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Arora A, Kumar S, Kumar S, Dua A, Singh BK. Synthesis, characterization and photophysical studies of dual-emissive base-modified fluorescent nucleosides. Org Biomol Chem 2024. [PMID: 38808609 DOI: 10.1039/d4ob00749b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
A straightforward and efficient methodology has been employed for the synthesis of a diverse set of base-modified fluorescent nucleoside conjugates via Cu(I)-catalysed cycloaddition reaction of 5-ethynyl-2',3',5'-tri-O-acetyluridine/3',5'-di-O-acetyl-2'-deoxyuridine with 4-(azidomethyl)-N9-(4'-aryl)-9,10-dihydro-2H,8H-chromeno[8,7-e][1,3]oxazin-2-ones in tBuOH to afford the desired 1,2,3-triazoles in 92-95% yields. Treatment with NaOMe/MeOH resulted in the final deprotected nucleoside analogues. The synthesized 1,2,3-triazoles demonstrated a significant emission spectrum, featuring two robust bands in the region from 350-500 nm (with excitation at 300 nm) in fluorescence studies. Photophysical investigations revealed a dual-emissive band with high fluorescence intensity, excellent Stokes shift (140-164 nm) and superior quantum yields (0.068-0.350). Furthermore, the electronic structures of the synthesized triazoles have been further verified by DFT studies. Structural characterization of all synthesized compounds was carried out using various analytical techniques, including IR, 1H-NMR, 13C-NMR, 1H-1H COSY, 1H-13C HETCOR experiments, and HRMS measurements. The dual-emissive nature of these nucleosides would be a significant contribution to nucleoside chemistry as there are limited literature reports on the same.
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Affiliation(s)
- Aditi Arora
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
| | - Sumit Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
| | - Sandeep Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
- Department of Chemistry, Ramjas College, University of Delhi, Delhi-110007, India
| | - Amita Dua
- Department of Chemistry, Dyal Singh College, University of Delhi, Delhi-110007, India
| | - Brajendra K Singh
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
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2
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Allert MJ, Kumar S, Wang Y, Beese LS, Hellinga HW. Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching. Commun Chem 2023; 6:168. [PMID: 37598249 PMCID: PMC10439942 DOI: 10.1038/s42004-023-00982-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023] Open
Abstract
Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.
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Affiliation(s)
- Malin J Allert
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Shivesh Kumar
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - You Wang
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Lorena S Beese
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA.
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3
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Fluorescent Probes as a Tool in Diagnostic and Drug Delivery Systems. Pharmaceuticals (Basel) 2023; 16:ph16030381. [PMID: 36986481 PMCID: PMC10056067 DOI: 10.3390/ph16030381] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Over the last few years, the development of fluorescent probes has received considerable attention. Fluorescence signaling allows noninvasive and harmless real-time imaging with great spectral resolution in living objects, which is extremely useful for modern biomedical applications. This review presents the basic photophysical principles and strategies for the rational design of fluorescent probes as visualization agents in medical diagnosis and drug delivery systems. Common photophysical phenomena, such as Intramolecular Charge Transfer (ICT), Twisted Intramolecular Charge Transfer (TICT), Photoinduced Electron Transfer (PET), Excited-State Intramolecular Proton Transfer (ESIPT), Fluorescent Resonance Energy Transfer (FRET), and Aggregation-Induced Emission (AIE), are described as platforms for fluorescence sensing and imaging in vivo and in vitro. The presented examples are focused on the visualization of pH, biologically important cations and anions, reactive oxygen species (ROS), viscosity, biomolecules, and enzymes that find application for diagnostic purposes. The general strategies regarding fluorescence probes as molecular logic devices and fluorescence–drug conjugates for theranostic and drug delivery systems are discussed. This work could be of help for researchers working in the field of fluorescence sensing compounds, molecular logic gates, and drug delivery.
