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Kyrychenko A, Ladokhin AS. Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions. CHEM REC 2024; 24:e202300232. [PMID: 37695081 PMCID: PMC11113672 DOI: 10.1002/tcr.202300232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.
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Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, United States
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52
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Pivovarenko VG, Klymchenko AS. Fluorescent Probes Based on Charge and Proton Transfer for Probing Biomolecular Environment. CHEM REC 2024; 24:e202300321. [PMID: 38158338 DOI: 10.1002/tcr.202300321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Fluorescent probes for sensing fundamental properties of biomolecular environment, such as polarity and hydration, help to study assembly of lipids into biomembranes, sensing interactions of biomolecules and imaging physiological state of the cells. Here, we summarize major efforts in the development of probes based on two photophysical mechanisms: (i) an excited-state intramolecular charge transfer (ICT), which is represented by fluorescent solvatochromic dyes that shift their emission band maximum as a function of environment polarity and hydration; (ii) excited-state intramolecular proton transfer (ESIPT), with particular focus on 5-membered cyclic systems, represented by 3-hydroxyflavones, because they exhibit dual emission sensitive to the environment. For both ICT and ESIPT dyes, the design of the probes and their biological applications are summarized. Thus, dyes bearing amphiphilic anchors target lipid membranes and report their lipid organization, while targeting ligands direct them to specific organelles for sensing their local environment. The labels, amino acid and nucleic acid analogues inserted into biomolecules enable monitoring their interactions with membranes, proteins and nucleic acids. While ICT probes are relatively simple and robust environment-sensitive probes, ESIPT probes feature high information content due their dual emission. They constitute a powerful toolbox for addressing multitude of biological questions.
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Affiliation(s)
- Vasyl G Pivovarenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, 01033, Kyiv, Ukraine
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, ITI SysChem, Université de Strasbourg, 67401, Illkirch, France
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53
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Ma YZ, Premadasa UI, Bryantsev VS, Miles AR, Ivanov IN, Elgattar A, Liao Y, Doughty B. Unravelling photoisomerization dynamics in a metastable-state photoacid. Phys Chem Chem Phys 2024; 26:4062-4070. [PMID: 38224171 DOI: 10.1039/d3cp04454h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Direct access to trans-cis photoisomerization in a metastable state photoacid (mPAH) remains challenging owing to the presence of competing excited-state relaxation pathways and multiple transient isomers with overlapping spectra. Here, we reveal the photoisomerization dynamics in an indazole mPAH using time-resolved fluorescence (TRF) spectroscopy by exploiting a unique property of this mPAH having fluorescence only from the trans isomer. The combination of these experimental results with time-dependent density function theory (TDDFT) calculations enables us to gain mechanistic insight into this key dynamical process.
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Affiliation(s)
- Ying-Zhong Ma
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.
| | - Uvinduni I Premadasa
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.
| | - Vyacheslav S Bryantsev
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.
| | - Audrey R Miles
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Ilia N Ivanov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Adnan Elgattar
- Department of Biomedical and Chemical Engineering, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Yi Liao
- Department of Biomedical and Chemical Engineering, Florida Institute of Technology, Melbourne, FL 32901, USA
| | - Benjamin Doughty
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.
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54
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Bao Y. Polymerization-Mediated Through-Space Charge Transfer: An Emerging Strategy for Light-Emitting Materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 38252874 DOI: 10.1021/acs.langmuir.3c03376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Through-space charge transfer (TSCT) has attracted increasing attention owing to its great potential in designing efficient light-emitting molecules and polymers. Complementary to through-bond charge transfer and Förster resonance energy transfer, TSCT offers an alternative approach for the manipulation of molecular fluorescence. Recently, the synergy between TSCT and polymer systems through polymerization-mediated charge transfer has fostered the advancements of innovative light-emitting functional materials featuring thermally activated delayed fluorescence and/or aggregation-induced emission. This perspective highlights the significant progress in tailoring emission properties through structural engineering of donor and acceptor groups within polymeric systems, leveraging the TSCT mechanism. This strategy has transcended the limitations of traditional charge transfer systems with its tolerance to extended donor-acceptor distance, paving the way for novel applications beyond organic light-emitting diodes. The discussion concludes with a forward-looking analysis of potential future research trajectories in the field of polymerization-mediated charge transfer for developing next-generation light-emitting materials.
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Affiliation(s)
- Yinyin Bao
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
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55
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Pascual G, Roy SK, Barcenas G, Wilson CK, Cervantes-Salguero K, Obukhova OM, Krivoshey AI, Terpetschnig EA, Tatarets AL, Li L, Yurke B, Knowlton WB, Mass OA, Pensack RD, Lee J. Effect of hydrophilicity-imparting substituents on exciton delocalization in squaraine dye aggregates covalently templated to DNA Holliday junctions. NANOSCALE 2024; 16:1206-1222. [PMID: 38113123 DOI: 10.1039/d3nr04499h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Molecular aggregates exhibit emergent properties, including the collective sharing of electronic excitation energy known as exciton delocalization, that can be leveraged in applications such as quantum computing, optical information processing, and light harvesting. In a previous study, we found unexpectedly large excitonic interactions (quantified by the excitonic hopping parameter Jm,n) in DNA-templated aggregates of squaraine (SQ) dyes with hydrophilic-imparting sulfo and butylsulfo substituents. Here, we characterize DNA Holliday junction (DNA-HJ) templated aggregates of an expanded set of SQs and evaluate their optical properties in the context of structural heterogeneity. Specifically, we characterized the orientation of and Jm,n between dyes in dimer aggregates of non-chlorinated and chlorinated SQs. Three new chlorinated SQs that feature a varying number of butylsulfo substituents were synthesized and attached to a DNA-HJ via a covalent linker to form adjacent and transverse dimers. Various characteristics of the dye, including its hydrophilicity (in terms of log Po/w) and surface area, and of the substituents, including their local bulkiness and electron withdrawing capacity, were quantified computationally. The orientation of and Jm,n between the dyes were estimated using a model based on Kühn-Renger-May theory to fit the absorption and circular dichroism spectra. The results suggested that adjacent dimer aggregates of all the non-chlorinated and of the most hydrophilic chlorinated SQ dyes exhibit heterogeneity; that is, they form a mixture of dimers subpopulations. A key finding of this work is that dyes with a higher hydrophilicity (lower log Po/w) formed dimers with smaller Jm,n and large center-to-center dye distance (Rm,n). Also, the results revealed that the position of the dye in the DNA-HJ template, that is, adjacent or transverse, impacted Jm,n. Lastly, we found that Jm,n between symmetrically substituted dyes was reduced by increasing the local bulkiness of the substituent. This work provides insights into how to maintain strong excitonic coupling and identifies challenges associated with heterogeneity, which will help to improve control of these dye aggregates and move forward their potential application as quantum information systems.
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Affiliation(s)
- Gissela Pascual
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Simon K Roy
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA
| | - German Barcenas
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Christopher K Wilson
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA
| | | | - Olena M Obukhova
- State Scientific Institution "Institute for Single Crystals" of the National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Alexander I Krivoshey
- State Scientific Institution "Institute for Single Crystals" of the National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | | | - Anatoliy L Tatarets
- State Scientific Institution "Institute for Single Crystals" of the National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Olga A Mass
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, USA.
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56
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Cheng X, Pu Y, Ye S, Xiao X, Zhang X, Chen H. Measuring Solvent Exchange in Silica Nanoparticles with Rotor-Based Fluorophore. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2305779. [PMID: 37774750 DOI: 10.1002/adma.202305779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/15/2023] [Indexed: 10/01/2023]
Abstract
Measuring the diffusivity of molecules is the first step toward understanding their dependence and controlling diffusion, but the challenge increases with the decrease of molecular size, particularly for non-fluorescent and non-reactive molecules such as solvents. Here, the capability to monitor the solvent exchange process within the micropores of silica with millisecond time resolution is demonstrated, by simply embedding a rotor-based fluorophore (thioflavin T) in colloidal silica nanoparticles. Basically, the silica provides an extreme case of viscous microenvironment, which is affected by the polarity of the solvents. The fluorescence intensity traces can be well fitted to the Fickian diffusion model, allowing analytical solution of the diffusion process, and revealing the diffusion coefficients. The validation experiments, involving the water-to-ethanol and ethanol-to-water solvent exchange, the comparison of different drying conditions, and the variation in the degree of cross-linking in silica, confirmed the effectiveness and sensitivity of this method for characterizing diffusion in silica micropores. This work focuses on the method development of measuring diffusivity and the high temporal resolution in tracking solvent exchange dynamics over a short distance (within 165 nm) opens enormous possibilities for further studies.
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Affiliation(s)
- Xuejun Cheng
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang, 310027, China
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Yingming Pu
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Songtao Ye
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Xiao Xiao
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Xin Zhang
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Hongyu Chen
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
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57
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Lampkin BJ, Kritzer JA. Engineered fluorogenic HaloTag ligands for turn-on labelling in live cells. Chem Commun (Camb) 2023; 60:200-203. [PMID: 38048049 PMCID: PMC10835756 DOI: 10.1039/d3cc05536a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Recent years have seen dramatic improvements in the design of organic fluorophores based on limiting non-radiative decay pathways. We sought to extend this understanding to benzothiadiazoles that have been used as turn-on fluorescent substrates for the self-labeling protein HaloTag. When conjugated to HaloTag, the benzothiadiazoles reside in a narrow tunnel that precludes twisted internal charge transfer, which allowed us to explore steric and electronic effects on other non-radiative decay pathways. By minimizing both non-radiative decay and nonspecific interactions with cellular components, we produced improved turn-on dyes with 136-fold increase in fluorescence over background in cells.
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Affiliation(s)
- Bryan J Lampkin
- Department of Chemistry, Tufts University, 62 Talbot Rd, Medford, MA 02155, USA.
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Rd, Medford, MA 02155, USA.
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58
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Das S, Batra A, Kundu S, Sharma R, Patra A. Unveiling autophagy and aging through time-resolved imaging of lysosomal polarity with a delayed fluorescent emitter. Chem Sci 2023; 15:102-112. [PMID: 38131076 PMCID: PMC10732132 DOI: 10.1039/d3sc02450d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/11/2023] [Indexed: 12/23/2023] Open
Abstract
Detecting the lysosomal microenvironmental changes like viscosity, pH, and polarity during their dynamic interorganelle interactions remains an intriguing area that facilitates the elucidation of cellular homeostasis. The subtle variation of physiological conditions can be assessed by deciphering the lysosomal microenvironments during lysosome-organelle interactions, closely related to autophagic pathways leading to various cellular disorders. Herein, we shed light on the dynamic lysosomal polarity in live cells and a multicellular model organism, Caenorhabditis elegans (C. elegans), through time-resolved imaging employing a thermally activated delayed fluorescent probe, DC-Lyso. The highly photostable and cytocompatible DC-Lyso rapidly labels the lysosomes (within 1 min of incubation) and exhibits red luminescence and polarity-sensitive long lifetime under the cellular environment. The distinct variation in the fluorescence lifetime of DC-Lyso suggests an increase in local polarity during the lysosomal dynamics and interorganelle interactions, including lipophagy and mitophagy. The lifetime imaging analysis reveals increasing lysosomal polarity as an indicator for probing the successive development of C. elegans during aging. The in vivo microsecond timescale imaging of various cancerous cell lines and C. elegans, as presented here, therefore, expands the scope of delayed fluorescent emitters for unveiling complex biological processes.
