1
|
Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
Collapse
Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| |
Collapse
|
2
|
Synthesis, structure, and photoluminescence properties of lanthanide based metal organic frameworks and a cadmium coordination polymer derived from 2,2′-diamino-trans 4,4′-stilbenedicarboxylate. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
3
|
Barsukova MO, Sapchenko SA, Kovalenko KA, Samsonenko DG, Potapov AS, Dybtsev DN, Fedin VP. Exploring the multifunctionality in metal–organic framework materials: how do the stilbenedicarboxylate and imidazolyl ligands tune the characteristics of coordination polymers? NEW J CHEM 2018. [DOI: 10.1039/c8nj00494c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A synergistic effect causes MOF materials to demonstrate excellent iodine vapor retention and luminescence properties.
Collapse
Affiliation(s)
- Marina O. Barsukova
- Nikolaev Institute of Inorganic Chemistry
- Siberian Branch of the Russian Academy of Sciences
- Novosibirsk
- Russia
- Faculty of Natural Sciences
| | - Sergey A. Sapchenko
- Nikolaev Institute of Inorganic Chemistry
- Siberian Branch of the Russian Academy of Sciences
- Novosibirsk
- Russia
- Faculty of Natural Sciences
| | - Konstantin A. Kovalenko
- Nikolaev Institute of Inorganic Chemistry
- Siberian Branch of the Russian Academy of Sciences
- Novosibirsk
- Russia
- Faculty of Natural Sciences
| | - Denis G. Samsonenko
- Nikolaev Institute of Inorganic Chemistry
- Siberian Branch of the Russian Academy of Sciences
- Novosibirsk
- Russia
- Faculty of Natural Sciences
| | | | - Danil N. Dybtsev
- Nikolaev Institute of Inorganic Chemistry
- Siberian Branch of the Russian Academy of Sciences
- Novosibirsk
- Russia
- Faculty of Natural Sciences
| | - Vladimir P. Fedin
- Nikolaev Institute of Inorganic Chemistry
- Siberian Branch of the Russian Academy of Sciences
- Novosibirsk
- Russia
- Faculty of Natural Sciences
| |
Collapse
|
4
|
Eichinger A, Neumaier I, Pschenitza M, Niessner R, Knopp D, Skerra A. Enge molekulare Erkennung von Benzo[ a
]pyren durch einen hochaffinen Antikörper. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Andreas Eichinger
- Munich Center for Integrated Protein Science (CIPS-M) und Lehrstuhl für Biologische Chemie; Technische Universität München; 85354 Freising, Weihenstephan Deutschland
| | - Irmgard Neumaier
- Munich Center for Integrated Protein Science (CIPS-M) und Lehrstuhl für Biologische Chemie; Technische Universität München; 85354 Freising, Weihenstephan Deutschland
| | - Michael Pschenitza
- Lehrstuhl für Analytische Chemie; Technische Universität München; 81377 München Deutschland
| | - Reinhard Niessner
- Lehrstuhl für Analytische Chemie; Technische Universität München; 81377 München Deutschland
| | - Dietmar Knopp
- Lehrstuhl für Analytische Chemie; Technische Universität München; 81377 München Deutschland
| | - Arne Skerra
- Munich Center for Integrated Protein Science (CIPS-M) und Lehrstuhl für Biologische Chemie; Technische Universität München; 85354 Freising, Weihenstephan Deutschland
| |
Collapse
|
5
|
Eichinger A, Neumaier I, Pschenitza M, Niessner R, Knopp D, Skerra A. Tight Molecular Recognition of Benzo[a]pyrene by a High-Affinity Antibody. Angew Chem Int Ed Engl 2017; 56:10592-10597. [PMID: 28603847 DOI: 10.1002/anie.201703893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/26/2017] [Indexed: 01/19/2023]
Abstract
Benzo[a]pyrene, which is produced during the incomplete combustion of organic material, is an abundant noxious pollutant because of its carcinogenic metabolic degradation products. The high-affinity (KD ≈3 nm) monoclonal antibody 22F12 allows facile bioanalytical quantification of benzo[a]pyrene even in complex matrices. We report the functional and X-ray crystallographic analysis of 22F12 in complex with 3-hydroxybenzo[a]pyrene after cloning of the V-genes and production as a recombinant Fab fragment. The polycyclic aromatic hydrocarbon is bound in a deep pocket between the light and heavy chains, surrounded mainly by aromatic and aliphatic amino acid side chains. Interestingly, the hapten-antibody interface is less densely packed than expected and reveals polar, H-bond-like interactions with the polycyclic aromatic π-electron system, which may allow the antibody to maintain a large, predominantly hydrophobic binding site in an aqueous environment while providing sufficient complementarity to its ligand.
Collapse
Affiliation(s)
- Andreas Eichinger
- Munich Center for Integrated Protein Science, CIPS-M, und Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising, Weihenstephan, Germany
| | - Irmgard Neumaier
- Munich Center for Integrated Protein Science, CIPS-M, und Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising, Weihenstephan, Germany
| | - Michael Pschenitza
- Lehrstuhl für Analytische Chemie, Technische Universität München, 81377, München, Germany
| | - Reinhard Niessner
- Lehrstuhl für Analytische Chemie, Technische Universität München, 81377, München, Germany
| | - Dietmar Knopp
- Lehrstuhl für Analytische Chemie, Technische Universität München, 81377, München, Germany
| | - Arne Skerra
- Munich Center for Integrated Protein Science, CIPS-M, und Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising, Weihenstephan, Germany
| |
Collapse
|
6
|
Li C, Tebo AG, Gautier A. Fluorogenic Labeling Strategies for Biological Imaging. Int J Mol Sci 2017; 18:ijms18071473. [PMID: 28698494 PMCID: PMC5535964 DOI: 10.3390/ijms18071473] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/27/2022] Open
Abstract
The spatiotemporal fluorescence imaging of biological processes requires effective tools to label intracellular biomolecules in living systems. This review presents a brief overview of recent labeling strategies that permits one to make protein and RNA strongly fluorescent using synthetic fluorogenic probes. Genetically encoded tags selectively binding the exogenously applied molecules ensure high labeling selectivity, while high imaging contrast is achieved using fluorogenic chromophores that are fluorescent only when bound to their cognate tag, and are otherwise dark. Beyond avoiding the need for removal of unbound synthetic dyes, these approaches allow the development of sophisticated imaging assays, and open exciting prospects for advanced imaging, particularly for multiplexed imaging and super-resolution microscopy.