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4
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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Allert MJ, Hellinga HW. Discovery of Thermostable, Fluorescently Responsive Glucose Biosensors by Structure-Assisted Function Extrapolation. Biochemistry 2022; 61:276-293. [PMID: 35084821 DOI: 10.1021/acs.biochem.1c00738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate assignment of protein function from sequence remains a fascinating and difficult challenge. The periplasmic-binding protein (PBP) superfamily present an interesting case of function prediction because they are both ubiquitous in prokaryotes and tend to diversify through gene duplication "explosions" that can lead to large numbers of paralogs in a genome. An engineered version of the moderately thermostable glucose-binding PBP from Escherichia coli has been used successfully as a reagentless fluorescent biosensor both in vitro and in vivo. To develop more robust sensors that meet the challenges of real-world applications, we report the discovery of thermostable homologues that retain a glucose-mediated conformationally coupled fluorescence response. Accurately identifying a glucose-binding PBP homologue among closely related paralogs is challenging. We demonstrate that a structure-based method that filters sequences by residues that bind glucose in an archetype structure is highly effective. Using fully sequenced bacterial genomes, we found that this filter reduced high paralog numbers to single hits in a genome, consistent with the accurate separation of glucose binding from other functions. We expressed engineered proteins for eight homologues, chosen to represent different degrees of sequence identity, and tested their glucose-mediated fluorescence responses. We accurately predicted the presence of glucose binding down to 31% sequence identity. We have also successfully identified suitable candidates for next-generation robust, fluorescent glucose sensors.
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Affiliation(s)
- Malin J Allert
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina 27710, United States
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, North Carolina 27710, United States
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Chumak A, Khodzhaeva R, Kharchenko O, Kotlyar V, Kolomoitsev O, Doroshenko A. Complexation of 1,3-dihetaryl-5-phenyl-2-pyrazoline Derivatives with Polyvalent Metal Ions: Quantum Chemical Modeling and Experimental Investigation. FRENCH-UKRAINIAN JOURNAL OF CHEMISTRY 2022. [DOI: 10.17721/fujcv10i1p155-174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
1,3,5-Triaryl-2-pyrazoline derivatives with a pyridine ring in position 1 and 2-benzimidazolyl or 2-benzothiazolyl bicycles in position 3 were synthesized. Spectral properties in solvents of similar polarity, i.e. aprotic acetonitrile and in protic methanol, were studied, complexation with cadmium and mercury ions in acetonitrile was elucidated as well. Quantum-chemical modeling with application of the elements of Bader's atoms-in-molecules (AIM) theory of the title molecules conformational structure and 1:1 stoichiometry complexes formed with polyvalent metals of various nature (Mg, Zn, Cd, Pb, Hg, Ba) was conducted. The principal possibility of “nitrogen-sulfur” switching of the metal ions binding sites for the benzothiazole derivative was revealed, and makes possible to classify this compound as “smart ligand”.
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7
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Zhu Q. Optical Characteristics and Applications of AIE Racemic C6-Unsubstituted Tetrahydropyrimidines. Front Chem 2021; 9:800177. [PMID: 34900949 PMCID: PMC8664540 DOI: 10.3389/fchem.2021.800177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/02/2021] [Indexed: 11/13/2022] Open
Abstract
Racemic C6-unsubstituted tetrahydropyrimidines (THPs) are the products of an efficient five-component reaction that we developed. THPs show strong AIE characteristics, that is, completely no fluorescence in different solvents but strong emission with fluorescence quantum yields (Φ F) up to 100% upon aggregation. However, the Φ F values of their pure enantiomers are lower than 46%. Unlike common AIE compounds with crowded aryl rotors on a π-bond or on an aryl ring, THPs have three completely non-crowded aryl rotors on a non-aromatic chiral central ring (tetrahydropyrimidine). In this mini review, we first discuss the AIE characteristics of THPs and the influences of molecular structures on their molecular packing modes and optical properties, and then present their applications and forecast the development of other racemic AIE compounds.
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Affiliation(s)
- Qiuhua Zhu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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8
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Chumak AY, Mudrak VO, Kotlyar VM, Doroshenko AO. 4’-Nitroflavonol fluorescence: Excited state intramolecular proton transfer reaction from the non-emissive excited state. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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Wu CH, Chen Y, Pyrshev KA, Chen YT, Zhang Z, Chang KH, Yesylevskyy SO, Demchenko AP, Chou PT. Fluorescence Probes Exhibit Photoinduced Structural Planarization: Sensing In Vitro and In Vivo Microscopic Dynamics of Viscosity Free from Polarity Interference. ACS Chem Biol 2020; 15:1862-1873. [PMID: 32543829 DOI: 10.1021/acschembio.0c00100] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate the construction of wavelength λ-ratiometric images that allow visualizing the distribution of microscopic dynamics within living cells and tissues by using the newly developed principle of fluorescence response. The bent-to-planar motion in the excited state of incorporated fluorescence probes leads to elongation of the π-delocalization, resulting in microviscosity-dependent but polarity-insensitive interplay between well-separated blue and red bands in emission spectra. This allows constructing the exceptionally contrasted images of cellular dynamics. Moreover, the application of probes with increased affinity toward biological membranes allowed detecting the differences in dynamics between the plasma membrane and intracellular membrane structures. Such λ-ratiometric microviscosity imaging was extended for mapping the living tissues and observing their inflammation-dependent changes.