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Affiliation(s)
- Subhadeep Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Madhya Pradesh 462066 India
| | - Abhilasha Batra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Madhya Pradesh 462066 India
| | - Subhankar Kundu
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Madhya Pradesh 462066 India
| | - Rati Sharma
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Madhya Pradesh 462066 India
| | - Abhijit Patra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Madhya Pradesh 462066 India
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59
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Fabre N, Trojanowicz R, Moreaud L, Fiorini-Debuisschert C, Vassant S, Charra F. Structure and Photonic Properties of a Perylenediimide Monolayer Assembled by the Langmuir-Blodgett Technique. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18252-18262. [PMID: 38051255 DOI: 10.1021/acs.langmuir.3c02038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The photonic responses of densely packed dye molecule assemblies are strongly dependent on their organization and environment. The precise control of molecular orientations and distances relative to the substrate and to each other is thus a key point in the design of photonic molecular materials. Herein, we report the preparation of a homogeneous and well-organized single monolayer of the perylenediimide (PDI) derivative by means of the Langmuir-Blodgett technique. Its optical properties disclose an intense charge-transfer excitonic absorption band related to important intermolecular coupling. Furthermore, an important immunity to photobleaching is observed for such a molecular assembly. The dipolar orientations of the molecules along the substrate have been unambiguously determined by angle-of-incidence-resolved polarized absorption and back-focal-plane fluorescence mapping. In addition, time-resolved spectroscopy reveals a fast two-dimensional diffusion of excitons consistent with strong π-stacking of adjacent PDI molecules.
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Affiliation(s)
- Nicolas Fabre
- Université Paris-Saclay, CEA-CNRS, Service de Physique de l'État condensé (SPEC), Gif-sur-Yvette F-91191, France
| | - Remigiusz Trojanowicz
- Université Paris-Saclay, CEA-CNRS, Service de Physique de l'État condensé (SPEC), Gif-sur-Yvette F-91191, France
| | - Laureen Moreaud
- Université Paris-Saclay, CEA-CNRS, Service de Physique de l'État condensé (SPEC), Gif-sur-Yvette F-91191, France
| | - Céline Fiorini-Debuisschert
- Université Paris-Saclay, CEA-CNRS, Service de Physique de l'État condensé (SPEC), Gif-sur-Yvette F-91191, France
| | - Simon Vassant
- Université Paris-Saclay, CEA-CNRS, Service de Physique de l'État condensé (SPEC), Gif-sur-Yvette F-91191, France
| | - Fabrice Charra
- Université Paris-Saclay, CEA-CNRS, Service de Physique de l'État condensé (SPEC), Gif-sur-Yvette F-91191, France
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60
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Suo Y, Chen A, La Clair JJ, Burkart MD. Substrate Sequestration and Chain Flipping in Human Mitochondrial Acyl Carrier Protein. Biochemistry 2023; 62:3548-3553. [PMID: 38039071 DOI: 10.1021/acs.biochem.3c00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Outside of their involvement in energy production, mitochondria play a critical role for the cell through their access to a discrete pathway for fatty acid biosynthesis. Despite decades of study in bacterial fatty acid synthases (the putative evolutionary mitochondrial precursor), our understanding of human mitochondrial fatty acid biosynthesis remains incomplete. In particular, the role of the key carrier protein, human mitochondrial acyl carrier protein (mACP), which shuttles the substrate intermediates through the pathway, has not been well-studied in part due to challenges in protein expression and purification. Herein, we report a reliable method for recombinant Escherichia coli expression and purification of mACP. Fundamental characteristics, including substrate sequestration and chain-flipping activity, are demonstrated in mACP using solvatochromic response. This study provides an efficient approach toward understanding the fundamental protein-protein interactions of mACP and its partner proteins, ultimately leading to a molecular understanding of human mitochondrial diseases such as mitochondrial fatty acid oxidation deficiencies.
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Affiliation(s)
- Yixing Suo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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61
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Zhou M, Song C, Qin T, Xun Z, Liu B. Fast and sensitive detection of nitroxynil using a chalcone-based supramolecular fluorescent sensor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 302:122974. [PMID: 37327726 DOI: 10.1016/j.saa.2023.122974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023]
Abstract
Nitroxynil as a veterinary drug has been widely used for treatment of parasitic worms in food-producing sheep and cattle. However, the residual nitroxynil in edible animal products can lead to severe adverse effects on human health. Thus, development of an effective analytical tool for nitroxynil is of great significance. In the present study, we designed and synthesized a novel albumin-based fluorescent sensor, which was capable of detecting nitroxynil with the fast response (<10 s), high sensitivity (limit of detection ∼8.7 ppb), high selectivity, and excellent anti-interference property. The sensing mechanism was clarified by using the molecular docking technique and mass spectra. Moreover, this sensor showed the detection accuracy comparable to standard HPLC method, and meanwhile exhibited much shorter response time and higher sensitivity. All the results demonstrated that this novel fluorescent senor could serve as a practical analytical tool for determination of nitroxynil in real food samples.
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Affiliation(s)
- Mei Zhou
- Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Material Science and Engineering, Shenzhen University, Shenzhen 518060, China
| | - Chao Song
- Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Material Science and Engineering, Shenzhen University, Shenzhen 518060, China
| | - Tianyi Qin
- Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Material Science and Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhiqing Xun
- Guangzhou Quality Supervision and Testing Institute, 1-2 Zhujiang Rd, Guangzhou 511447, China
| | - Bin Liu
- Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Material Science and Engineering, Shenzhen University, Shenzhen 518060, China.
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62
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Chepeleva LV, Demidov OO, Snizhko AD, Tarasenko DO, Chumak AY, Kolomoitsev OO, Kotliar VM, Gladkov ES, Kyrychenko A, Roshal AD. Binding interactions of hydrophobically-modified flavonols with β-glucosidase: fluorescence spectroscopy and molecular modelling study. RSC Adv 2023; 13:34107-34121. [PMID: 38020002 PMCID: PMC10661682 DOI: 10.1039/d3ra06276g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
Natural flavonoids are capable of inhibiting glucosidase activity, so they can be used for treating diabetes mellitus and hypertension. However, molecular-level details of their interactions with glucosidase enzymes remain poorly understood. This paper describes the synthesis and spectral characterization of a series of fluorescent flavonols and their interaction with the β-glucosidase enzyme. To tune flavonol-enzyme interaction modes and affinity, we introduced different polar halogen-containing groups or bulky aromatic/alkyl substituents in the peripheral 2-aryl ring of a flavonol moiety. Using fluorescence spectroscopy methods in combination with molecular docking and molecular dynamics simulations, we examined the binding affinity and identified probe binding patterns, which are critical for steric blockage of the key catalytic residues of the enzyme. Using a fluorescent assay, we demonstrated that the binding of flavonol 2e to β-glucosidase decreased its enzymatic activity up to 3.5 times. In addition, our molecular docking and all-atom molecular dynamics simulations suggest that the probe binding is driven by hydrophobic interactions with aromatic Trp and Tyr residues within the catalytic glycone binding pockets of β-glucosidase. Our study provides a new insight into structure-property relations for flavonol-protein interactions, which govern their enzyme binding, and outlines a framework for a rational design of new flavonol-based potent inhibitors for β-glucosidases.
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Affiliation(s)
- Liudmyla V Chepeleva
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Oleksii O Demidov
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Arsenii D Snizhko
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Dmytro O Tarasenko
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Andrii Y Chumak
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Oleksii O Kolomoitsev
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Volodymyr M Kotliar
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
| | - Eugene S Gladkov
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
- State Scientific Institution "Institute for Single Crystals", National Academy of Sciences of Ukraine 60 Nauky Ave. Kharkiv 61072 Ukraine
| | - Alexander Kyrychenko
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
- State Scientific Institution "Institute for Single Crystals", National Academy of Sciences of Ukraine 60 Nauky Ave. Kharkiv 61072 Ukraine
| | - Alexander D Roshal
- Institute of Chemistry, V.N. Karazin Kharkiv National University 4 Svobody Sq. Kharkiv 61022 Ukraine
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63
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Hu Y, Zhang RQ, Liu SL, Wang ZG. In-situ quantification of lipids in live cells through imaging approaches. Biosens Bioelectron 2023; 240:115649. [PMID: 37678059 DOI: 10.1016/j.bios.2023.115649] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/03/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Lipids are important molecules that are widely distributed within the cell, and they play a crucial role in several biological processes such as cell membrane formation, signaling, cell motility and division. Monitoring the spatiotemporal dynamics of cellular lipids in real-time and quantifying their concentrations in situ is crucial since the local concentration of lipids initiates various signaling pathways that regulate cellular processes. In this review, we first introduced the historical background of lipid quantification methods. We then delve into the current state of the art of in situ lipid quantification, including the establishment and utility of fluorescence imaging techniques based on sensors of lipid-binding domains labeled with organic dyes or fluorescent proteins, and Raman and magnetic resonance imaging (MRI) techniques that do not require lipid labeling. Next, we highlighted the biological applications of live-cell lipid quantification techniques in the study of in situ lipid distribution, lipid transformation, and lipid-mediated signaling pathways. Finally, we discussed the technical challenges and prospects for the development of lipid quantification in live cells, with the aim of promoting the development of in situ lipid quantification in live cells, which may have a profound impact on the biological and medical fields.
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Affiliation(s)
- Yusi Hu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Centre for New Organic Matter, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry and School of Medicine, Nankai University, Tianjin, 300071, China
| | - Rui-Qiao Zhang
- Qingdao Academy of Agricultural Sciences, Qingdao, 266100, China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Centre for New Organic Matter, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry and School of Medicine, Nankai University, Tianjin, 300071, China.
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Centre for New Organic Matter, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry and School of Medicine, Nankai University, Tianjin, 300071, China.
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64
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Dang Z, Liu X, Du Y, Wang Y, Zhou D, Zhang Y, Zhu S. Ultra-Bright Heptamethine Dye Clusters Based on a Self-Adaptive Co-Assembly Strategy for NIR-IIb Biomedical Imaging. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2306773. [PMID: 37713682 DOI: 10.1002/adma.202306773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/05/2023] [Indexed: 09/17/2023]
Abstract
Despite the wide range of applications of bright NIR-II polymethine scaffolds in biomedical imaging, their solvatochromism and aggregation-caused quenching (ACQ) effects in aqueous solutions limit their inherent brightness using traditional encapsulation methods, and effective hydrophilization strategies are still scarce. Here, a new set of Flav dyes is synthesized and PEGylated, followed by manufacturing DSPE@FlavP2000 nanoparticles using a self-adaptive co-assembly strategy to overcome these limitations. FlavP2000 can autonomously adjust its conformation when co-assembled with DSPE-PEG2000 , resulting in high-efficiency luminescence (≈44.9% fluorescence of Flav in DMSO). DSPE@FlavP2000 enables NIR-IIb (>1500 nm) angiography with high signal-to-noise ratios. Notably, this co-assembly can occur in situ between FlavP2000 with proteins in the living body based on a novel mechanism of brightness activation induced by disassembly (BAD), achieving consistent brightness as DSPE@FlavP2000 in blood or serum. The self-adaptive co-assembly strategy can be enhanced by incorporating an IPA moiety, which dynamically binds to albumin to prolong the dye's blood circulation time. Thus, the "enhanced" BAD is successfully applied to long-term vascular imaging and sciatic nerve imaging. Both the self-adaptive co-assembly strategy and BAD phenomenon improve the selectivity and availability of the hydrophilization methods, paving the way for efficient biological applications of polymethine dyes.
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Affiliation(s)
- Zetao Dang
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, The First Hospital of Jilin University, Changchun, 130021, P. R. China
| | - Xiangping Liu
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Yijing Du
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, The First Hospital of Jilin University, Changchun, 130021, P. R. China
| | - Yajun Wang
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Ding Zhou
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, Changchun, 130021, P. R. China
| | - Yuewei Zhang
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, The First Hospital of Jilin University, Changchun, 130021, P. R. China
- School of Chemistry and Pharmaceutical Engineering, Jilin Institute of Chemical Technology, Jilin, 132022, P. R. China
| | - Shoujun Zhu
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, The First Hospital of Jilin University, Changchun, 130021, P. R. China
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital of Jilin University, Changchun, 130021, P. R. China
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65
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Kimura R, Yoneda Y, Kuramochi H, Saito S. Environment-sensitive fluorescence of COT-fused perylene bisimide based on symmetry-breaking charge separation. Photochem Photobiol Sci 2023; 22:2541-2552. [PMID: 37656334 DOI: 10.1007/s43630-023-00468-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/09/2023] [Indexed: 09/02/2023]
Abstract
Flexible and aromatic photofunctional system (FLAP) is composed of flapping rigid aromatic wings fused with a flexible 8π ring at the center such as cyclooctatetraene (COT). A series of FLAP have been actively studied for the interesting dynamic behaviors. Here, we synthesized a new flapping molecule bearing naphtho-perylenebisimide wings (NPBI-FLAP), in which two perylene units are arranged side by side. As a reference compound, we also prepared COT-fused NPBI (NPBI-COT) that contains only single perylene unit. In both compounds, inherent strong fluorescence of the NPBI moiety is almost quenched and the FL lifetime becomes much shortened in highly polar solvents (acetone and DMF). Through the analyses of environment-sensitive fluorescence, electrochemical reduction/oxidation, and femtosecond transient absorption, the fluorescence quenching behavior was attributed to rapid symmetry-breaking charge separation (SB-CS) for NPBI-FLAP and to intramolecular charge transfer (ICT) for NPBI-COT. Most of the excited species of these compounds decay with the bent geometry, which is in contrast with the excited-state planarization behavior of a previously reported COT-fused peryleneimides with the double-headed arrangement of the perylene moieties. These results indicate that changing the fusion manners between COT and other π skeletons offers new functional molecules with distinct dynamics.
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Affiliation(s)
- Ryo Kimura
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwake, Sakyo, Kyoto, 606-8502, Japan
| | - Yusuke Yoneda
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, 444-8585, Japan
| | - Hikaru Kuramochi
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, 444-8585, Japan.
| | - Shohei Saito
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwake, Sakyo, Kyoto, 606-8502, Japan.
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66
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Liu J, Chen B, Zhang R, Li Y, Chen R, Zhu S, Wen S, Luan T. Recent progress in analytical strategies of arsenic-binding proteomes in living systems. Anal Bioanal Chem 2023; 415:6915-6929. [PMID: 37410126 DOI: 10.1007/s00216-023-04812-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/10/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023]
Abstract
Arsenic (As) is one of the most concerning elements due to its high exposure risks to organisms and ecosystems. The interaction between arsenicals and proteins plays a pivotal role in inducing their biological effects on living systems, e.g., arsenicosis. In this review article, the recent advances in analytical techniques and methods of As-binding proteomes were well summarized and discussed, including chromatographic separation and purification, biotin-streptavidin pull-down probes, in situ imaging using novel fluorescent probes, and protein identification. These analytical technologies could provide a growing body of knowledge regarding the composition, level, and distribution of As-binding proteomes in both cells and biological samples, even at the organellar level. The perspectives on analysis of As-binding proteomes are also proposed, e.g., isolation and identification of minor proteins, in vivo targeted protein degradation (TPD) technologies, and spatial As-binding proteomics. The application and development of sensitive, accurate, and high-throughput methodologies of As-binding proteomics would enable us to address the key molecular mechanisms underlying the adverse health effects of arsenicals.
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Affiliation(s)
- Jiahui Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Baowei Chen
- Southern Marine Science and Engineering Guangdong Laboratory, School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, China
| | - Ruijia Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yizheng Li
- Southern Marine Science and Engineering Guangdong Laboratory, School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, China
| | - Ruohong Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Siqi Zhu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shijun Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Tiangang Luan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
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67
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Biswas S, Baruah M, Shil A, Sarkar S, Ali M, Samanta A, Bhuniya S. Polarity-Driven Two-Photon Fluorescent Probe for Monitoring the Perturbation in Lipid Droplet Levels during Mitochondrial Dysfunction and Acute Pancreatitis. ACS Sens 2023; 8:3793-3803. [PMID: 37815484 DOI: 10.1021/acssensors.3c01245] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Lipid droplets (LDs) act as an energy reservoir in cancer cells; on the other hand, mitochondria are hyperactive to fulfill the energy demand to accelerate cell proliferation. We are interested in unfolding the relationship between the cellular energy reservoir and energy producer through fluorescence labeling. Thus, a dual organelle-targeted fluorescent probe MLD-1 has been rationally developed. It visualized the crosstalk between mitochondrial dysfunction and the fluctuation of LDs in live cells. Its two-photon ability allowed us to acquire deep tissue images. For the first time, we have shown that the probe has the ability to track the accumulation of LDs in different mouse organs during pancreatic inflammation. MLD-1, being a selectively polarity-driven, chemo- and photostable LD probe, may offer great possibilities for studying LD-associated biology in due course.
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Affiliation(s)
- Shayeri Biswas
- Centre for Interdisciplinary Sciences, JIS Institute of Advanced Studies and Research, JIS University, Arch Waterfront, GP Block, Sector V, Bidhannagar, Kolkata 700091, India
| | - Mousumi Baruah
- Molecular Sensors and Therapeutics Research Laboratory, Department of Chemistry, Shiv Nadar Institution of Eminence, Delhi NCR, NH 91, Tehsil Dadri, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Anushree Shil
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Gyungbuk 37673, Republic of Korea
| | - Sourav Sarkar
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Gyungbuk 37673, Republic of Korea
| | - Mudassar Ali
- Molecular Sensors and Therapeutics Research Laboratory, Department of Chemistry, Shiv Nadar Institution of Eminence, Delhi NCR, NH 91, Tehsil Dadri, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Animesh Samanta
- Molecular Sensors and Therapeutics Research Laboratory, Department of Chemistry, Shiv Nadar Institution of Eminence, Delhi NCR, NH 91, Tehsil Dadri, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Sankarprasad Bhuniya
- Centre for Interdisciplinary Sciences, JIS Institute of Advanced Studies and Research, JIS University, Arch Waterfront, GP Block, Sector V, Bidhannagar, Kolkata 700091, India
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68
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Yang C, Zhang H. A review on machine learning-powered fluorescent and colorimetric sensor arrays for bacteria identification. Mikrochim Acta 2023; 190:451. [PMID: 37880465 DOI: 10.1007/s00604-023-06021-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023]
Abstract
Biosensors have been widely used for bacteria determination with great success. However, the "lock-and-key" methodology used by biosensors to identify bacteria has a significant limitation: it can only detect one species of bacteria. In recent years, optical (fluorescent and colorimetric) sensor arrays are gradually gaining attention from researchers as a new type of biosensor. They can acquire multiple features of a target simultaneously, form a feature pattern, and determine the bacteria species with the help of pattern recognition/machine learning algorithms. Previous reviews in this area have focused on the interaction between the sensor array and bacteria or the materials used to make the sensors. This review, on the other hand, will provide researchers with a better understanding of the field by discussing fluorescent and colorimetric sensor arrays based on the mechanism of optical signal generation. These sensor arrays will be compared based on the identified species. Finally, we will discuss the limitations of these sensor arrays and explore possible solutions.
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Affiliation(s)
- Changmao Yang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan, 430074, China
| | - Houjin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan, 430074, China.
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69
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Schiavone DV, Gallardo J, Kapkayeva DM, Baucom JC, Murelli RP. Lactam-fused tropolones: a new tunable, environmentally sensitive fluorophore class. Org Biomol Chem 2023; 21:7900-7907. [PMID: 37750360 DOI: 10.1039/d3ob01263h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Fluorescent small-molecules capable of altering their profiles in response to environmental changes are exceptionally valuable tool compounds throughout the scientific community. The following manuscriipt describes a new class of fluorescent small molecules based on lactam-fused tropolones that are responsive to a dynamic range of environmental changes. These molecules can be easily obtained through a rapid annulation procedure between appropriately functionalized tropolones and primary amines, which is often complete within minutes at room temperature. Molecules generated through this approach have been identified with fluoresence emission across the visible light spectra, and can be tuned based on either the tropolone or amine component. They are also highly responsive to changes in solvent, pH, and certain divalent metal ions. Tropolone-fused lactams thus represent a new class of tunable fluorescent small molecules that could find value throughout the scientific community.
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Affiliation(s)
- Daniel V Schiavone
- Department of Chemistry and Biochemistry, Brooklyn College, The City University of New York, Brooklyn, New York, USA.
- PhD Program in Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
| | - Joel Gallardo
- Department of Chemistry and Biochemistry, Brooklyn College, The City University of New York, Brooklyn, New York, USA.
- PhD Program in Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
| | - Diana M Kapkayeva
- Department of Chemistry and Biochemistry, Brooklyn College, The City University of New York, Brooklyn, New York, USA.
| | - John-Charles Baucom
- Department of Chemistry and Biochemistry, Brooklyn College, The City University of New York, Brooklyn, New York, USA.
