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Sevinçli ZŞ, Amudi K, Öncel BC, Yurtcu E, İşeri ÖD, Menges N. Selective RNA binding and imaging with imidazopyrazine-based fluorescent molecule. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2025; 340:126382. [PMID: 40373550 DOI: 10.1016/j.saa.2025.126382] [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: 03/15/2025] [Revised: 05/08/2025] [Accepted: 05/09/2025] [Indexed: 05/17/2025]
Abstract
We report the synthesis and characterization of novel imidazopyrazine-based fluorescent molecules 5a and 5b targeting RNA and DNA binding. Molecule 5b showed superior photophysical properties with stable fluorescence and high quantum yield in various solvents. UV-Vis and fluorescence spectroscopy revealed strong RNA binding with time-dependent fluorescence quenching and increasing absorbance, suggesting groove binding or π-π stacking interactions. Furthermore, agarose gel electrophoresis further confirmed selective RNA binding of 5b. Imaging studies demonstrated that 5b penetrated into viable MCF-7 cells and selectively stained RNA and retained fluorescence for up to 8 h under ambient conditions. These findings advance the study of RNA dynamics in living cells, highlighting the potential of 5b for RNA-specific bioimaging and sensing applications.
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Affiliation(s)
- Zekiye Şeyma Sevinçli
- Pharmaceutical Chemistry Section, Faculty of Pharmacy, Van Yuzuncu Yil University, Van 65100, Turkiye
| | - Karina Amudi
- Science and Technology Research and Application Center (BITAM), Necmettin Erbakan University, Konya 42090, Turkiye
| | - Buse Ceyda Öncel
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Başkent University, Ankara 06790, Turkiye
| | - Erkan Yurtcu
- Medical Biology Department, School of Medicine, Kırıkkale University, Kırıkkale 71451, Turkiye
| | - Özlem Darcansoy İşeri
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Başkent University, Ankara 06790, Turkiye
| | - Nurettin Menges
- Science and Technology Research and Application Center (BITAM), Necmettin Erbakan University, Konya 42090, Turkiye; Biomedical Engineering Section, Faculty of Engineering, Necmettin Erbakan University, Konya 42090, Turkiye.
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2
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Xu N, Qiao Q, Wang C, Zhou W, Bao P, Li J, Wu S, Liu X, Xu Z. Bright and Versatile Azetidinecarboxamide-Based Fluorophore-Ligand Conjugates for High-Resolution Cell Imaging. Angew Chem Int Ed Engl 2025; 64:e202505579. [PMID: 40166893 DOI: 10.1002/anie.202505579] [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: 03/10/2025] [Revised: 03/28/2025] [Accepted: 04/01/2025] [Indexed: 04/02/2025]
Abstract
Fluorophore-ligand conjugates play a pivotal role in cellular imaging, providing high target specificity. However, simultaneously achieving conjugates with high brightness and ligand-targeting diversity presents significant challenges. Traditional strategies often require complex, multistep modifications for fluorophore enhancement and ligand conjugation. Here, we present an azetidinecarboxamide strategy that addresses these challenges by integrating brightness enhancement and ligand conjugation capabilities within a single molecular framework. The azetidinecarboxamide core suppresses twisted intramolecular charge transfer (TICT), thereby enhancing fluorescence quantum yield. Its carbonyl group provides a versatile site for conjugating a wide range of targeting ligands, enabling the rapid development of diverse and tunable fluorophore-ligand conjugates. This streamlined approach reduces synthetic complexity, accelerates probe development, and is compatible with a wide variety of fluorophores, such as coumarin, naphthalimide, NBD, rhodol, rhodamine, and silicon-rhodamine, facilitating the creation of high-performance, multifunctional probes for advanced cellular imaging.
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Affiliation(s)
- Ning Xu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Qinglong Qiao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Chao Wang
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
- State Key Laboratory of Fine Chemicals, College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518055, China
| | - Wei Zhou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Pengjun Bao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Jin Li
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Shaowei Wu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Zhaochao Xu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
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3
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Ma H, Ni WP, Lin Q, Sun R, Ge JF. Near-infrared fluorescent probes based on naphthyridine derivatives for mitochondrial nucleic acid imaging. Analyst 2025; 150:642-649. [PMID: 39829413 DOI: 10.1039/d4an01450b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Most current nucleic acid-responsive fluorescent probes are enhanced ones with short emission wavelengths. Therefore, the development of novel near-infrared, turn-on response nucleic acid fluorescent probes is of great significance. Herein, three cationic fluorescent dyes 1a-1c were synthesized by reacting naphthalidine salt with suitable aldehydes. These probes exhibited excellent photostability, maintaining over 95% of their absorption rate after 5 h of irradiation. Notably, probes 1a-1c exhibited an OFF-ON fluorescence response to DNA and RNA. The maximum emission wavelength could reach the near-infrared region (661-762 nm), with large Stokes shifts (153-222 nm) upon binding to DNA/RNA. The fluorescence intensity was enhanced 143 fold and 127 fold for 1b upon interaction with DNA and RNA, respectively. Co-staining and nucleic acid digestion assays showed that probes 1a-1c could target the mitochondria of fixed cells with low cytotoxicity. These findings may be useful for the early screening of genetic mutations related to mitochondrial diseases.