Collapse
Affiliation(s)
- Chenge Li
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France.
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France.
| | - Alison G Tebo
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France.
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France.
| | - Arnaud Gautier
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France.
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France.
| |
Collapse
|
7
|
Mathis II SR, Golafale ST, Bacsa J, Steiner A, Ingram CW, Doty FP, Auden E, Hattar K. Mesoporous stilbene-based lanthanide metal organic frameworks: synthesis, photoluminescence and radioluminescence characteristics. Dalton Trans 2017; 46:491-500. [DOI: 10.1039/c6dt03755k] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mesoporous non-interpenetrating stilbene-based lanthanide metal organic frameworks exhibits photo and radioluminescence behavior.
Collapse
Affiliation(s)
- Stephan R. Mathis II
- Center for Functional Nanoscale Materials
- Department of Chemistry
- Clark Atlanta University
- Atlanta
- USA
| | - Saki T. Golafale
- Center for Functional Nanoscale Materials
- Department of Chemistry
- Clark Atlanta University
- Atlanta
- USA
| | - John Bacsa
- Department of Chemistry
- Emory University
- Atlanta
- USA
| | | | - Conrad W. Ingram
- Center for Functional Nanoscale Materials
- Department of Chemistry
- Clark Atlanta University
- Atlanta
- USA
| | | | | | | |
Collapse
|
8
|
Jarenmark M, Carlström G, Fredin LA, Hedberg Wallenstein J, Doverbratt I, Abrahamsson M, Persson P. Diastereomerization Dynamics of a Bistridentate RuII Complex. Inorg Chem 2016; 55:3015-22. [DOI: 10.1021/acs.inorgchem.5b02893] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Joachim Hedberg Wallenstein
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | | | - Maria Abrahamsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | | |
Collapse
|
9
|
Jullien L, Gautier A. Fluorogen-based reporters for fluorescence imaging: a review. Methods Appl Fluoresc 2015; 3:042007. [PMID: 29148509 DOI: 10.1088/2050-6120/3/4/042007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fluorescence bioimaging has recently jumped into a new area of spatiotemporal resolution and sensitivity thanks to synergistic advances in both optical physics and probe/biosensor design. This review focuses on the recent development of genetically encodable fluorescent reporters that bind endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activate their fluorescence. We highlight the innovative engineering and design that gave rise to these new natural and synthetic fluorescent reporters, and describe some of the emerging applications in imaging and biosensing.
Collapse
Affiliation(s)
- Ludovic Jullien
- École Normale Supérieure-PSL Research University, Department of Chemistry, 24 rue Lhomond, F-75005 Paris, France. Sorbonne Universités, UPMC Univ Paris 06, UMR 8640 PASTEUR, F-75005 Paris, France. CNRS, UMR 8640 PASTEUR, F-75005 Paris, France
| | | |
Collapse
|
10
|
Chen Q, Trinh MT, Paley DW, Preefer MB, Zhu H, Fowler BS, Zhu XY, Steigerwald ML, Nuckolls C. Strain-induced stereoselective formation of blue-emitting cyclostilbenes. J Am Chem Soc 2015; 137:12282-8. [PMID: 26373838 DOI: 10.1021/jacs.5b06258] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the synthesis of two conjugated macrocycles that are formed from the end-to-end linking of stilbenes. We have named these macrocycles cyclostilbenes. The two cyclostilbene isomers created in this study differ in the configuration of the double bond in their subunits. These macrocycles are formed selectively through a stepwise reductive elimination from a tetraplatinum precursor and subsequent photoisomerization. Single-crystal X-ray diffraction reveals the formation of channel architectures in the solid state that can be filled with guest molecules. The cyclostilbene macrocycles emit blue light with fluorescence quantum yields that are high (>50%) and have photoluminescence lifetimes of ∼0.8-1.5 ns. The breadth and large Stokes shift in fluorescence emission, along with broad excited-state absorption, result from strong electronic-vibronic coupling in the strained structures of the cyclostilbenes.
Collapse
Affiliation(s)
- Qishui Chen
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - M Tuan Trinh
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Daniel W Paley
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Molleigh B Preefer
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Haiming Zhu
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Brandon S Fowler
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - X-Y Zhu
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Michael L Steigerwald
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Colin Nuckolls
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| |
Collapse
|
11
|
Créminon C, Taran F. Enzyme immunoassays as screening tools for catalysts and reaction discovery. Chem Commun (Camb) 2015; 51:7996-8009. [DOI: 10.1039/c5cc00599j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This feature article summarizes the development and use of immunoassay techniques (ELISA) as screening tools for fast identification of efficient catalysts in libraries and for the discovery of new chemical reactions.
Collapse
Affiliation(s)
| | - Frédéric Taran
- CEA
- iBiTecS
- Service de Chimie Bioorganique et de Marquage
- Gif sur Yvette
- France
| |
Collapse
|
12
|
Garg K, Ganapathi E, Rajakannu P, Ravikanth M. Stereochemical modulation of emission behaviour in E/Z isomers of diphenyldipyrroethene from aggregation induced emission to crystallization induced emission. Phys Chem Chem Phys 2015; 17:19465-73. [DOI: 10.1039/c5cp02400e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have successfully separated and characterized E- and Z-isomers of diphenyldipyrroethene molecules and studies show that the E-isomer behaves as AIEgen, whereas the Z-isomer behaves as CIEgen.
Collapse
Affiliation(s)
- K. Garg
- Department of Chemistry
- Indian institute of Technology Bombay
- Powai
- India
| | - E. Ganapathi
- Department of Chemistry
- Indian institute of Technology Bombay
- Powai
- India
| | - P. Rajakannu
- Department of Chemistry
- Indian institute of Technology Bombay
- Powai
- India
| | - M. Ravikanth
- Department of Chemistry
- Indian institute of Technology Bombay
- Powai
- India
| |
Collapse
|
13
|
Agnihotri H, Palakollu V, Kanvah S. Selective photoisomerization of methyl substituted nitro diphenylbutadienes. J Photochem Photobiol A Chem 2014. [DOI: 10.1016/j.jphotochem.2014.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
14
|
Mei J, Hong Y, Lam JWY, Qin A, Tang Y, Tang BZ. Aggregation-induced emission: the whole is more brilliant than the parts. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:5429-79. [PMID: 24975272 DOI: 10.1002/adma.201401356] [Citation(s) in RCA: 1847] [Impact Index Per Article: 184.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/25/2014] [Indexed: 05/20/2023]
Abstract
"United we stand, divided we fall."--Aesop. Aggregation-induced emission (AIE) refers to a photophysical phenomenon shown by a group of luminogenic materials that are non-emissive when they are dissolved in good solvents as molecules but become highly luminescent when they are clustered in poor solvents or solid state as aggregates. In this Review we summarize the recent progresses made in the area of AIE research. We conduct mechanistic analyses of the AIE processes, unify the restriction of intramolecular motions (RIM) as the main cause for the AIE effects, and derive RIM-based molecular engineering strategies for the design of new AIE luminogens (AIEgens). Typical examples of the newly developed AIEgens and their high-tech applications as optoelectronic materials, chemical sensors and biomedical probes are presented and discussed.
Collapse
Affiliation(s)
- Ju Mei
- Department of Chemistry, HKUST Jockey Club Institute for Advanced Study, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science & Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong, China
| | | | | | | | | | | |
Collapse
|
15
|
Samanta SR, Choudhury R, Ramamurthy V. Photoisomerization and Photooxygenation of 1,4-Diaryl-1,3-dienes in a Confined Space. J Phys Chem A 2014; 118:10554-62. [DOI: 10.1021/jp505196v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shampa R. Samanta
- Department
of Chemistry, University of Miami, Room No. 315 Cox Science Building, Coral Gables, Florida 33146, United States
| | - Rajib Choudhury
- Department
of Chemistry, University of Miami, Room No. 315 Cox Science Building, Coral Gables, Florida 33146, United States
| | - V. Ramamurthy
- Department
of Chemistry, University of Miami, Room No. 315 Cox Science Building, Coral Gables, Florida 33146, United States
| |
Collapse
|
16
|
Zhu L, Yuan Z, Simmons JT, Sreenath K. Zn(II)-coordination modulated ligand photophysical processes - the development of fluorescent indicators for imaging biological Zn(II) ions. RSC Adv 2014; 4:20398-20440. [PMID: 25071933 PMCID: PMC4111279 DOI: 10.1039/c4ra00354c] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Molecular photophysics and metal coordination chemistry are the two fundamental pillars that support the development of fluorescent cation indicators. In this article, we describe how Zn(II)-coordination alters various ligand-centered photophysical processes that are pertinent to developing Zn(II) indicators. The main aim is to show how small organic Zn(II) indicators work under the constraints of specific requirements, including Zn(II) detection range, photophysical requirements such as excitation energy and emission color, temporal and spatial resolutions in a heterogeneous intracellular environment, and fluorescence response selectivity between similar cations such as Zn(II) and Cd(II). In the last section, the biological questions that fluorescent Zn(II) indicators help to answer are described, which have been motivating and challenging this field of research.
Collapse
Affiliation(s)
- Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, United States
| | - Zhao Yuan
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, United States
| | - J. Tyler Simmons
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, United States
| | - Kesavapillai Sreenath
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, United States
| |
Collapse
|
17
|
Hayashi G, Okamoto A. Probe design for the effective fluorescence imaging of intracellular RNA. CHEM REC 2013; 13:209-17. [PMID: 23495145 DOI: 10.1002/tcr.201200026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Indexed: 01/18/2023]
Abstract
Over the past two decades, the spatiotemporal analysis of fluorescently labeled single RNA species has provided a broad insight into the synthesis, localization, degradation, and transport of RNA. To elucidate the dynamic behavior of functional RNAs in living cells, researchers throughout the world have proposed numerous fluorometric strategies for intracellular RNA imaging. Because, like most other biological molecules, RNA is intrinsically nonfluorescent, the development of methods for the labeling of RNAs of interest with fluorescent molecules is essential. Several artificial tag sequences have been attached onto the 3' end of target RNAs and used as scaffolds for interacting with their fluorescent counterparts. In this Personal Account, we focus on the methods that have been developed to show how RNAs expressed in cells can be labeled and visualized by fluorescent proteins, small molecules, or nucleic acids. Each of these methods is designed to increase the sensitivity and specificity for imaging or to decrease the background fluorescence.
Collapse
Affiliation(s)
- Gosuke Hayashi
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo 153-8904, Japan
| | | |
Collapse
|
18
|
Shank NI, Pham HH, Waggoner AS, Armitage BA. Twisted cyanines: a non-planar fluorogenic dye with superior photostability and its use in a protein-based fluoromodule. J Am Chem Soc 2012; 135:242-51. [PMID: 23252842 DOI: 10.1021/ja308629w] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The cyanine dye thiazole orange (TO) is a well-known fluorogenic stain for DNA and RNA, but this property precludes its use as an intracellular fluorescent probe for non-nucleic acid biomolecules. Further, as is the case with many cyanines, the dye suffers from low photostability. Here, we report the synthesis of a bridge-substituted version of TO named α-CN-TO, where the central methine hydrogen of TO is replaced by an electron withdrawing cyano group, which was expected to decrease the susceptibility of the dye toward singlet oxygen-mediated degradation. An X-ray crystal structure shows that α-CN-TO is twisted drastically out of plane, in contrast to TO, which crystallizes in the planar conformation. α-CN-TO retains the fluorogenic behavior of the parent dye TO in viscous glycerol/water solvent, but direct irradiation and indirect bleaching studies showed that α-CN-TO is essentially inert to visible light and singlet oxygen. In addition, the twisted conformation of α-CN-TO mitigates nonspecific binding and fluorescence activation by DNA and a previously selected TO-binding protein and exhibits low background fluorescence in HeLa cell culture. α-CN-TO was then used to select a new protein that binds and activates fluorescence from the dye. The new α-CN-TO/protein fluoromodule exhibits superior photostability to an analogous TO/protein fluoromodule. These properties indicate that α-CN-TO will be a useful fluorogenic dye in combination with specific RNA and protein binding partners for both in vitro and cell-based applications. More broadly, structural features that promote nonplanar conformations can provide an effective method for reducing nonspecific binding of cationic dyes to nucleic acids and other biomolecules.