- PhD Program in Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
| | - Ryan P Murelli
- Department of Chemistry and Biochemistry, Brooklyn College, The City University of New York, Brooklyn, New York, USA.
- PhD Program in Chemistry, The Graduate Center, The City University of New York, New York, NY, USA
- PhD Program in Biochemistry, The Graduate Center, The City University of New York, New York, NY, USA
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70
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Zhang F, Chen F, Zhong M, Shen R, Zhao Z, Wei H, Zhang B, Fang J. Imaging of Carbonic Anhydrase Level in Epilepsy with an Environment-Sensitive Fluorescent Probe. Anal Chem 2023; 95:14833-14841. [PMID: 37747928 DOI: 10.1021/acs.analchem.3c01368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Carbonic anhydrases (CAs) participate in various physiological and pathological activities by catalyzing the interconversion between carbon dioxide and bicarbonate ions. Under normal circumstances, they guarantee that the relevant biological reactions in our body occur within an appropriate time scale. Abnormal expression or activity alteration of CAs is closely related to the pathogenesis of diverse diseases. This work reports an inhibitor-directed fluorescent probe FMRs-CA for the detection of CAs. Excellent selectivity, favorable biocompatibility, and desirable blood-brain barrier (BBB) penetration endow the probe with the ability to image the fluctuation of CAs in cells and mice. We achieved in situ visualization of the increased CAs in hypoxic cells with this probe. Additionally, probe FMRs-CA was mainly enriched within the liver and gradually metabolized by the liver. With the help of FMRs-CA, the increase of CAs in epileptic mouse brains was revealed first from the perspective of imaging, providing the mechanism connection between abnormal CA expressions and epilepsy.
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Affiliation(s)
- Fang Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Fan Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Miao Zhong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Ruipeng Shen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Zhengjia Zhao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Haopai Wei
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Baoxin Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Jianguo Fang
- School of Chemistry and Chemical Engineering, Nanjing University of Science & Technology, Nanjing, Jiangsu 210094, China
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71
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Chen XX, Gomila RM, García-Arcos JM, Vonesch M, Gonzalez-Sanchis N, Roux A, Frontera A, Sakai N, Matile S. Fluorogenic In Situ Thioacetalization: Expanding the Chemical Space of Fluorescent Probes, Including Unorthodox, Bifurcated, and Mechanosensitive Chalcogen Bonds. JACS AU 2023; 3:2557-2565. [PMID: 37772186 PMCID: PMC10523495 DOI: 10.1021/jacsau.3c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023]
Abstract
Progress with fluorescent flippers, small-molecule probes to image membrane tension in living systems, has been limited by the effort needed to synthesize the twisted push-pull mechanophore. Here, we move to a higher oxidation level to introduce a new design paradigm that allows the screening of flipper probes rapidly, at best in situ. Late-stage clicking of thioacetals and acetals allows simultaneous attachment of targeting units and interfacers and exploration of the critical chalcogen-bonding donor at the same time. Initial studies focus on plasma membrane targeting and develop the chemical space of acetals and thioacetals, from acyclic amino acids to cyclic 1,3-heterocycles covering dioxanes as well as dithiolanes, dithianes, and dithiepanes, derived also from classics in biology like cysteine, lipoic acid, asparagusic acid, DTT, and epidithiodiketopiperazines. From the functional point of view, the sensitivity of membrane tension imaging in living cells could be doubled, with lifetime differences in FLIM images increasing from 0.55 to 1.11 ns. From a theoretical point of view, the complexity of mechanically coupled chalcogen bonding is explored, revealing, among others, intriguing bifurcated chalcogen bonds.
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Affiliation(s)
- Xiao-Xiao Chen
- Department
of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Rosa M. Gomila
- Departament
de Química, Universitat de les Illes
Balears, SP-07122 Palma de Mallorca, Spain
| | | | - Maxime Vonesch
- Department
of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | | | - Aurelien Roux
- Department
of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Antonio Frontera
- Departament
de Química, Universitat de les Illes
Balears, SP-07122 Palma de Mallorca, Spain
| | - Naomi Sakai
- Department
of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Stefan Matile
- Department
of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
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72
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Dong B, Wang Y, Wei H, Kong X, Li S, Yue T. A D-π-A-π-D type structure-based fluorescent probe for revealing the fluctuations of the ER polarity during ferroptosis. Anal Chim Acta 2023; 1275:341571. [PMID: 37524463 DOI: 10.1016/j.aca.2023.341571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/02/2023]
Abstract
Ferroptosis is a novel Fe(II)-mediated oxidative cell death form, and is closely related with endoplasmic reticulum (ER). Exploring the fluctuation of ER polarity during ferroptosis is highly important for the in-depth study of the biological roles of ER in ferroptosis. Herein, we present a ratiometric probe (BNS) for revealing the changes of the ER polarity in the living cells experiencing ferroptosis. BNS employed a D-π-A-π-D type structure as the polarity-sensitive fluorophore, and selected p-toluenesulfonamide as the ER-targeting unit. Theoretical calculations suggested that the response mechanism of BNS to polarity was based on ICT, and two ICT processes appeared when BNS was at excited state. Cell imaging results demonstrated that BNS possessed desirable ER-targeting capability, and erastin-induced ferroptosis could increase the ER polarity of the living cells. Moreover, similarly to vitamin E (VE) and deferoxamine (DFO), dihydrolipoic acid (DHLA) could inhibit the changes of the ER polarity during erastin-induced ferroptosis. We expect that the probe could provide a convenient method to rapidly monitor ferroptosis and design novel drugs for the treatment of ferroptosis-relevant diseases.
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Affiliation(s)
- Baoli Dong
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, China.
| | - Yan Wang
- Shandong Chemical Technology Academy, Qingdao University of Science and Technology (Jinan), Jinan, Shandong, 250014, China
| | - Hua Wei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, China
| | - Xiuqi Kong
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, China
| | - Shijing Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, China
| | - Tao Yue
- Shandong Chemical Technology Academy, Qingdao University of Science and Technology (Jinan), Jinan, Shandong, 250014, China.
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73
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Wang T, Zhao J, Wu L, Liu W, Li Y, Yang Y. Polymer-Stabilized Cholesteric Liquid Crystal Films with Double Reflection Bands Prepared Based on the Competition between Photopolymerization and Photoisomerization. ACS APPLIED MATERIALS & INTERFACES 2023; 15:44314-44321. [PMID: 37674445 DOI: 10.1021/acsami.3c09576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Composite colors have been widely found in nature. Herein, polymer-stabilized cholesteric liquid crystal (PSCLC) films with composite structural colors were prepared through a one-step photopolymerization approach. The CLC mixtures were prepared using a mixture of acrylates and a mixture of two chiral dopants. One of the chiral dopants is polymerizable, and the other one is photoisomerizable. After photopolymerization, the PSCLC films with double Bragg reflection bands were obtained on the surface of a substrate. The competition between the photopolymerization of the acrylates and the photoisomerization of the chiral dopant was proposed to drive the formation of the double reflection bands. Without oxygen inhibition, the polymerization of the acrylates near the substrate surface was carried out. However, due to oxygen inhibition, the polymerization of the acrylates near the air was retarded. Then, the photoisomerization of the chiral dopant was carried out prior to the polymerization of the acrylates. The wavelengths of the double reflection bands were tunable by changing the concentrations of the acrylates and chiral dopants and the polymerization temperature. Colorful patterns with composite structural colors were prepared, which were suitable for decoration and anti-counterfeiting.
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Affiliation(s)
- Tingting Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Jinghua Zhao
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Limin Wu
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, Jiangsu 224051, P. R. China
| | - Wei Liu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Yi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| | - Yonggang Yang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
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74
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Zhou W, O’Neill CL, Ding T, Zhang O, Rudra JS, Lew MD. Resolving the nanoscale structure of β-sheet assemblies using single-molecule orientation-localization microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557571. [PMID: 37745382 PMCID: PMC10515885 DOI: 10.1101/2023.09.13.557571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Synthetic peptides that self-assemble into cross-β fibrils have remarkable utility as engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarity to amyloid species has been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers, KFE8L and KFE8D, and the pathological amyloid-beta peptide Aβ42. SMOLM reveals that the orientations of Nile red, as it transiently binds to both KFE8 and Aβ42, are consistent with a helical (bilayer) ribbon structure and convey the precise tilt of the fibrils' inner and outer backbones. SMOLM also finds polymorphic branched and curved morphologies of KFE8 whose backbones exhibit much more heterogeneity than those of more typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross β-rich fibrils.
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Affiliation(s)
- Weiyan Zhou
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Conor L. O’Neill
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Jai S. Rudra
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
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75
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Ohsato H, Kawauchi K, Yamada S, Konno T. Diverse Synthetic Transformations Using 4-Bromo-3,3,4,4-tetrafluorobut-1-ene and Its Applications in the Preparation of CF 2 CF 2 -Containing Sugars, Liquid Crystals, and Light-Emitting Materials. CHEM REC 2023; 23:e202300080. [PMID: 37140105 DOI: 10.1002/tcr.202300080] [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: 03/01/2023] [Revised: 04/16/2023] [Indexed: 05/05/2023]
Abstract
Organic molecules with fluoroalkylene scaffolds, especially a tetrafluoroethylene (CF2 CF2 ) moiety, in their molecular structures exhibit unique biological activities, or can be applied to functional materials such as liquid crystals and light-emitting materials. Although several methods for the syntheses of CF2 CF2 -containing organic molecules have been reported to date, they have been limited to methods using explosives and fluorinating agents. Therefore, there is an urgent need to develop simple and efficient approaches to synthesize CF2 CF2 -containing organic molecules from readily available fluorinated substrates using carbon-carbon bond formation reactions. This personal account summarizes the simple and efficient transformation of functional groups at both ends of 4-bromo-3,3,4,4-tetrafluorobut-1-ene and discusses its synthetic applications to biologically active fluorinated sugars and functional materials, such as liquid crystals and light-emitting molecules.
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Affiliation(s)
- Haruka Ohsato
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Kazuma Kawauchi
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Shigeyuki Yamada
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
| | - Tsutomu Konno
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan
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76
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Monari A, Burger A, Dumont E. Rationalizing the environment-dependent photophysical behavior of a DNA luminescent probe by classical and non-adiabatic molecular dynamics simulations. Photochem Photobiol Sci 2023; 22:2081-2092. [PMID: 37166569 DOI: 10.1007/s43630-023-00431-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/26/2023] [Indexed: 05/12/2023]
Abstract
Environment-sensitive fluorescent nucleoside analogs are of utmost importance to investigate the structure of nucleic acids, their intrinsic flexibility, and sequence-specific DNA- and RNA-binding proteins. The latter play indeed a key role in transcription, translation as well as in the regulation of RNA stability, localization and turnover, and many other cellular processes. The sensitivity of the embedded fluorophore to polarity, hydration, and base stacking is clearly dependent on the specific excited-state relaxation mechanism and can be rationalized combining experimental and computational techniques. In this work, we elucidate the mechanisms leading to the population of the triplet state manifold for a versatile nucleobase surrogate, namely the 2-thienyl-3-hydroxychromone in gas phase, owing to non-adiabatic molecular dynamics simulations. Furthermore, we analyze its behavior in the B-DNA environment via classical molecular dynamics simulations, which evidence a rapid extrusion of the adenine facing the 2-thienyl-3-hydroxychromone nucleobase surrogate. Our simulations provide new insights into the dynamics of this family of chromophores, which could give rise to an integrated view and a fine tuning of their photochemistry, and namely the role of excited-state intramolecular proton transfer for the rational design of the next generation of fluorescent nucleoside analogs.