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Affiliation(s)
- Huan Ma
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
| | - Wen-Pei Ni
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
| | - Qi Lin
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
| | - Ru Sun
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
| | - Jian-Feng Ge
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 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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4
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Sopić M, Vladimirov S, Munjas J, Mitić T, Hall IF, Jusic A, Ruzic D, Devaux Y. Targeting noncoding RNAs to treat atherosclerosis. Br J Pharmacol 2025; 182:220-245. [PMID: 38720437 DOI: 10.1111/bph.16412] [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: 10/26/2023] [Revised: 03/06/2024] [Accepted: 04/05/2024] [Indexed: 12/13/2024] Open
Abstract
Noncoding RNAs (ncRNAs) are pivotal for various pathological processes, impacting disease progression. The potential for leveraging ncRNAs to prevent or treat atherosclerosis and associated cardiovascular diseases is of great significance, especially given the increasing prevalence of atherosclerosis in an ageing and sedentary population. Together, these diseases impose a substantial socio-economic burden, demanding innovative therapeutic solutions. This review explores the potential of ncRNAs in atherosclerosis treatment. We commence by examining approaches for identifying and characterizing atherosclerosis-associated ncRNAs. We then delve into the functional aspects of ncRNAs in atherosclerosis development and progression. Additionally, we review current RNA and RNA-targeting molecules in development or under approval for clinical use, offering insights into their pharmacological potential. The importance of improved ncRNA delivery strategies is highlighted. Finally, we suggest avenues for advanced research to accelerate the use of ncRNAs in treating atherosclerosis and mitigating its societal impact. LINKED ARTICLES: This article is part of a themed issue Non-coding RNA Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v182.2/issuetoc.
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Affiliation(s)
- Miron Sopić
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Sandra Vladimirov
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Jelena Munjas
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Tijana Mitić
- BHF/University Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ignacio Fernando Hall
- BHF/University Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Amela Jusic
- HAYA Therapeutics SA, SuperLab Suisse - Bâtiment Serine, Lausanne, Vaud, Switzerland
| | - Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Luxembourg, Luxembourg
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5
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Suzuki M, Sato Y, Nishizawa S. Benzo[c,d]Indole-Quinoline-Based Deep-Red Emissive Probes for Live-Cell Imaging of Nucleolar RNA. Methods Mol Biol 2025; 2875:111-123. [PMID: 39535644 DOI: 10.1007/978-1-0716-4248-1_10] [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] [Indexed: 11/16/2024]
Abstract
Small molecular weight fluorescent probes capable of binding to RNAs have been powerful tools for understanding the intracellular behaviors of RNAs. In this chapter, we describe the fluorescence imaging of nucleolar RNA in living cells using deep-red emissive probes with benzo[c,d]indole-quinoline (BIQ) monomethine cyanine scaffolds. These probes feature a significant fluorescence "off-on" ability upon binding to RNAs (>100-fold) in the deep-red spectral region (λem > 650 nm). In addition, they have many advantages for fluorescence sensing of RNAs and nucleolar RNA imaging, such as longer emission wavelength, higher photostability, and better counterstaining compatibility for live cell imaging, compared to a commercially available RNA-binding probe, SYTO RNA select.
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Affiliation(s)
- Michiyuki Suzuki
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan.