Collapse
Affiliation(s)
- Nathaniel I Shank
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | | | | | | |
Collapse
|
19
|
Srinivas U, Arun Kumar P, Srinivas K, Bhanuprakash K, Jayathirtha Rao V. Conformational analysis of 2-anthryl-ethylene derivatives: Photochemical and computational investigation. J STRUCT CHEM+ 2012. [DOI: 10.1134/s0022476612050058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
20
|
Petyaev IM, Tsibezov VV, Osipov SN, Kyle NH, Vorobjeva DV, Bashmakov YK. Generation of Monoclonal Antibody Against trans-Resveratrol. Hybridoma (Larchmt) 2012; 31:449-54. [DOI: 10.1089/hyb.2012.0007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Valeriy V. Tsibezov
- Ivanovsky Institute Of Virology, Ministry of Health, Moscow, Russian Federation
| | - Sergey N. Osipov
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Science, Moscow, Russian Federation
| | | | - Daria V. Vorobjeva
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Science, Moscow, Russian Federation
| | | |
Collapse
|
21
|
Lin CJ, Liu YH, Peng SM, Yang JS. Photoluminescence and trans → cis Photoisomerization of Aminostyrene-Conjugated Phenylpyridine C^N Ligands and Their Complexes with Platinum(II): The Styryl Position and the Amino Substituent Effects. J Phys Chem B 2012; 116:8222-32. [DOI: 10.1021/jp304893c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Che-Jen Lin
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Hung Liu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Shie-Ming Peng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Jye-Shane Yang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
22
|
Wang J, Mei J, Hu R, Sun JZ, Qin A, Tang BZ. Click synthesis, aggregation-induced emission, E/Z isomerization, self-organization, and multiple chromisms of pure stereoisomers of a tetraphenylethene-cored luminogen. J Am Chem Soc 2012; 134:9956-66. [PMID: 22606988 DOI: 10.1021/ja208883h] [Citation(s) in RCA: 345] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
It has been difficult to decipher the mechanistic issue whether E/Z isomerization is involved in the aggregation-induced emission (AIE) process of a tetraphenylethene (TPE) derivative, due to the difficulty in the synthesis of its pure E and Z conformers. In this work, pure stereoisomers of a TPE derivative named 1,2-bis{4-[1-(6-phenoxyhexyl)-4-(1,2,3-triazol)yl]phenyl}-1,2-diphenylethene (BPHTATPE) are successfully synthesized. Both isomers show remarkable AIE effect (α(AIE) ≥ 322) and high fluorescence quantum yield in the solid state (Φ(F) 100%). The conformers readily undergo E/Z isomerization upon exposure to a powerful UV light and treatment at a high temperature (>200 °C). Such conformational change, however, is not observed under normal fluorescence spectrum measurement conditions, excluding the involvement of the E/Z isomerization in the AIE process of the TPE-based luminogen. The molecules of (E)-BPHTATPE self-organize into ordered one-dimensional nanostructures such as microfibers and nanorods that show obvious optical waveguide effect. BPHTATPE shows rich chromic effects, including mechano-, piezo-, thermo-, vapo-, and chronochromisms. Its emission peak is bathochromically shifted by simple grinding and pressurization and the spectral change is reversed by fuming with a polar solvent, heating at a high temperature, or storing at room temperature for some time. The multiple chromic processes are all associated with changes in the modes of molecular packing.
Collapse
Affiliation(s)
- Jian Wang
- MoE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | | | | | | | | | | |
Collapse
|
23
|
Chen XH, Roloff A, Seitz O. Consecutive Signal Amplification for DNA Detection Based on De Novo Fluorophore Synthesis and Host-Guest Chemistry. Angew Chem Int Ed Engl 2012; 51:4479-83. [DOI: 10.1002/anie.201108845] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Indexed: 01/27/2023]
|
24
|
Chen XH, Roloff A, Seitz O. Konsekutive Signalverstärkung für die DNA-Detektion basierend auf einer De-novo-Fluorophorsynthese und Wirt-Gast-Chemie. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108845] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
25
|
Tzeli D, Theodorakopoulos G, Petsalakis ID, Ajami D, Rebek J. Conformations and Fluorescence of Encapsulated Stilbene. J Am Chem Soc 2012; 134:4346-54. [DOI: 10.1021/ja211164b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Demeter Tzeli
- Theoretical
and Physical Chemistry
Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou, Athens 116 35, Greece
| | - Giannoula Theodorakopoulos
- Theoretical
and Physical Chemistry
Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou, Athens 116 35, Greece
| | - Ioannis D. Petsalakis
- Theoretical
and Physical Chemistry
Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou, Athens 116 35, Greece
| | - Dariush Ajami
- The Skaggs Institute for Chemical Biology & Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Julius Rebek
- The Skaggs Institute for Chemical Biology & Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
26
|
Tolbert LM, Baldridge A, Kowalik J, Solntsev KM. Collapse and recovery of green fluorescent protein chromophore emission through topological effects. Acc Chem Res 2012; 45:171-81. [PMID: 21861536 DOI: 10.1021/ar2000925] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Housed within the 11-stranded β-barrel of the green fluorescent protein (GFP) is the arylideneimidazolidinone (AMI) chromophore, the component responsible for fluorescence. This class of small-molecule chromophore has drawn significant attention for its remarkable photophysical and photochemical properties, both within the intact protein and after its denaturation. All of the proteins so far isolated that have visible light fluorescence have been found to contain an AMI chromophore. These proteins comprise an extensive rainbow, ranging from GFP, which contains the simplest chromophore, p-hydroxybenzylideneimidazolidinone (p-HOBDI), to proteins having molecules with longer conjugation lengths and a variety of intraprotein interactions. The fluorescence invariably almost vanishes upon removal of the protective β-barrel. The role of the barrel in hindering internal conversion has been the subject of numerous studies, especially in our laboratories and those of our collaborators. A better understanding of these chromophores has been facilitated by the development of numerous synthetic protocols. These syntheses, which commonly use the Erlenmeyer azlactone method, have evolved in recent years with the development of a [2 + 3] cycloaddition exploited in our laboratory. The synthetic AMI chromophores have allowed delineation of the complex photophysics of GFP and its derivatives. Upon denaturation, AMI chromophores are marked by 4 orders of magnitude of diminution in emission quantum yield (EQY). This result is attributed to internal conversion resulting from conformational freedom in the released chromophore, which is not allowed within the restrictive β-barrel. To date, the photophysical properties of the AMI chromophore remain elusive and have been attributed to a variety of mechanisms, including cis-trans isomerization, triplet formation, hula twisting, and proton transfer. Advanced studies involving gas-phase behavior, solvent effects, and protonation states have significantly increased our understanding of the chromophore photophysics, but a comprehensive picture is only slowly emerging. Most importantly, mechanisms in structurally defined chromophores may provide clues as to the origin of the "blinking" behavior of the fluorescent proteins themselves. One approach to examining the effect of conformational freedom on rapid internal conversion of the chromophores is to restrict the molecules, both through structural modifications and through adjustments of the supramolecular systems. We thus include here a discussion of studies involving the crystalline state, inclusion within natural protein-binding pockets, complexation with metal ions, and sequestration within synthetic cavities; all of this research affirms the role of restricting conformational freedom in partially restoring the EQY. Additionally, new photochemistry is observed within these restricted systems. Many of the studies carried out in our laboratories show promise for these molecules to be adapted as molecular probes, wherein inclusion turns on the fluorescence and provides a signaling mechanism. In this Account, we present an overview of the AMI chromophores, including synthesis, overall photophysics, and supramolecular behavior. A significant amount of work remains for researchers to fully understand the properties of these chromophores, but important progress achieved thus far in photophysics and photochemistry is underscored here.
Collapse
Affiliation(s)
- Laren M. Tolbert
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Anthony Baldridge
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Janusz Kowalik
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Kyril M. Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| |
Collapse
|
27
|
Tseng NW, Liu J, Ng JCY, Lam JWY, Sung HHY, Williams ID, Tang BZ. Deciphering mechanism of aggregation-induced emission (AIE): Is E–Zisomerisation involved in an AIE process? Chem Sci 2012. [DOI: 10.1039/c1sc00690h] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
|
28
|
Imaging of RNA in live cells. Curr Opin Chem Biol 2011; 15:806-12. [PMID: 22055496 DOI: 10.1016/j.cbpa.2011.10.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 10/11/2011] [Accepted: 10/17/2011] [Indexed: 01/07/2023]
Abstract
Fluorescence microscopy and molecular tagging technologies have ushered in a new era in our understanding of protein localization and function in cells. This review summarizes recent efforts to extend some of these methods (and to create new ones) to imaging of RNA in live cells. Both fluorescent proteins and hybridization probes allow noncovalent labeling of specific RNA molecules with fluorescent dyes that allow detection and tracking in real time.
Collapse
|
29
|
Zanotti KJ, Silva GL, Creeger Y, Robertson KL, Waggoner AS, Berget PB, Armitage BA. Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments. Org Biomol Chem 2011; 9:1012-20. [PMID: 21180706 PMCID: PMC3163152 DOI: 10.1039/c0ob00444h] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluoromodules are complexes formed upon the noncovalent binding of a fluorogenic dye to its cognate biomolecular partner, which significantly enhances the fluorescence quantum yield of the dye. Previously, several single-chain, variable fragment (scFv) antibodies were selected from a yeast cell surface-displayed library that activated fluorescence from a family of unsymmetrical cyanine dyes covering much of the visible and near-IR spectrum. The current work expands our repertoire of genetically encodable scFv-dye pairs by selecting and characterizing a group of scFvs that activate fluorogenic violet-absorbing, blue-fluorescing cyanine dyes, based on oxazole and thiazole heterocycles. The dye binds to both yeast cell surface-displayed and soluble scFvs with low nanomolar K(d) values. These dye-protein fluoromodules exhibit high quantum yields, approaching unity for the brightest system. The promiscuity of these scFvs with other fluorogenic cyanine dyes was also examined. Fluorescence microscopy demonstrates that the yeast cell surface-displayed scFvs can be used for multicolor imaging. The prevalence of 405 nm lasers on confocal imaging and flow cytometry systems make these new reagents potentially valuable for cell biological studies.
Collapse
Affiliation(s)
- Kimberly J. Zanotti
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Gloria L. Silva
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Yehuda Creeger
- Department of Molecular Biosensor and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Kelly L. Robertson
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Alan S. Waggoner
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Department of Molecular Biosensor and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Peter B. Berget
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Department of Molecular Biosensor and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| | - Bruce A. Armitage
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
- Department of Molecular Biosensor and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213
| |
Collapse
|
30
|
Ejima H, Matsuno H, Serizawa T. Biological identification of peptides that specifically bind to poly(phenylene vinylene) surfaces: recognition of the branched or linear structure of the conjugated polymer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:17278-17285. [PMID: 20949958 DOI: 10.1021/la102018f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Peptides that bind to poly(phenylene vinylene) (PPV) were identified by the phage display method. Aromatic amino acids were enriched in these peptide sequences, suggesting that a π-π interaction is the key interaction between the peptides and PPV. The surface plasmon resonance (SPR) experiments using chemically synthesized peptides demonstrated that the Hyp01 peptide, with the sequence His-Thr-Asp-Trp-Arg-Leu-Gly-Thr-Trp-His-His-Ser, showed an affinity constant (7.7 × 10(5) M(-1)) for the target, hyperbranched PPV (hypPPV) film. This value is 15-fold greater than its affinity for linear PPV (linPPV). In contrast, the peptide screened for linPPV (Lin01) showed the reverse specificity for linPPV. These results suggested that the Hyp01 and Lin01 peptides selectively recognized the linear or branched structure of PPVs. The Ala-scanning experiment, circular dichroism (CD) spectrometry, and molecular modeling of the Hyp01 peptide indicated that adequate location of two Trp residues by forming the polyproline type II (P(II)) helical conformation allowed the peptide to specifically interact with hypPPV.