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Affiliation(s)
- Antonio Monari
- Université Paris Cité and CNRS, ITODYS, 75006, Paris, France.
| | - Alain Burger
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, 06108, Nice, France
| | - Elise Dumont
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, 06108, Nice, France.
- Institut Universitaire de France, 5 Rue Descartes, 75005, Paris, France.
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77
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Vidyakina AA, Shtyrov AA, Ryazantsev MN, Khlebnikov AF, Kolesnikov IE, Sharoyko VV, Spiridonova DV, Balova IA, Bräse S, Danilkina NA. Development of Fluorescent Isocoumarin-Fused Oxacyclononyne - 1,2,3-Triazole Pairs. Chemistry 2023; 29:e202300540. [PMID: 37293937 DOI: 10.1002/chem.202300540] [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: 02/18/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/10/2023]
Abstract
Fluorescent isocoumarin-fused cycloalkynes, which are reactive in SPAAC and give fluorescent triazoles regardless of the azide nature, have been developed. The key structural feature that converts the non-fluorescent cycloalkyne/triazole pair to its fluorescent counterpart is the pi-acceptor group (COOMe, CN) at the C6 position of the isocoumarin ring. The design of the fluorescent cycloalkyne/triazole pairs is based on the theoretical study of the S1 state deactivation mechanism of the non-fluorescent isocoumarin-fused cycloalkyne IC9O using multi-configurational ab initio and DFT methodologies. The calculations revealed that deactivation proceeds through the electrocyclic ring opening of the α-pyrone cycle and is accompanied by a redistribution of electron density in the fused benzene ring. We proposed that the S1 excited state deactivation barrier could be increased by introducing a pi-acceptor group into a position that is in direct conjugation with the formed C=O group and has a reduced electron density in the transition state. As a proof of concept, we designed and synthesized two fluorescent isocoumarin-fused cycloalkynes IC9O-COOMe and IC9O-CN bearing pi-acceptors at the C6 position. The importance of the nature of a pi-acceptor group was shown by the example of much less fluorescent CF3 -substituted cycloalkyne IC9O-CF3 .
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Affiliation(s)
- Aleksandra A Vidyakina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Andrey A Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, Sankt-Peterburg, 194021 Saint Petersburg, Russia
| | - Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, Sankt-Peterburg, 194021 Saint Petersburg, Russia
| | - Alexander F Khlebnikov
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Ilya E Kolesnikov
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Vladimir V Sharoyko
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Dar'ya V Spiridonova
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Irina A Balova
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
- Institute of Biological and Chemical Systems-, Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Natalia A Danilkina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Sankt-Peterburg, 199034 Saint Petersburg, Russia
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78
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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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79
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Baranova AA, Tyurin AP, Korshun VA, Alferova VA. Sensing of Antibiotic-Bacteria Interactions. Antibiotics (Basel) 2023; 12:1340. [PMID: 37627760 PMCID: PMC10451291 DOI: 10.3390/antibiotics12081340] [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: 07/05/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Sensing of antibiotic-bacteria interactions is an important area of research that has gained significant attention in recent years. Antibiotic resistance is a major public health concern, and it is essential to develop new strategies for detecting and monitoring bacterial responses to antibiotics in order to maintain effective antibiotic development and antibacterial treatment. This review summarizes recent advances in sensing strategies for antibiotic-bacteria interactions, which are divided into two main parts: studies on the mechanism of action for sensitive bacteria and interrogation of the defense mechanisms for resistant ones. In conclusion, this review provides an overview of the present research landscape concerning antibiotic-bacteria interactions, emphasizing the potential for method adaptation and the integration of machine learning techniques in data analysis, which could potentially lead to a transformative impact on mechanistic studies within the field.
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Affiliation(s)
| | | | | | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (A.P.T.); (V.A.K.)
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80
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Steparuk EV, Meshcheryakova EA, Viktorova VV, Ulitko MV, Obydennov DL, Sosnovskikh VY. Oxidative Ring-Opening Transformation of 5-Acyl-4-pyrones as an Approach for the Tunable Synthesis of Hydroxylated Pyrones and Furans. J Org Chem 2023; 88:11590-11602. [PMID: 37504952 DOI: 10.1021/acs.joc.3c00907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
A selective and tunable approach for oxidation of 4-pyrones has been developed via ring-opening transformations leading to various hydroxylated oxaheterocycles. The first step of the strategy includes the base-catalyzed epoxidation of 5-acyl-4-pyrones in the presence of hydrogen peroxide for the effective synthesis of pyrone epoxides in high yields. The epoxides bearing the CO2Et group are reactive molecules that can undergo both pyrone and oxirane ring-opening via deformylation to produce hydroxylated 2-pyrones or 4-pyrones. The acid-promoted transformation led to 3-hydroxy-4-pyrones (24-76% yields), whereas the K2CO3-catalyzed ring-opening process of 2-carbethoxy-4-pyrone epoxides proceeded as an attack of alcohol at the C-3 position bearing the CO2Et group to give functionalized 6-acyl-5-hydroxy-2-pyrones (27-87% yields). The base-catalyzed reaction of 2-aryl-4-pyrone epoxides was followed by ring contraction and the dearoylation process to produce 3-hydroxyfuran-2-carbaldehydes in 42-80% yields. The transformation of 3-aroylchromone epoxides led to flavonols and 3-hydroxybenzofuran-2-carbaldehyde in the acidic and basic conditions, respectively. The prepared hydroxylated heterocycles demonstrated high reactivity for further transformations and low cytotoxicity and are promising fluorophores or UV filters.
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Affiliation(s)
- Elena V Steparuk
- Institute of Natural Sciences and Mathematics, Ural Federal University, 51 Lenina Ave., 620000 Ekaterinburg, Russian Federation
| | - Ekaterina A Meshcheryakova
- Institute of Natural Sciences and Mathematics, Ural Federal University, 51 Lenina Ave., 620000 Ekaterinburg, Russian Federation
| | - Viktoria V Viktorova
- Institute of Natural Sciences and Mathematics, Ural Federal University, 51 Lenina Ave., 620000 Ekaterinburg, Russian Federation
| | - Maria V Ulitko
- Institute of Natural Sciences and Mathematics, Ural Federal University, 51 Lenina Ave., 620000 Ekaterinburg, Russian Federation
| | - Dmitrii L Obydennov
- Institute of Natural Sciences and Mathematics, Ural Federal University, 51 Lenina Ave., 620000 Ekaterinburg, Russian Federation
| | - Vyacheslav Y Sosnovskikh
- Institute of Natural Sciences and Mathematics, Ural Federal University, 51 Lenina Ave., 620000 Ekaterinburg, Russian Federation
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81
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Islam J, Conroy P, Fercher C, Kim M, Yaari Z, Jones M, Bell TDM, Caradoc-Davies T, Law R, Whisstock J, Heller D, Mahler S, Corrie S. Design of Polarity-Dependent Immunosensors Based on the Structural Analysis of Engineered Antibodies. ACS Chem Biol 2023; 18:1863-1871. [PMID: 37440171 DOI: 10.1021/acschembio.3c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
"Reagentless" immunosensors are emerging to address the challenge of practical and sensitive detection of important biomarkers in real biological samples without the need for multistep assays and user intervention, with applications ranging from research tools to point-of-care diagnostics. Selective target binding to an affinity reagent is detected and reported in one step without the need for washing or additional reporters. In this study, we used a structure-guided approach to identify a mutation site in an antibody fragment for the polarity-dependent fluorophore, Anap, such that upon binding of the protein target cardiac troponin I, the Anap-labeled antibody would produce a detectable and dose-dependent shift in emission wavelength. We observed a significant emission wavelength shift of the Anap-labeled anti-cTnI mutant, with a blue shift of up to 37 nm, upon binding to the cTnI protein. Key differences in the resulting emission spectra between target peptides in comparison to whole proteins were also found; however, the affinity and binding characteristics remained unaffected when compared to the wild-type antibody. We also highlighted the potential flexibility of the approach by incorporating a near-infrared dye, IRDye800CW, into the same mutation site, which also resulted in a dose-dependent wavelength shift upon target incubation. These reagents can be used in experiments and devices to create simpler and more efficient biosensors across a range of research, medical laboratory, and point-of-care platforms.
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Affiliation(s)
- Jiaul Islam
- Department of Chemical and Biological Engineering, Monash University, Melbourne 3800, Australia
| | - Paul Conroy
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Christian Fercher
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Mijin Kim
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Centre, New York 10065, United States
| | - Zvi Yaari
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Centre, New York 10065, United States
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Martina Jones
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Toby D M Bell
- School of Chemistry, Monash University, Melbourne 3800, Australia
| | - Tom Caradoc-Davies
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
- Australian Synchrotron - ANSTO, Melbourne 3168, Australia
| | - Ruby Law
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - James Whisstock
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
| | - Daniel Heller
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Centre, New York 10065, United States
| | - Stephen Mahler
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne 3800, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Simon Corrie
- Department of Chemical and Biological Engineering, Monash University, Melbourne 3800, Australia
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82
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Auvray M, Naud-Martin D, Fontaine G, Bolze F, Clavier G, Mahuteau-Betzer F. Ultrabright two-photon excitable red-emissive fluorogenic probes for fast and wash-free bioorthogonal labelling in live cells. Chem Sci 2023; 14:8119-8128. [PMID: 37538830 PMCID: PMC10395273 DOI: 10.1039/d3sc01754k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
Fluorogenic bioorthogonal reactions are promising tools for tracking small molecules or biomolecules in living organisms. Two-photon excitation, by shifting absorption towards the red, significantly increases the signal-to-noise ratio and decreases photodamage, while allowing imaging about 10 times deeper than with a confocal microscope. However, efficient two-photon excitable fluorogenic probes are currently lacking. We report here the design and synthesis of fluorogenic probes based on a two-photon excitable fluorophore and a tetrazine quenching moiety. These probes react with bicyclo[6.1.0]no-4-yn-9ylmethanol (BCN) with a good to impressive kinetic rate constant (up to 1.1 × 103 M-1 s-1) and emit in the red window with moderate to high turn-on ratios. TDDFT allowed the rationalization of both the kinetic and fluorogenic performance of the different probes. The best candidate displays a 13.8-fold turn-on measured by quantifying fluorescence intensities in live cells under one-photon excitation, whereas a value of 3 is sufficient for high contrast live-cell imaging. In addition, live-cell imaging under two-photon excitation confirmed that there was no need for washing to monitor the reaction between BCN and this probe since an 8.0-fold turn-on was measured under two-photon excitation. Finally, the high two-photon brightness of the clicked adduct (>300 GM) allows the use of a weak laser power compatible with in vivo imaging.