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Rubio V, McInchak N, Fernandez G, Benavides D, Herrera D, Jimenez C, Mesa H, Meade J, Zhang Q, Stawikowski MJ. Development and characterization of fluorescent cholesteryl probes with enhanced solvatochromic and pH-sensitive properties for live-cell imaging. Sci Rep 2024; 14:30777. [PMID: 39730504 DOI: 10.1038/s41598-024-80958-2] [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: 08/19/2024] [Accepted: 11/22/2024] [Indexed: 12/29/2024] Open
Abstract
We present novel fluorescent cholesteryl probes (CNDs) with a modular design based on the solvatochromic 1,8-phthalimide scaffold. We have explored how different modules-linkers and head groups-affect the ability of these probes to integrate into lipid membranes and how they distribute intracellularly in mouse astrocytes and fibroblasts targeting lysosomes and lipid droplets. Each compound was assessed for its solvatochromic behavior in organic solvents and model membranes. Molecular dynamics simulations and lipid partitioning using giant unilamellar vesicles showed how these analogs behave in model membranes compared to cholesterol. Live-cell imaging demonstrated distinct staining patterns and cellular uptake behaviors, further validating the utility of these probes in biological systems. We compared the empirical results with those of BODIPY-cholesterol, a well-regarded fluorescent cholesterol analog. The internalization efficiency of fluorescent CND probes varies in different cell types and is affected mainly by the head groups. Our results demonstrate that the modular design significantly simplifies the creation of fluorescent cholesteryl probes bearing distinct spectral, biophysical, and cellular targeting features. It is a valuable toolkit for imaging in live cells, measuring cellular membrane dynamics, and studying cholesterol-related processes.
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Affiliation(s)
- Vicente Rubio
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA
| | - Nicholas McInchak
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA
| | - Genesis Fernandez
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA
| | - Dana Benavides
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA
| | - Diana Herrera
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA
| | - Catherine Jimenez
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA
| | - Haylee Mesa
- Stiles-Nicholson Brain Institute, Florida Atlantic University, 5353 Parkside Dr, Jupiter, FL, 33458, USA
| | - Jonathan Meade
- Stiles-Nicholson Brain Institute, Florida Atlantic University, 5353 Parkside Dr, Jupiter, FL, 33458, USA
| | - Qi Zhang
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA
- Stiles-Nicholson Brain Institute, Florida Atlantic University, 5353 Parkside Dr, Jupiter, FL, 33458, USA
| | - Maciej J Stawikowski
- Department of Chemistry and Biochemistry, Charles E. Schmidt College of Science, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA.
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7
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Xie Z, Zhao Z, Zhang J, Li Z, Meng L, Zhang Y, Zhang J, Deng X, Hong C, Sun S. Real-Time Fluorescence Visualization of the Dynamic Distribution of Zn 2+ Ions during Osteoblast Differentiation. Anal Chem 2024; 96:17730-17738. [PMID: 39445477 DOI: 10.1021/acs.analchem.4c03996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
The differentiation and maturation of osteoblasts are essential for bone formation. Zn2+ plays a crucial role in cell differentiation and is involved in osteogenic differentiation. The concentration and distribution of Zn2+ in the nucleus and cytoplasm indicate the differentiation states of osteoblasts. However, there is an absence of a real-time method for monitoring the dynamic fluctuations of endogenous Zn2+ within the nucleus. Here, a novel Zn2+ fluorescent probe (NTAD-N1) with nuclear membrane permeability was designed and developed, allowing for distribution throughout the entire cell, including the nucleus. The NTAD-N1 probe successfully showed the dynamic distribution and concentration changes of Zn2+ in the nucleus and cytoplasm of preosteoblast MC3T3-E1 during the 21-day differentiation period. The results showed that free Zn2+ increased significantly during differentiation of osteoblasts (2-21 days). Importantly, after 4 days of differentiation, osteoblasts are mainly distributed in the nucleus, which is confirmed by metallothionein expression. Subsequently, the level of free Zn2+ in the cytoplasm remained at a high level, which promoted the increase in alkaline phosphatase activity and inhibited the activity of cis-aconitase in the tricarboxylic acid cycle, resulting in the accumulation of citric acid. This series of events promotes the formation of mineralized nodules. In the process of osteoblast differentiation, the detection time of Zn2+ (≤7 days) is ahead of the late marker of alkaline phosphatase (14 days) and mineralized nodules (14-21 days). This indicates that Zn2+ can be used as a biomarker and an intervention point for early differentiation of osteoblasts.
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Affiliation(s)
- Zhenzhen Xie
- Key Laboratory of Xinjiang Phytomedicine Resources of Ministry of Education, School of Pharmacy/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832002, China
| | - Zhihao Zhao
- Key Laboratory of Xinjiang Phytomedicine Resources of Ministry of Education, School of Pharmacy/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832002, China
| | - Jiaru Zhang
- Key Laboratory of Xinjiang Phytomedicine Resources of Ministry of Education, School of Pharmacy/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832002, China
| | - Zuoping Li
- Key Laboratory of Xinjiang Phytomedicine Resources of Ministry of Education, School of Pharmacy/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832002, China
| | - Lanxin Meng
- Key Laboratory of Xinjiang Phytomedicine Resources of Ministry of Education, School of Pharmacy/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832002, China
| | - Yuling Zhang
- Key Laboratory of Xinjiang Phytomedicine Resources of Ministry of Education, School of Pharmacy/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832002, China
| | - Jing Zhang
- School of Medicine, