensland, Brisbane, QLD 4072, Australia
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49
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Wanjari PP, Gibb BC, Ashbaugh HS. Simulation optimization of spherical non-polar guest recognition by deep-cavity cavitands. J Chem Phys 2014; 139:234502. [PMID: 24359375 DOI: 10.1063/1.4844215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Biomimetic deep-cavity cavitand hosts possess unique recognition and encapsulation properties that make them capable of selectively binding a range of non-polar guests within their hydrophobic pocket. Adamantane based derivatives which snuggly fit within the pocket of octa-acid deep cavity cavitands exhibit some of the strongest host binding. Here we explore the roles of guest size and attractiveness on optimizing guest binding to form 1:1 complexes with octa-acid cavitands in water. Specifically we simulate the water-mediated interactions of the cavitand with adamantane and a range of simple Lennard-Jones guests of varying diameter and attractive well-depth. Initial simulations performed with methane indicate hydrated methanes preferentially reside within the host pocket, although these guests frequently trade places with water and other methanes in bulk solution. The interaction strength of hydrophobic guests increases with increasing size from sizes slightly smaller than methane to Lennard-Jones guests comparable in size to adamantane. Over this guest size range the preferential guest binding location migrates from the bottom of the host pocket upwards. For guests larger than adamantane, however, binding becomes less favorable as the minimum in the potential-of-mean force shifts to the cavitand face around the portal. For a fixed guest diameter, the Lennard-Jones well-depth is found to systematically shift the guest-host potential-of-mean force to lower free energies, however, the optimal guest size is found to be insensitive to increasing well-depth. Ultimately our simulations show that adamantane lies within the optimal range of guest sizes with significant attractive interactions to match the most tightly bound Lennard-Jones guests studied.
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Affiliation(s)
- Piyush P Wanjari
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
| | - Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA
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50
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Santos FS, Ramasamy E, Ramamurthy V, Rodembusch FS. Excited state chemistry of flavone derivatives in a confined medium: ESIPT emission in aqueous media. Photochem Photobiol Sci 2014; 13:992-6. [PMID: 24901799 DOI: 10.1039/c4pp00096j] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The excited state behavior of two flavone derivatives 3-hydroxyflavone and 4'-N,N-diethylaminoflavonol in a confined medium indicates that supramolecular effects could alter the nature of the fluorescence emission. Within the octa acid host the neutral unionized species of these two dyes are present showing large Stokes shifted emission due to intramolecular proton transfer, a pattern different from that in aqueous medium.
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Affiliation(s)
- Fabiano S Santos
- Department of Chemistry, University of Miami, Coral Gables, Florida 33124, USA
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