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Affiliation(s)
- Marie Auvray
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
| | - Delphine Naud-Martin
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
| | - Gaëlle Fontaine
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
| | - Frédéric Bolze
- UMR7199, Faculté de Pharmacie 67401 Illkirch-Graffenstaden France
| | | | - Florence Mahuteau-Betzer
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer Institut Curie, Université PSL 91400 Orsay France
- CNRS UMR9187, Inserm U1196, Chemistry and Modeling for the Biology of Cancer, Université Paris-Saclay 91400 Orsay France
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83
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Melero A, Jiménez-Rojo N. Cracking the membrane lipid code. Curr Opin Cell Biol 2023; 83:102203. [PMID: 37437490 DOI: 10.1016/j.ceb.2023.102203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 07/14/2023]
Abstract
Why has nature acquired such a huge lipid repertoire? Although it would be theoretically possible to make a lipid bilayer fulfilling barrier functions with only one glycerophospholipid, there are diverse and numerous different lipid species. Lipids are heterogeneously distributed across the evolutionary tree with lipidomes evolving in parallel to organismal complexity. Moreover, lipids are different between organs and tissues and even within the same cell, different organelles have characteristic lipid signatures. At the molecular level, membranes are asymmetric and laterally heterogeneous. This lipid asymmetry at different scales indicates that these molecules may play very specific molecular functions in biology. Some of these roles have been recently uncovered: lipids have been shown to be essential in processes such as hypoxia and ferroptosis or in protein sorting and trafficking but many of them remain still unknown. In this review we will discuss the importance of understanding lipid diversity in biology across scales and we will share a toolbox with some of the emerging technologies that are helping us to uncover new lipid molecular functions in cell biology and, step by step, crack the membrane lipid code.
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Affiliation(s)
- Alejandro Melero
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Noemi Jiménez-Rojo
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain; Instituto Biofisika (UPV/EHU, CSIC), 48940, Leioa, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
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84
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Sartori AR, Radujević A, George SM, Anzenbacher P. Azacrown-calixpyrrole isosteres: receptors and sensors for anions. Chem Sci 2023; 14:7545-7552. [PMID: 37449063 PMCID: PMC10337727 DOI: 10.1039/d3sc01970e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Calix[4]pyrroles (CPs) and polyammonium azacrowns (ACs) are well-known receptors for anions. CPs bind anions by directional hydrogen bonds that do not always work well for aqueous analytes. The positive charge in polyammonium ACs allows for a stronger but non-directional anion-ammonium electrostatic attraction but lack selectivity. Bridging the gap between CPs and ACs could increase affinity and potentially preserve the selectivity of anion binding. We have synthesized a flexible calixpyrrole-azacrown near isosteric receptor and incorporated an environmentally sensitive dansyl fluorophore to enable fluorescence measurements. Anion binding was evaluated using NMR and fluorescence titrations. The isosteric receptor shows a strong affinity for aqueous phosphates and phosphonates (Na+ salts) in the order HAsO42- > H2PO4- > H2P2O72- > glyphosate2- > AMP- > methylphosphonate- ≫ ADP2- or ATP3- but does not bind halides. This is in stark contrast to CP which shows a strong preference for halides over oxyanions. The anion binding by the new receptor was accompanied by analyte-specific changes in fluorescence intensity and spectral width and by a wavelength shift. These parameters were used in qualitative and quantitative sensing of aqueous anions. By applying machine-learning algorithms, such as linear discriminant analysis and support vector machine linear regression, this one sensor can differentiate between 10 different analytes and accurately quantify herbicide glyphosate and methylphosphonate, a product of sarin, soman or cyclosarin hydrolysis. In fact, glyphosate can be quantified even in the presence of competing anions such as orthophosphate (LODs were ≤ 1 μM).
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Affiliation(s)
- Austin R Sartori
- Bowling Green State University, Center for Photochemical Sciences Bowling Green Ohio 43403 USA
| | - Aco Radujević
- Bowling Green State University, Center for Photochemical Sciences Bowling Green Ohio 43403 USA
| | - Sandra M George
- Bowling Green State University, Center for Photochemical Sciences Bowling Green Ohio 43403 USA
| | - Pavel Anzenbacher
- Bowling Green State University, Center for Photochemical Sciences Bowling Green Ohio 43403 USA
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85
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Hao HC, Zhang G, Sun R, Xu YJ, Ge JF. Multiple organelle-targeted 1,8-naphthyridine derivatives for detecting the polarity of organelles. J Mater Chem B 2023. [PMID: 37401500 DOI: 10.1039/d3tb00601h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Four 1,8-naphthyridine derivatives (1a-1d) with different organelle targeting abilities were obtained using the Knoevenagel condensation reaction of 1,8-naphthyridine with 4-(N,N-diethylamino)benzaldehyde (2a), 4-(N,N-diphenylamino)benzaldehyde (2b), 4-(piperazin-1-yl)benzaldehyde (2c) and 4-(ethyl(4-formylphenyl)amino)-N-(2-((4-methylphenyl)sulfonamido)ethyl)butanamide (2d), respectively. The maximal absorption bands of dyes 1a-1d were observed at 375-447 nm, while their maximum emission peaks were situated at 495-605 nm. The optical properties showed that the fluorescence emission of dyes 1a-1d is shifted toward greater wavelengths as the system polarity (Δf) increased. Meanwhile, with increasing polarity of the mixed 1,4-dioxane/H2O system, the fluorescence intensity of dyes 1a-1d gradually decreased. Furthermore, the fluorescence intensity of 1a-1d enhanced by 12-239 fold as the polarity of 1,4-dioxane/H2O mixtures declined. 1a-1d had a large Stokes shift (up to 229 nm) in polar solvents in comparison to nonpolar solvents. The colocalization imaging experiments demonstrated that dyes 1a-1d (3-10 μM) were located in mitochondria, lipid droplets, lysosomes and the endoplasmic reticulum in living HeLa cells, respectively; and they could monitor the polarity fluctuation of the corresponding organelles. Consequently, this work proposes a molecular design idea with different organelle targeting capabilities based on the same new fluorophore, and this molecular design idea may provide more alternatives for polarity-sensitive fluorescent probes with organelle targeting.
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Affiliation(s)
- Hao-Chi Hao
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, No. 199 Ren'Ai Road, Suzhou 215123, China.
| | - Gang Zhang
- School of Radiation Medicine and Protection, Medical College of Soochow University, Soochow University, Suzhou 215123, China
| | - Ru Sun
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, No. 199 Ren'Ai Road, Suzhou 215123, China.
| | - Yu-Jie Xu
- School of Radiation Medicine and Protection, Medical College of Soochow University, Soochow University, Suzhou 215123, China
| | - Jian-Feng Ge
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, No. 199 Ren'Ai Road, Suzhou 215123, China.
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou 215163, China
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86
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Zhan W, Gao G, Liu Z, Liu X, Xu L, Wang M, Xu HD, Tang R, Cao J, Sun X, Liang G. Enzymatic Self-Assembly of Adamantane-Peptide Conjugate for Combating Staphylococcus aureus Infection. Adv Healthc Mater 2023; 12:e2203283. [PMID: 36880480 DOI: 10.1002/adhm.202203283] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/28/2023] [Indexed: 03/08/2023]
Abstract
Staphylococcus aureus (S. aureus) remains a leading cause of bacterial infections. However, eradication of S. aureus infections with common antibiotics is increasingly difficult due to outbreaks of drug resistance. Therefore, new antibiotic classes and antibacterial strategies are urgently in demand. Herein, it is shown that an adamantane-peptide conjugate, upon dephosphorylation by alkaline phosphatase (ALP) constitutively expressed on S. aureus, generates fibrous assemblies in situ to combat S. aureus infection. By attaching adamantane to a phosphorylated tetrapeptide Nap-Phe-Phe-Lys-Tyr(H2 PO3 )-OH, the rationally designed adamantane-peptide conjugate Nap-Phe-Phe-Lys(Ada)-Tyr(H2 PO3 )-OH (Nap-FYp-Ada) is obtained. Upon bacterial ALP activation, Nap-FYp-Ada is dephosphorylated and self-assembles into nanofibers on the surface of S. aureus. As revealed by cell assays, the assemblies of adamantane-peptide conjugates interact with cell lipid membrane and thereby disrupt membrane integrity to kill S. aureus. Animal experiments further demonstrate the excellent potential of Nap-FYp-Ada in the treatment of S. aureus infection in vivo. This work provides an alternative approach to design antimicrobial agents.
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Affiliation(s)
- Wenjun Zhan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
| | - Ge Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
| | - Xiaoyang Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
| | - Lingling Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
| | - Manli Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
| | - Hai-Dong Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
| | - Runqun Tang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
| | - Jingyuan Cao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
| | - Xianbao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
| | - Gaolin Liang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, P. R. China
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87
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Polita A, Stancikaitė M, Žvirblis R, Maleckaitė K, Dodonova-Vaitkūnienė J, Tumkevičius S, Shivabalan AP, Valinčius G. Designing a green-emitting viscosity-sensitive 4,4-difluoro-4-bora-3a,4a-diaza- s-indacene (BODIPY) probe for plasma membrane viscosity imaging. RSC Adv 2023; 13:19257-19264. [PMID: 37377877 PMCID: PMC10291278 DOI: 10.1039/d3ra04126c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023] Open
Abstract
Viscosity is a key characteristic of lipid membranes - it governs the passive diffusion of solutes and affects the lipid raft formation and membrane fluidity. Precise determination of viscosity values in biological systems is of great interest and viscosity-sensitive fluorescent probes offer a convenient solution for this task. In this work we present a novel membrane-targeting and water-soluble viscosity probe BODIPY-PM, which is based on one of the most frequently used probes BODIPY-C10. Despite its regular use, BODIPY-C10 suffers from poor integration into liquid-ordered lipid phases and lack of water solubility. Here, we investigate the photophysical characteristics of BODIPY-PM and demonstrate that solvent polarity only slightly affects the viscosity-sensing qualities of BODIPY-PM. In addition, with fluorescence lifetime imaging microscopy (FLIM), we imaged microviscosity in complex biological systems - large unilamellar vesicles (LUVs), tethered bilayer membranes (tBLMs) and live lung cancer cells. Our study showcases that BODIPY-PM preferentially stains the plasma membranes of live cells, equally well partitions into both liquid-ordered and liquid-disordered phases and reliably distinguishes lipid phase separation in tBLMs and LUVs.