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Affiliation(s)
- Cheng-Ham Wu
- Department of Chemistry, National Taiwan University, Taipei 10607, Taiwan
| | - Yi Chen
- Department of Chemistry, National Taiwan University, Taipei 10607, Taiwan
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology, Shanghai 200237, P. R. China
| | - Kyrylo A. Pyrshev
- Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv 01030, Ukraine
- Institute of Physics, National Academy of Sciences of Ukraine, Kyiv 03028, Ukraine
| | - Yi-Ting Chen
- Department of Chemistry, National Taiwan University, Taipei 10607, Taiwan
| | - Zhiyun Zhang
- Department of Chemistry, National Taiwan University, Taipei 10607, Taiwan
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology, Shanghai 200237, P. R. China
| | - Kai-Hsin Chang
- Department of Chemistry, National Taiwan University, Taipei 10607, Taiwan
| | - Semen O. Yesylevskyy
- Laboratoire Chrono Environnement UMR CNRS 6249, Universite′ de Bourgogne Franche-Comte′, 16 route de Gray, 25030 Besançon Cedex, France
- Institute of Physics, National Academy of Sciences of Ukraine, Kyiv 03028, Ukraine
| | - Alexander P. Demchenko
- Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv 01030, Ukraine
- Yuriy Fedkovych National University, 58012 Chernivtsi, Ukraine
| | - Pi-Tai Chou
- Department of Chemistry, National Taiwan University, Taipei 10607, Taiwan
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10
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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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11
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Dubrovkin JM, Tomin VI. Direct excitation of higher excited state and kinetics of photoreactions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 226:117573. [PMID: 31655372 DOI: 10.1016/j.saa.2019.117573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
Excited-state reactions (ESR) play an essential role in chemical, physical, and biological processes. The mathematical models are usually used to study ESR in kinetics and steady-state regimes. In these models, the excitation pulse populates the first excited state (the first singlet level) of the primary molecular form. Recently, researchers' paid growing attention to the reactions excited via the higher energy levels. We modeled these reactions using the system of linear differential equations. Exact analytical expressions of the kinetics of N* and P* populations were derived for the general case when excitation performed via the higher Sn singlet state by the delta pulse. The graphical forms of these expressions were N and P time-dependent pulses. We detected the changes of the pulses' shapes, their maxima locations, the time behavior of the populations, and the total yield of the P* population. The changes occur due to the populating of the product excited state in the kinetic and thermodynamic reaction regimes. Numerical analysis performed for different ESR parameters revealed peculiarities of the N* and P* populations. Kinetics properties of these population characterize systems with varying rates of reversible ESR and various contributions of anti-Kasha (AK) reaction (from the Sn state) to P* population. Modeling data presented in graphical form, allowed to understand better (a) the impact of the AK reaction on the kinetic properties of the excited states of the molecular systems operating in various mode of ESR (kinetic, reversible and intermediate); (b) the photochemical processes' mechanisms. Also, this modeling allowed establishing the criteria for revealing the effect of the AK reaction for improving the efficiency of anti-Kasha processes.
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Affiliation(s)
- Joseph M Dubrovkin
- Multidisciplinary Department, The Western Galilee College, 2421, Acre, Israel.
| | - Vladimir I Tomin
- Institute of Physics, Pomeranian University, Słupsk, 76_200, Poland
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12
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Allert MJ, Hellinga HW. Describing Complex Structure-Function Relationships in Biomolecules at Equilibrium. J Mol Biol 2020; 432:1926-1951. [PMID: 31940471 DOI: 10.1016/j.jmb.2019.12.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/03/2019] [Accepted: 12/17/2019] [Indexed: 11/17/2022]
Abstract
One of the great ambitions of structural biology is to describe structure-function relationships quantitatively. Statistical thermodynamics is a powerful, general tool for computing the behavior of biological macromolecules at equilibrium because it establishes a direct link between structure and function. Complex behavior emerges as equilibria of multiple reactions are coupled. Analytical treatment of linked equilibria scales poorly with increasing numbers of reactions and states as the algebraic constructs rapidly become unwieldy. We therefore developed a generalizable, but straightforward computational method to handle arbitrarily complex systems. To demonstrate this approach, we collected a multidimensional fluorescence landscape of an engineered fluorescent glucose biosensor and showed that its features could be modeled with ten intricately linked ligand-binding and conformational exchange reactions. This protein represents a minimalist model of sufficient complexity to encompass fundamental biomolecular structure-function relationships: two-state and multistate conformational ensembles, conformational hierarchies, osmolytes, coupling between different binding sites and coupling between ligand binding and conformational change. The successful fit of this complex, multifaceted system demonstrates generality of the method.
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Affiliation(s)
- Malin J Allert
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC, 27710, USA
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC, 27710, USA.
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13
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Chen Y, Chen DG, Chen YA, Wu CH, Chang KH, Meng FY, Chen MC, Lin JA, Huang CY, Su J, Tian H, Chou PT. Mono-Heteroatom Substitution for Harnessing Excited-State Structural Planarization of Dihydrodibenzo[a,c]phenazines. Chemistry 2019; 25:16755-16764. [PMID: 31663166 DOI: 10.1002/chem.201904900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Indexed: 01/24/2023]
Abstract
With the aim of generalizing the structure-properties relationship of bending heterocyclic molecules that undergo prominent photoinduced structural planarization (PISP), a series of new dihydrodibenzo[ac]phenazine derivatives in which one nitrogen atom is replaced by oxygen (PNO), sulfur (PNS), selenium (PNSe), or dimethylmethanediyl (PNC) was strategically designed and synthesized. Compounds PNO, PNS, and PNSe have significantly nonplanar geometries in the ground state, which undergo PISP to give a planarlike conformer and hence a large emission Stokes shift. A combination of femtosecond early relaxation dynamics and computational approaches established an R*→I* (intermediate)→P* sequential kinetic pattern for PNS and PNSe, whereas PNO undergoes R*→P* one-step kinetics. The polarization ability of the substituted heteroatoms, which is in the order O<S<Se, correlates with their increase in π conjugation, and hence the Stokes shift of the emission is in the order PNO<PNS<PNSe. Compound PNSe with the largest PISP barrier was shown to be a highly sensitive viscosity probe. Further evidence for heteroatom-harnessing PISP is given by PNC, in which the dimethylmethanediyl substituent lacks lone pair electrons for π extension, showing the normal emission of the bent structure. The results led to the conclusion that PISP is ubiquitous in dihydrodibenzo[ac]phenazines, for which the driving force is elongation of the π delocalization to gain stabilization in the excited state.
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Affiliation(s)
- Yi Chen
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology Shanghai, 200237, Shanghai, P. R. China.,Department of Chemistry, National Taiwan University, Taipei, 10617, R.O.C., Taiwan
| | - Deng-Gao Chen
- Department of Chemistry, National Taiwan University, Taipei, 10617, R.O.C., Taiwan
| | - Yi-An Chen
- Department of Chemistry, National Taiwan University, Taipei, 10617, R.O.C., Taiwan
| | - Cheng-Ham Wu
- Department of Chemistry, National Taiwan University, Taipei, 10617, R.O.C., Taiwan
| | - Kai-Hsin Chang
- Department of Chemistry, National Taiwan University, Taipei, 10617, R.O.C., Taiwan
| | - Fan-Yi Meng
- Department of Chemistry, National Taiwan University, Taipei, 10617, R.O.C., Taiwan
| | - Meng-Chi Chen
- Department of Chemistry, National Taiwan University, Taipei, 10617, R.O.C., Taiwan
| | - Jia-An Lin
- Department of Chemistry, National Taiwan University, Taipei, 10617, R.O.C., Taiwan
| | - Chun-Ying Huang
- Department of Chemistry, National Taiwan University, Taipei, 10617, R.O.C., Taiwan
| | - Jianhua Su
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology Shanghai, 200237, Shanghai, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology Shanghai, 200237, Shanghai, P. R. China
| | - Pi-Tai Chou
- Department of Chemistry, National Taiwan University, Taipei, 10617, R.O.C., Taiwan
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14
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4’-Methoxy-3-hydroxyflavone excited state intramolecular proton transfer reaction in alcoholic solutions: Intermolecular versus intramolecular hydrogen bonding effect. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.111964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Bag SS, Gogoi H. Design of "Click" Fluorescent Labeled 2'-deoxyuridines via C5-[4-(2-Propynyl(methyl)amino)]phenyl Acetylene as a Universal Linker: Synthesis, Photophysical Properties, and Interaction with BSA. J Org Chem 2018; 83:7606-7621. [PMID: 29877080 DOI: 10.1021/acs.joc.7b03097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microenvironment-sensitive fluorescent nucleosides present attractive advantages over single-emitting dyes for sensing inter-biomolecular interactions involving DNA. Herein, we report the rational design and synthesis of triazolyl push-pull fluorophore-labeled uridines via the intermediacy of C5-[4-(2-propynyl(methyl)amino)]phenyl acetylene as a universal linker. The synthesized nucleosides showed interesting solvatochromic characteristic and/or intramolecular charge transfer (ICT) features. A few of them also exhibited dual-emitting characteristics evidencing our designing concept. The HOMO-LUMO distribution showed that the emissive states of these nucleosides were characterized with more significant electron redistribution between the C5-[4-(2-propynyl(methyl)amino)]phenyl triazolyl donor moiety and the aromatic chromophores linked to it, leading to modulated emission property. The solvent polarity sensitivity of these nucleosides was also tested. The synthesized triazolyl benzonitrile (10C), naphthyl (10E), and pyrenyl (10G) nucleosides were found to exhibit interesting ICT and dual (LE/ICT) emission properties. The dual-emitting pyrenyl nucleoside maintained a good ratiometric response in the BSA protein microenvironment, enabling the switch-on ratiometric sensing of BSA as the only protein biomolecule. Thus, it is expected that the new fluorescent nucleoside analogues would be useful in designing DNA probes for nucleic acid analysis or studying DNA-protein interactions via a drastic change in fluorescence response due to a change in micropolarity.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bioorganic Chemistry Laboratory, Department of Chemistry , Indian Institute of Technology Guwahati 781039 , India
| | - Hiranya Gogoi
- Bioorganic Chemistry Laboratory, Department of Chemistry , Indian Institute of Technology Guwahati 781039 , India
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16
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Bricks JL, Slominskii YL, Panas ID, Demchenko AP. Fluorescent J-aggregates of cyanine dyes: basic research and applications review. Methods Appl Fluoresc 2017; 6:012001. [DOI: 10.1088/2050-6120/aa8d0d] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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17
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Demchenko AP, Tomin VI, Chou PT. Breaking the Kasha Rule for More Efficient Photochemistry. Chem Rev 2017; 117:13353-13381. [DOI: 10.1021/acs.chemrev.7b00110] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Alexander P. Demchenko
- Palladin
Institute of Biochemistry, National Academy of Sciences of Ukraine, 9 Leontovicha Street, Kyiv 01030, Ukraine
| | - Vladimir I. Tomin
- Institute
of Physics, Pomeranian University in Słupsk, ul. Arciszewskiego, 22b, Słupsk 76-200, Poland
| | - Pi-Tai Chou
- Department
of Chemistry, National Taiwan University, 1 Roosevelt Road Section 4, Taipei 106, Taiwan
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18
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Tomin VI, Dubrovkin JM. Kinetics of Anti-Kasha Photoreactions. Direct Excitation of a Higher Excited State. ChemistrySelect 2017. [DOI: 10.1002/slct.201701518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Luby BM, Charron DM, MacLaughlin CM, Zheng G. Activatable fluorescence: From small molecule to nanoparticle. Adv Drug Deliv Rev 2017; 113:97-121. [PMID: 27593264 DOI: 10.1016/j.addr.2016.08.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/15/2016] [Accepted: 08/27/2016] [Indexed: 12/23/2022]
Abstract
Molecular imaging has emerged as an indispensable technology in the development and application of drug delivery systems. Targeted imaging agents report the presence of biomolecules, including therapeutic targets and disease biomarkers, while the biological behaviour of labelled delivery systems can be non-invasively assessed in real time. As an imaging modality, fluorescence offers additional signal specificity and dynamic information due to the inherent responsivity of fluorescence agents to interactions with other optical species and with their environment. Harnessing this responsivity is the basis of activatable fluorescence imaging, where interactions between an engineered fluorescence agent and its biological target induce a fluorogenic response. Small molecule activatable agents are frequently derivatives of common fluorophores designed to chemically react with their target. Macromolecular scale agents are useful for imaging proteins and nucleic acids, although their biological delivery can be difficult. Nanoscale activatable agents combine the responsivity of fluorophores with the unique optical and physical properties of nanomaterials. The molecular imaging application and overall complexity of biological target dictate the most advantageous fluorescence agent size scale and activation strategy.
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Affiliation(s)
- Benjamin M Luby
- Princess Margaret Cancer Centre and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Danielle M Charron
- Princess Margaret Cancer Centre and Techna Institute, University Health Network, Toronto, ON, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Christina M MacLaughlin
- Princess Margaret Cancer Centre and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Gang Zheng
- Princess Margaret Cancer Centre and Techna Institute, University Health Network, Toronto, ON, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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20
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Barthes NPF, Gavvala K, Bonhomme D, Dabert-Gay AS, Debayle D, Mély Y, Michel BY, Burger A. Design and Development of a Two-Color Emissive FRET Pair Based on a Photostable Fluorescent Deoxyuridine Donor Presenting a Mega-Stokes Shift. J Org Chem 2016; 81:10733-10741. [DOI: 10.1021/acs.joc.6b01807] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicolas P. F. Barthes
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Krishna Gavvala
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Dominique Bonhomme
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Anne Sophie Dabert-Gay
- Institut
de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Université Côte d'Azur, CNRS, 660 Route des Lucioles, 06560 Valbonne, France
| | - Delphine Debayle
- Institut
de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Université Côte d'Azur, CNRS, 660 Route des Lucioles, 06560 Valbonne, France
| | - Yves Mély
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Benoît Y. Michel
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Alain Burger
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
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21
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Novel PAMAM Dendron as a Bichromophoric Probe Based on Rhodamine 6G and 1,8-Naphthalimide. J Fluoresc 2016; 26:1091-100. [DOI: 10.1007/s10895-016-1799-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/27/2016] [Indexed: 10/24/2022]
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22
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Finkler B, Riemann I, Vester M, Grüter A, Stracke F, Jung G. Monomolecular pyrenol-derivatives as multi-emissive probes for orthogonal reactivities. Photochem Photobiol Sci 2016; 15:1544-1557. [DOI: 10.1039/c6pp00290k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chameleons in a test tube: up to four easily distinguishable emission colors result from conversion by two hydrolytic enzymes at opposite reaction sites.
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Affiliation(s)
- Björn Finkler
- Biophysical Chemistry
- Saarland University
- 66123 Saarbrücken
- Germany
| | | | - Michael Vester
- Biophysical Chemistry
- Saarland University
- 66123 Saarbrücken
- Germany
| | - Andreas Grüter
- Biophysical Chemistry
- Saarland University
- 66123 Saarbrücken
- Germany
| | | | - Gregor Jung
- Biophysical Chemistry
- Saarland University
- 66123 Saarbrücken
- Germany
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23
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2-Carbamido-1,3-indandione - a Fluorescent Molecular Probe and Sunscreen Candidate. J Fluoresc 2015; 25:1601-14. [PMID: 26342735 DOI: 10.1007/s10895-015-1645-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
Abstract
The present work reports theoretical and experimental studies on the photophysical properties of two tautomeric forms of 2-carbamido-1,3-indandione (CAID). By means of UV-vis, steady-state and time-dependent fluorescence spectroscopy it is shown that both enol forms, 2-(hydroxylaminomethylidene)-indan-1,3-dione and 2-carboamide-1-hydroxy-3-oxo-indan, coexist in solution. On the base of spectroscopic studies of CAID interaction with human serum albumin and DNA sequences, it was shown that the compound has potential and it is suitable for use as fluorescent molecular probe for investigation of different biomolecules. CAID shows relatively high photostability within 3 h irradiation period. Such behavior of the investigated compound supposes possibilities for using of the CAID molecule as sunscreen because of strong absorption in UVA, UVB and UVC light spectra.
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24
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Barthes NPF, Karpenko IA, Dziuba D, Spadafora M, Auffret J, Demchenko AP, Mély Y, Benhida R, Michel BY, Burger A. Development of environmentally sensitive fluorescent and dual emissive deoxyuridine analogues. RSC Adv 2015. [DOI: 10.1039/c5ra02709h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We designed and developed fluorescent deoxyuridine analogues with strong sensitivity to hydration for the major groove labelling of DNA.
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Affiliation(s)
- N. P. F. Barthes
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - I. A. Karpenko
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - D. Dziuba
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - M. Spadafora
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - J. Auffret
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | | | - Y. Mély
- Laboratoire de Biophotonique et Pharmacologie
- UMR 7213
- Faculté de Pharmacie
- Université de Strasbourg
- CNRS
| | - R. Benhida
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - B. Y. Michel
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - A. Burger
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
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