Collapse
Affiliation(s)
- Hirotaka Ejima
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | | | | |
Collapse
|
31
|
Choi S, Ong DST, Kelly JW. A stilbene that binds selectively to transthyretin in cells and remains dark until it undergoes a chemoselective reaction to create a bright blue fluorescent conjugate. J Am Chem Soc 2010; 132:16043-51. [PMID: 20964336 DOI: 10.1021/ja104999v] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a non-fluorescent, second generation stilbene that very selectively binds to transthyretin in complex biological environments and remains dark until it chemoselectively reacts with the pK(a)-perturbed Lys-15 ε-amino group of transthyretin to form a bright blue fluorescent conjugate. Stilbene A2 is mechanistically unusual in that it remains non-fluorescent in cell lysates lacking transthyretin, even though there is likely some proteome binding. Thus, it is especially useful for cellular imaging, as background fluorescence is undetectable until A2 reacts with transthyretin. The mechanistic basis for the effective lack of environment-sensitive fluorescence of A2 when bound to, but before reacting with, transthyretin is reported. Stilbene A2 exhibits sufficiently rapid transthyretin conjugation kinetics at 37 °C to enable pulse-chase experiments to be performed, in this case demonstrating that transthyretin is secreted from HeLa cells. As the chase compound, we employed C1, a cell-permeable, highly selective, non-covalent, transthyretin-binding dihydrostilbene that cannot become fluorescent. The progress reported is viewed as a first and necessary step toward our long-term goal of creating a one-chain, one-binding-site transthyretin tag, whose fluorescence can be regulated by adding A2 or an analogous molecule. Fusing proteins of interest to a one-chain, one-binding-site transthyretin tag regulated by A2 should be useful for studying folding, trafficking, and degradation in the cellular secretory pathway, utilizing pulse-chase experiments. Immediate applications of A2 include utilizing its conjugate fluorescence to quantify transthyretin concentration in human plasma, reflecting nutritional status, and determining the binding stoichiometry of kinetic stabilizer drugs to transthyretin in plasma.
Collapse
Affiliation(s)
- Sungwook Choi
- Department of New Drug Discovery and Development, Chungnam National University, Daejon, 305-764, Republic of Korea
| | | | | |
Collapse
|
32
|
Yun-Xing Y, Xiao-Qiang Y, Dong W, Xian Z, Qi F, Min-Hua J. Synthesis and Properties of a New Two-photon-absorbed Material DMAEAS. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20030210209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
33
|
Szent-Gyorgyi C, Schmidt BF, Fitzpatrick JAJ, Bruchez MP. Fluorogenic dendrons with multiple donor chromophores as bright genetically targeted and activated probes. J Am Chem Soc 2010; 132:11103-9. [PMID: 20698676 PMCID: PMC2920033 DOI: 10.1021/ja9099328] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Indexed: 11/27/2022]
Abstract
We have developed a class of dendron-based fluorogenic dyes (termed dyedrons) comprised of multiple cyanine (Cy3) donors coupled to a single malachite green (MG) acceptor that fluoresce only when the MG is noncovalently but specifically bound to a cognate single chain antibody (scFv). These cell-impermeant dyedrons exploit efficient intramolecular energy transfer from Cy3 donors to stoichiometrically amplify the fluorescence of MG chromophores that are activated by binding to the scFv. These chromophore enhancements, coupled with our optimized scFv, can significantly increase fluorescence emission generated by the dyedron/scFv complex to brightness levels several-fold greater than that for single fluorescent proteins and targeted small molecule fluorophores. Efficient intramolecular quenching of free dyedrons enables sensitive homogeneous (no wash) detection under typical tissue culture conditions, with undetectable nonspecific activation.
Collapse
Affiliation(s)
- Christopher Szent-Gyorgyi
- Carnegie Mellon University, Molecular Biosensors and Imaging Center, Pittsburgh, Pennsylvania 15213, USA
| | | | | | | |
Collapse
|
34
|
Armen RS, Schiller SM, Brooks CL. Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes. Proteins 2010; 78:1926-38. [PMID: 20310065 DOI: 10.1002/prot.22706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Orthogonal aminoacyl-tRNA synthetase/tRNA pairs from archaea have been evolved to facilitate site specific in vivo incorporation of unnatural amino acids into proteins in Escherichia coli. Using this approach, unnatural amino acids have been successfully incorporated with high translational efficiency and fidelity. In this study, CHARMM-based molecular docking and free energy calculations were used to evaluate rational design of specific protein-ligand interactions for aminoacyl-tRNA synthetases. A series of novel unnatural amino acid ligands were docked into the p-benzoyl-L-phenylalanine tRNA synthetase, which revealed that the binding pocket of the enzyme does not provide sufficient space for significantly larger ligands. Specific binding site residues were mutated to alanine to create additional space to accommodate larger target ligands, and then mutations were introduced to improve binding free energy. This approach was used to redesign binding sites for several different target ligands, which were then tested against the standard 20 amino acids to verify target specificity. Only the synthetase designed to bind Man-alpha-O-Tyr was predicted to be sufficiently selective for the target ligand and also thermodynamically stable. Our study suggests that extensive redesign of the tRNA synthatase binding pocket for large bulky ligands may be quite thermodynamically unfavorable.
Collapse
Affiliation(s)
- Roger S Armen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | | |
Collapse
|
35
|
Huang GJ, Yang JS. The N-Arylamino Conjugation Effect in the Photochemistry of Fluorescent Protein Chromophores and Aminostilbenes. Chem Asian J 2010; 5:2075-85. [DOI: 10.1002/asia.201000209] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
36
|
Abhinandan KR, Martin ACR. Analysis and prediction of VH/VL packing in antibodies. Protein Eng Des Sel 2010; 23:689-97. [PMID: 20591902 DOI: 10.1093/protein/gzq043] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The packing of V(H) and V(L) domains in antibodies can vary, influencing the topography of the antigen-combining site. However, until recently, this has largely been ignored in modelling antibody structure. We present an analysis of the degree of variability observed in known structures together with a machine-learning approach to predict the packing angle. A neural network was trained on sets of interface residues and a genetic algorithm designed to perform 'feature selection' to define which sets of interface residues could be used most successfully to perform the prediction. While this training procedure was very computationally intensive, prediction is performed in a matter of seconds. Thus, not only do we provide a rapid method for predicting the packing angle, but also we define a set of residues that may be important in antibody humanization in order to obtain the correct binding site topography.
Collapse
Affiliation(s)
- K R Abhinandan
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK
| | | |
Collapse
|
37
|
Shabbir SH, Joyce LA, da Cruz GM, Lynch VM, Sorey S, Anslyn EV. Pattern-based recognition for the rapid determination of identity, concentration, and enantiomeric excess of subtly different threo diols. J Am Chem Soc 2010; 131:13125-31. [PMID: 19691315 DOI: 10.1021/ja904545d] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A pattern-based recognition approach for the rapid determination of the identity, concentration, and enantiomeric excess of chiral vicinal diols, specifically threo diols, has been developed. A diverse enantioselective sensor array was generated using three chiral boronic acid receptors and three pH indicators. The optical response produced by the sensor array was analyzed by two pattern-recognition algorithms: principal component analysis and artificial neural networks. Principal component analysis demonstrated good chemoselective and enantioselective separation of the analytes, and an artificial neural network was used to accurately determine the concentrations and enantiomeric excesses of five unknown samples with an average absolute error of +/-0.08 mM in concentration and 3.6% in enantiomeric excess. The speed of the analysis was enhanced by using a 96-well plate format, portending applications in high-throughput screening for asymmetric-catalyst discovery. X-ray crystallography and (11)B NMR spectroscopy was utilized to study the enantioselective nature of the boronic acid host 2.
Collapse
Affiliation(s)
- Shagufta H Shabbir
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | | | | | | | | | | |
Collapse
|
38
|
Baldridge A, Solntsev KM, Song C, Tanioka T, Kowalik J, Hardcastle K, Tolbert LM. Inhibition of twisting of a green fluorescent protein-like chromophore by metal complexation. Chem Commun (Camb) 2010; 46:5686-8. [DOI: 10.1039/b927313a] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
39
|
Falco CN, Dykstra KM, Yates BP, Berget PB. scFv-based fluorogen activating proteins and variable domain inhibitors as fluorescent biosensor platforms. Biotechnol J 2009; 4:1328-36. [PMID: 19606431 DOI: 10.1002/biot.200900075] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Single chain antibodies (scFvs) are engineered proteins composed of IgG variable heavy (V(H)) and variable light (V(L)) domains tethered together by a flexible peptide linker. We have characterized the individual V(H) or V(L) domain activities of several scFvs isolated from a yeast surface-display library for their ability to bind environmentally sensitive fluorogenic dyes causing them to fluoresce. For many of the scFvs, both V(H) and V(L) domains are required for dye binding and fluorescence. The analysis of other scFvs, however, revealed that either the V(H) or the V(L) domain alone is sufficient to cause the fluorogenic dye activation. Furthermore, the inactive complementary domains in the original scFvs either contribute nothing to, or actually inhibit the activity of these active single domains. We have explored the interactions between active variable domains and inactive complementary domains by extensive variable domain swapping through in vitro gene manipulations to create hybrid scFvs. In this study, we demonstrate that significant alteration of the fluorogenic dye activation by the active V(H) or V(L) domains can occur by partnering with different V(H) or V(L) complementary domains in the scFv format. Hybrid scFvs can be generated that have fluorogen-activating domains that are completely inhibited by interactions with other domains. Such hybrid scFvs are excellent platforms for the development of several types of genetically encoded, fluorescence-generating biosensors.
Collapse
Affiliation(s)
- Crystal N Falco
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | | | | |
Collapse
|
40
|
TSUMOTO K, UI M. Rational Fragment-design Method Based on a Thermodynamic Analysis. YAKUGAKU ZASSHI 2009; 129:1311-7. [DOI: 10.1248/yakushi.129.1311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kouhei TSUMOTO
- Graduate School of Frontier Sciences, The University of Tokyo
| | - Mihoko UI
- Graduate School of Frontier Sciences, The University of Tokyo
| |
Collapse
|
41
|
Bertin A, Steibel J, Michou-Gallani AI, Gallani JL, Felder-Flesch D. Development of a Dendritic Manganese-Enhanced Magnetic Resonance Imaging (MEMRI) Contrast Agent: Synthesis, Toxicity (in Vitro) and Relaxivity (in Vitro, in Vivo) Studies. Bioconjug Chem 2009; 20:760-7. [DOI: 10.1021/bc8004683] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Annabelle Bertin
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR CNRS/ULP 7504, 23 rue du Lœss BP 43, 67034 Strasbourg Cedex 2, France, Laboratoire d’Imagerie et de Neurosciences Cognitives, UMR CNRS/ULP 7191, 12 rue Goethe, 67000 Strasbourg, France, and siRNA Therapeutics, NIBR Biologics Center, Novartis Institutes for Biomedical Research, Inc., 4002 Basel, Switzerland