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Affiliation(s)
- Artūras Polita
- Institute of Biochemistry, Life Sciences Center, Vilnius University Saulėtekio Av. 7 Vilnius LT-10257 Lithuania
| | - Milda Stancikaitė
- Center of Physical Sciences and Technology Saulėtekio Av. 3 Vilnius LT-10257 Lithuania
| | - Rokas Žvirblis
- Life Sciences Center, Institute of Biotechnology, Vilnius University Saulėtekio Av. 7 Vilnius LT-10257 Lithuania
| | - Karolina Maleckaitė
- Center of Physical Sciences and Technology Saulėtekio Av. 3 Vilnius LT-10257 Lithuania
| | - Jelena Dodonova-Vaitkūnienė
- Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University Naugarduko St. 24 Vilnius LT-03225 Lithuania
| | - Sigitas Tumkevičius
- Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University Naugarduko St. 24 Vilnius LT-03225 Lithuania
| | - Arun Prabha Shivabalan
- Institute of Biochemistry, Life Sciences Center, Vilnius University Saulėtekio Av. 7 Vilnius LT-10257 Lithuania
| | - Gintaras Valinčius
- Institute of Biochemistry, Life Sciences Center, Vilnius University Saulėtekio Av. 7 Vilnius LT-10257 Lithuania
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88
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Abstract
A wide range of biomaterials and engineered cell surfaces are composed of bioconjugates embedded in liposome membranes, surface-immobilized bilayers, or the plasma membranes of living cells. This review article summarizes the various ways that Nature anchors integral and peripheral proteins in a cell membrane and describes the strategies devised by chemical biologists to label a membrane protein in living cells. Also discussed are modern synthetic and semisynthetic methods to produce lipidated proteins. Subsequent sections describe methods to anchor a three-component synthetic construct that is composed of a lipophilic membrane anchor, hydrophilic linker, and exposed functional component. The surface exposed payload can be a fluorophore, aptamer, oligonucleotide, polypeptide, peptide nucleic acid, polysaccharide, branched dendrimer, or linear polymer. Hydrocarbon chains are commonly used as the membrane anchor, and a general experimental trend is that a two chain lipid anchor has higher membrane affinity than a cholesteryl or single chain lipid anchor. Amphiphilic fluorescent dyes are effective molecular probes for cell membrane imaging and a zwitterionic linker between the fluorophore and the lipid anchor promotes high persistence in the plasma membrane of living cells. A relatively new advance is the development of switchable membrane anchors as molecular tools for fundamental studies or as technology platforms for applied biomaterials.
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Affiliation(s)
- Rananjaya S Gamage
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jordan L Chasteen
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
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89
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Frawley AT, Leslie KG, Wycisk V, Galiani S, Shrestha D, Eggeling C, Anderson HL. A Photoswitchable Solvatochromic Dye for Probing Membrane Ordering by RESOLFT Super-resolution Microscopy. Chemphyschem 2023; 24:e202300125. [PMID: 36946252 DOI: 10.1002/cphc.202300125] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/23/2023]
Abstract
A switchable solvatochromic fluorescent dyad can be used to map ordering of lipids in vesicle membranes at a resolution better than the diffraction limit. Combining a Nile Red fluorophore with a photochromic spironaphthoxazine quencher allows the fluorescence to be controlled using visible light, via photoswitching and FRET quenching. Synthetic lipid vesicles of varying composition were imaged with an average 2.5-fold resolution enhancement, compared to the confocal images. Ratiometric detection was used to probe the membrane polarity, and domains of different lipid ordering were distinguished within the same membrane.
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Affiliation(s)
- Andrew T Frawley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Kathryn G Leslie
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Virginia Wycisk
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Silvia Galiani
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Dilip Shrestha
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien-Platz 4, 07743, Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Strasse 9, 07745, Jena, Germany
- Jena Center for Soft Matter (JCSM), Philosophenweg 7, 07743, Jena, Germany
| | - Harry L Anderson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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90
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Zhang D, Chen Z, Du Z, Bao B, Su N, Chen X, Ge Y, Lin Q, Yang L, Hua Y, Wang S, Hua X, Zuo F, Li N, Liu R, Jiang L, Bao C, Zhao Y, Loscalzo J, Yang Y, Zhu L. Design of a palette of SNAP-tag mimics of fluorescent proteins and their use as cell reporters. Cell Discov 2023; 9:56. [PMID: 37311750 DOI: 10.1038/s41421-023-00546-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/18/2023] [Indexed: 06/15/2023] Open
Abstract
Naturally occurring fluorescent proteins (FPs) are the most widely used tools for tracking cellular proteins and sensing cellular events. Here, we chemically evolved the self-labeling SNAP-tag into a palette of SNAP-tag mimics of fluorescent proteins (SmFPs) that possess bright, rapidly inducible fluorescence ranging from cyan to infrared. SmFPs are integral chemical-genetic entities based on the same fluorogenic principle as FPs, i.e., induction of fluorescence of non-emitting molecular rotors by conformational locking. We demonstrate the usefulness of these SmFPs in real-time tracking of protein expression, degradation, binding interactions, trafficking, and assembly, and show that these optimally designed SmFPs outperform FPs like GFP in many important ways. We further show that the fluorescence of circularly permuted SmFPs is sensitive to the conformational changes of their fusion partners, and that these fusion partners can be used for the development of single SmFP-based genetically encoded calcium sensors for live cell imaging.
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Affiliation(s)
- Dasheng Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhengda Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zengmin Du
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Yihui Ge
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Lipeng Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yujie Hua
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xin Hua
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Fangting Zuo
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ningfeng Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Jiang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chunyan Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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91
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Perfilov MM, Zaitseva ER, Baleeva NS, Kublitski VS, Smirnov AY, Bogdanova YA, Krasnova SA, Myasnyanko IN, Mishin AS, Baranov MS. Meta-CF 3-Substituted Analogues of the GFP Chromophore with Remarkable Solvatochromism. Int J Mol Sci 2023; 24:9923. [PMID: 37373071 DOI: 10.3390/ijms24129923] [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: 05/18/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
In this work, we have shown that the introduction of a trifluoromethyl group into the me-ta-position of arylidene imidazolones (GFP chromophore core) leads to a dramatic increase in their fluorescence in nonpolar and aprotic media. The presence of a pronounced solvent-dependent gradation of fluorescence intensity makes it possible to use these substances as fluorescent polarity sensors. In particular, we showed that one of the created compounds could be used for selective labeling of the endoplasmic reticulum of living cells.
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Affiliation(s)
- Maxim M Perfilov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Elvira R Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Vadim S Kublitski
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, Moscow 121205, Russia
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Svetlana A Krasnova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
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92
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Real Hernandez LM, Levental I. Lipid packing is disrupted in copolymeric nanodiscs compared with intact membranes. Biophys J 2023; 122:2256-2266. [PMID: 36641625 PMCID: PMC10257115 DOI: 10.1016/j.bpj.2023.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/02/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Discoidal lipid-protein nanoparticles known as nanodiscs are widely used tools in structural and membrane biology. Amphipathic, synthetic copolymers have recently become an attractive alternative to membrane scaffold proteins for the formation of nanodiscs. Such copolymers can directly intercalate into, and form nanodiscs from, intact membranes without detergents. Although these copolymer nanodiscs can extract native membrane lipids, it remains unclear whether native membrane properties are also retained. To determine the extent to which bilayer lipid packing is retained in nanodiscs, we measured the behavior of packing-sensitive fluorescent dyes in various nanodisc preparations compared with intact lipid bilayers. We analyzed styrene-maleic acid (SMA), diisobutylene-maleic acid (DIBMA), and polymethacrylate (PMA) as nanodisc scaffolds at various copolymer-to-lipid ratios and temperatures. Measurements of Laurdan spectral shifts revealed that dimyristoyl-phosphatidylcholine (DMPC) nanodiscs had increased lipid headgroup packing compared with large unilamellar vesicles (LUVs) above the lipid melting temperature for all three copolymers. Similar effects were observed for DMPC nanodiscs stabilized by membrane scaffolding protein MSP1E1. Increased lipid headgroup packing was also observed when comparing nanodiscs with intact membranes composed of binary mixtures of 1-palmitoyl-2-oleoyl-phosphocholine (POPC) and di-palmitoyl-phosphocholine (DPPC), which show fluid-gel-phase coexistence. Similarly, Laurdan reported increased headgroup packing in nanodiscs for biomimetic mixtures containing cholesterol, most notable for relatively disordered membranes. The magnitudes of these ordering effects were not identical for the various copolymers, with SMA being the most and DIBMA being the least perturbing. Finally, nanodiscs derived from mammalian cell membranes showed similarly increased lipid headgroup packing. We conclude that nanodiscs generally do not completely retain the physical properties of intact membranes.
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Affiliation(s)
- Luis M Real Hernandez
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia.
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93
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MacKeigan TP, Morgan ML, Stys PK. Quantitation of Tissue Amyloid via Fluorescence Spectroscopy Using Controlled Concentrations of Thioflavin-S. Molecules 2023; 28:molecules28114483. [PMID: 37298959 DOI: 10.3390/molecules28114483] [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: 05/04/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Amyloids are misfolded proteins that aggregate into fibrillar structures, the accumulation of which is associated with the pathogenesis of many neurodegenerative diseases, such as Alzheimer's disease (AD). Early, sensitive detection of these misfolded aggregates is of great interest to the field, as amyloid deposition begins well before the presentation of clinical symptoms. Thioflavin-S (ThS) is a fluorescent probe commonly used to detect amyloid pathology. Protocols for ThS staining vary, but they often use high staining concentrations followed by differentiation, which causes varying levels of non-specific staining and potentially leaves more subtle amyloid deposition unidentified. In this study, we developed an optimized ThS staining protocol for the sensitive detection of β-amyloids in the widely used 5xFAD Alzheimer's mouse model. Controlled dye concentrations together with fluorescence spectroscopy and advanced analytical methods enabled not only the visualization of plaque pathology, but also the detection of subtle and widespread protein misfolding throughout the 5xFAD white matter and greater parenchyma. Together, these findings demonstrate the efficacy of a controlled ThS staining protocol and highlight the potential use of ThS for the detection of protein misfolding that precedes clinical manifestation of disease.