| | - Jérôme Steibel
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR CNRS/ULP 7504, 23 rue du Lœss BP 43, 67034 Strasbourg Cedex 2, France, Laboratoire d’Imagerie et de Neurosciences Cognitives, UMR CNRS/ULP 7191, 12 rue Goethe, 67000 Strasbourg, France, and siRNA Therapeutics, NIBR Biologics Center, Novartis Institutes for Biomedical Research, Inc., 4002 Basel, Switzerland
| | - Anne-Isabelle Michou-Gallani
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR CNRS/ULP 7504, 23 rue du Lœss BP 43, 67034 Strasbourg Cedex 2, France, Laboratoire d’Imagerie et de Neurosciences Cognitives, UMR CNRS/ULP 7191, 12 rue Goethe, 67000 Strasbourg, France, and siRNA Therapeutics, NIBR Biologics Center, Novartis Institutes for Biomedical Research, Inc., 4002 Basel, Switzerland
| | - Jean-Louis Gallani
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR CNRS/ULP 7504, 23 rue du Lœss BP 43, 67034 Strasbourg Cedex 2, France, Laboratoire d’Imagerie et de Neurosciences Cognitives, UMR CNRS/ULP 7191, 12 rue Goethe, 67000 Strasbourg, France, and siRNA Therapeutics, NIBR Biologics Center, Novartis Institutes for Biomedical Research, Inc., 4002 Basel, Switzerland
| | - Delphine Felder-Flesch
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR CNRS/ULP 7504, 23 rue du Lœss BP 43, 67034 Strasbourg Cedex 2, France, Laboratoire d’Imagerie et de Neurosciences Cognitives, UMR CNRS/ULP 7191, 12 rue Goethe, 67000 Strasbourg, France, and siRNA Therapeutics, NIBR Biologics Center, Novartis Institutes for Biomedical Research, Inc., 4002 Basel, Switzerland
| |
Collapse
|
42
|
Affiliation(s)
- Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, USA
| | | |
Collapse
|
43
|
Ozhalici-Unal H, Pow CL, Marks SA, Jesper LD, Silva GL, Shank NI, Jones EW, Burnette JM, Berget PB, Armitage BA. A rainbow of fluoromodules: a promiscuous scFv protein binds to and activates a diverse set of fluorogenic cyanine dyes. J Am Chem Soc 2008; 130:12620-1. [PMID: 18761447 DOI: 10.1021/ja805042p] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combined magnetic and fluorescence cell sorting were used to select Fluorogen Activating Proteins (FAPs) from a yeast surface-displayed library for binding to the fluorogenic cyanine dye Dimethyl Indole Red (DIR). Several FAPs were selected that bind to the dye with low nanomolar Kd values and enhance fluorescence more than 100-fold. One of these FAPs also exhibits considerable promiscuity, binding with high affinity to several other fluorogenic cyanine dyes with emission wavelengths covering most of the visible and near-IR regions of the spectrum. This significantly expands the number and wavelength range of scFv-based fluoromodules.
Collapse
Affiliation(s)
- Hayriye Ozhalici-Unal
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Hmadeh M, Traboulsi H, Elhabiri M, Braunstein P, Albrecht-Gary AM, Siri O. Synthesis, characterization and photophysical properties of benzidine-based compounds. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.04.058] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
45
|
Hillig RC, Urlinger S, Fanghänel J, Brocks B, Haenel C, Stark Y, Sülzle D, Svergun DI, Baesler S, Malawski G, Moosmayer D, Menrad A, Schirner M, Licha K. Fab MOR03268 Triggers Absorption Shift of a Diagnostic Dye via Packaging in a Solvent-shielded Fab Dimer Interface. J Mol Biol 2008; 377:206-19. [DOI: 10.1016/j.jmb.2007.12.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 12/20/2007] [Accepted: 12/21/2007] [Indexed: 11/28/2022]
|
46
|
Armitage BA, Berget PB. CHEMISTRY: An Enlightening Structure-Function Relationship. Science 2008; 319:1195-6. [DOI: 10.1126/science.1155093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
47
|
Debler EW, Kaufmann GF, Meijler MM, Heine A, Mee JM, Pljevaljcic G, Di Bilio AJ, Schultz PG, Millar DP, Janda KD, Wilson IA, Gray HB, Lerner RA. Deeply Inverted Electron-Hole Recombination in a Luminescent Antibody-Stilbene Complex. Science 2008; 319:1232-5. [DOI: 10.1126/science.1153445] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
48
|
Erdélyi M, Varedian M, Sköld C, Niklasson IB, Nurbo J, Persson Å, Bergquist J, Gogoll A. Chemistry and folding of photomodulable peptides – stilbene and thioaurone-type candidates for conformational switches. Org Biomol Chem 2008; 6:4356-73. [DOI: 10.1039/b812001c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
49
|
Szent-Gyorgyi C, Schmidt BF, Schmidt BA, Creeger Y, Fisher GW, Zakel KL, Adler S, Fitzpatrick JAJ, Woolford CA, Yan Q, Vasilev KV, Berget PB, Bruchez MP, Jarvik JW, Waggoner A. Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nat Biotechnol 2007; 26:235-40. [PMID: 18157118 DOI: 10.1038/nbt1368] [Citation(s) in RCA: 302] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 12/03/2007] [Indexed: 11/09/2022]
Abstract
Imaging of live cells has been revolutionized by genetically encoded fluorescent probes, most famously green and other fluorescent proteins, but also peptide tags that bind exogenous fluorophores. We report here the development of protein reporters that generate fluorescence from otherwise dark molecules (fluorogens). Eight unique fluorogen activating proteins (FAPs) have been isolated by screening a library of human single-chain antibodies (scFvs) using derivatives of thiazole orange and malachite green. When displayed on yeast or mammalian cell surfaces, these FAPs bind fluorogens with nanomolar affinity, increasing green or red fluorescence thousands-fold to brightness levels typical of fluorescent proteins. Spectral variation can be generated by combining different FAPs and fluorogen derivatives. Visualization of FAPs on the cell surface or within the secretory apparatus of mammalian cells can be achieved by choosing membrane permeant or impermeant fluorogens. The FAP technique is extensible to a wide variety of nonfluorescent dyes.
Collapse
Affiliation(s)
- Christopher Szent-Gyorgyi
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Tian F, Debler EW, Millar DP, Deniz AA, Wilson IA, Schultz PG. The effects of antibodies on stilbene excited-state energetics. Angew Chem Int Ed Engl 2007; 45:7763-5. [PMID: 17089439 DOI: 10.1002/anie.200602720] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Feng Tian
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR202, La Jolla, CA 92037, USA
| | | | | | | | | | | |
Collapse
|