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Affiliation(s)
- Tatiana P MacKeigan
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Megan L Morgan
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Peter K Stys
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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94
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Pelletier R, Danylchuk DI, Benaissa H, Broch F, Vauchelles R, Gautier A, Klymchenko AS. Genetic Targeting of Solvatochromic Dyes for Probing Nanoscale Environments of Proteins in Organelles. Anal Chem 2023. [PMID: 37229557 DOI: 10.1021/acs.analchem.3c00515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A variety of protein tags are available for genetically encoded protein labeling, which allow their precise localization and tracking inside the cells. A new dimension in protein imaging can be offered by combining protein tags with polarity-sensitive fluorescent probes, which provide information about local nanoscale environments of target proteins within the subcellular compartments (organelles). Here, we designed three fluorescent probes based on solvatochromic nile red dye, conjugated to a HaloTag reactive targeting group through polyethylene glycol linkers of varying lengths. The probe with medium linker length, NR12-Halo, was found to label specifically a large variety of proteins localized in defined cell compartments, such as plasma membranes (outer and inner leaflets), endoplasmic reticulum, Golgi apparatus, cytosol, microtubules, actin, and chromatin. Owing to its polarity-sensitive fluorophore, the probe clearly distinguished the proteins localized within apolar lipid membranes from other proteins. Moreover, it revealed dramatic changes in the environment during the life cycle of proteins from biosynthesis to their expected localization and, finally, to recycling inside lysosomes. Heterogeneity in the local polarity of some membrane proteins also suggested a formation of low-polar protein aggregates, for example, within cell-cell contacts. The approach also showed that mechanical stress (cell shrinking by osmotic shock) induced a general polarity decrease in membrane proteins, probably due to the condensation of biomolecules. Finally, the nanoenvironment of some membrane proteins was affected by a polyunsaturated fatty acid diet, which provided the bridge between organization of lipids and proteins. The developed solvatochromic HaloTag probe constitutes a promising tool for probing nanoscale environments of proteins and their interactions within subcellular structures.
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Affiliation(s)
- Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Hela Benaissa
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Fanny Broch
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Romain Vauchelles
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
| | - Arnaud Gautier
- CNRS, Laboratoire des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, Université PSL, Paris 75005 France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Strasbourg, Illkirch 67401, France
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95
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Liang Y, Willey S, Chung YC, Lo YM, Miao S, Rundell S, Tu LC, Bong D. Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA. Nat Commun 2023; 14:2987. [PMID: 37225690 DOI: 10.1038/s41467-023-38579-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
The most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sydney Willey
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Yu-Chieh Chung
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Yi-Meng Lo
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Li-Chun Tu
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
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96
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Sarkar A, Namboodiri V, Kumbhakar M. Single-Molecule Orientation Imaging Reveals Two Distinct Binding Configurations on Amyloid Fibrils. J Phys Chem Lett 2023:4990-4996. [PMID: 37220418 DOI: 10.1021/acs.jpclett.3c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Fluorescence readouts for an amyloid fibril sensor critically depend on its molecular interaction and local environment offered by the available structural motifs. Here we employ polarized points accumulation for imaging in nanoscale topography with intramolecular charge transfer probes transiently bound to amyloid fibrils to investigate the organization of fibril nanostructures and probe binding configurations. Besides the in-plane (θ ≈ 90°) mode for binding on the fibril surface parallel to the long fibril axis, we also observed a sizable population of over 60% out-of-plane (θ < 60°) dipoles for rotor probes experiencing a varying degree of orientational mobility. Highly confined dipoles exhibiting an out-of-plane configuration probably reflect tightly bound dipoles in the inner channel grooves, while the weakly bound ones on amyloid enjoy rotational flexibility. Our observation of an out-of-plane binding mode emphasizes the pivotal role played by the electron donor amino group toward fluorescence detection and hence the emergence of anchored probes alongside conventional groove binders.
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Affiliation(s)
- Aranyak Sarkar
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Vinu Namboodiri
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
| | - Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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97
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Fu J, Hu X, Guo T, Zhu W, Tian J, Liu M, Zhang X, Wei Y. A dual-function probe with aggregation-induced emission feature for Cu 2+ detection and chemodynamic therapy. Chem Commun (Camb) 2023; 59:6738-6741. [PMID: 37194318 DOI: 10.1039/d2cc06350f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Herein, a fluorescent probe (named TPACP) with aggregation-induced emission (AIE) feature was developed and utilized for the selective detection of Cu2+ with high sensitivity and fast-response. The resultant TPACP@Cu2+ complexes from coordination of TPACP with Cu2+ can also be potentially applied for chemodynamic and photodynamic therapy.
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Affiliation(s)
- Juan Fu
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China.
| | - Xin Hu
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China.
| | - Teng Guo
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China.
| | - Weifeng Zhu
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, China
| | - Jianwen Tian
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China.
| | - Meiying Liu
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China.
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, China
| | - Xiaoyong Zhang
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China.
| | - Yen Wei
- Department of Chemistry and the Tsinghua Center for Frontier Polymer Research, Tsinghua University, Beijing, 100084, P. R. China.
- Department of Chemistry and Center for Nanotechnology and Institute of Biomedical Technology, Chung-Yuan Christian University, Chung-Li 32023, Taiwan
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98
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Al-Marzooq F, Ghazawi A, Daoud L, Tariq S. Boosting the Antibacterial Activity of Azithromycin on Multidrug-Resistant Escherichia coli by Efflux Pump Inhibition Coupled with Outer Membrane Permeabilization Induced by Phenylalanine-Arginine β-Naphthylamide. Int J Mol Sci 2023; 24:ijms24108662. [PMID: 37240007 DOI: 10.3390/ijms24108662] [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: 04/20/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
The global spread of multidrug-resistant (MDR) bacteria increases the demand for the discovery of new antibiotics and adjuvants. Phenylalanine-arginine β-naphthylamide (PAβN) is an inhibitor of efflux pumps in Gram-negative bacteria, such as the AcrAB-TolC complex in Escherichia coli. We aimed to explore the synergistic effect and mechanism of action of PAβN combined with azithromycin (AZT) on a group of MDR E. coli strains. Antibiotic susceptibility was tested for 56 strains, which were screened for macrolide resistance genes. Then, 29 strains were tested for synergy using the checkerboard assay. PAβN significantly enhanced AZT activity in a dose-dependent manner in strains expressing the mphA gene and encoding macrolide phosphotransferase, but not in strains carrying the ermB gene and encoding macrolide methylase. Early bacterial killing (6 h) was observed in a colistin-resistant strain with the mcr-1 gene, leading to lipid remodeling, which caused outer membrane (OM) permeability defects. Clear OM damage was revealed by transmission electron microscopy in bacteria exposed to high doses of PAβN. Increased OM permeability was also proven by fluorometric assays, confirming the action of PAβN on OM. PAβN maintained its activity as an efflux pump inhibitor at low doses without permeabilizing OM. A non-significant increase in acrA, acrB, and tolC expression in response to prolonged exposure to PAβN was noted in cells treated with PAβN alone or with AZT, as a reflection of bacterial attempts to counteract pump inhibition. Thus, PAβN was found to be effective in potentiating the antibacterial activity of AZT on E. coli through dose-dependent action. This warrants further investigations of its effect combined with other antibiotics on multiple Gram-negative bacterial species. Synergetic combinations will help in the battle against MDR pathogens, adding new tools to the arsenal of existing medications.
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Affiliation(s)
- Farah Al-Marzooq
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Lana Daoud
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Saeed Tariq
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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99
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Chen Y, Li A, Li X, Tu L, Xie Y, Xu S, Li Z. Multi-Stimuli-Responsive Amphiphilic Pyridinium Salt and Its Application in the Visualization of Level 3 Details in Latent Fingerprints. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211917. [PMID: 36870363 DOI: 10.1002/adma.202211917] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/16/2023] [Indexed: 05/19/2023]
Abstract
Organic luminescent materials that can simultaneously achieve multimode mechanochromism and its water-vapor-induced recovery are desirable for practical applications but rarely reported. Herein, an amphiphilic compound, 4-(9H-carbazol-9-yl)-1-(2-hydroxyethyl)pyridin-1-ium bromide (CPAB), is designed by integrating a lipophilic aromatic unit and hydrophilic end in the molecular architecture. Self-recovered mechanochromism from brown to cyan is observed upon mechanical grinding in air. Comprehensive research by X-ray diffraction, infrared spectroscopy, and single-crystal analysis reveals that the photoluminescence switch originates from the variation in intermolecular hydrogen bonds and molecular packing mode. The amphiphilic nature of CPAB allows water molecules to enter the crystalline lattice, forming two polymorphs of the crystalline phase, namely CPAB-D and CPAB-W. The hydrosoluble CPAB exhibits excellent capability in probing the level 3 details of fingerprints because its lipophilic part can target the fatty acid residues of fingerprints, leading to strong aggregation-induced fluorescence. The research may inspire the design of latent fingerprint developers and application in forensics/anti-counterfeiting.
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Affiliation(s)
- Yi Chen
- Institute of Molecular Aggregation Science, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Tianjin University, Tianjin, 300072, P. R. China
| | - Aisen Li
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou, 350207, P. R. China
| | - Xiaoning Li
- Institute of Molecular Aggregation Science, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Tianjin University, Tianjin, 300072, P. R. China
| | - Liangjing Tu
- Institute of Molecular Aggregation Science, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Tianjin University, Tianjin, 300072, P. R. China
| | - Yujun Xie
- Institute of Molecular Aggregation Science, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Tianjin University, Tianjin, 300072, P. R. China
| | - Shuping Xu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Zhen Li
- Institute of Molecular Aggregation Science, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Tianjin University, Tianjin, 300072, P. R. China
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou, 350207, P. R. China
- Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
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100
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Lang XX, Sun SH, Cao HW, Chen YS, Li HY, Wang MQ. An environmentally insensitive fluorescent probe for G4 DNA detection: Design, synthesis, and mechanism studies. Anal Chim Acta 2023; 1252:341074. [PMID: 36935132 DOI: 10.1016/j.aca.2023.341074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/11/2023]
Abstract
G4 DNA structure highly localized to functionally important sites within the human genome, has been identified as a biomarker for regulation of multiple biological processes. Identification G4-responsive fluorescence probes has broad application prospects for addressing G4 biological functions, as well as developing of new families of anticancer drugs. However, some currently designed G4 DNA probes may suffer from serious solvent-dependent effect, and cause unspecific fluorescence that masks the specific signal from G4 DNA. Herein, with a bulky imidazole-cored molecular rotor fusing in D-A building block of carbazole-pyridinium, we constructed a new probe ACPS. This new probe with desirable environmentally insensitive property exhibited a "fluorescence-off" state in various polarity solvents. In the presence of G4 DNA, the intra-molecular rotations would be restricted, triggering intense fluorescence enhancement. Especially, probe ACPS bound to G4 DNA structures with superior selectivity, exhibiting much weaker fluorescence response in the presence of non-G4 DNA structures. This probe was also able to realize fluorescence visualization in cell imaging. Collectively, the probe design strategy eliminates the background fluorescence caused by uncontrollable environmental polarity change, thereby achieving high-fidelity sensing G4 DNA structures in complicated systems.
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Affiliation(s)
- Xue-Xian Lang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Shu-Hui Sun
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Hao-Wen Cao
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Yan-Song Chen
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Hong-Yao Li
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Ming-Qi Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China.
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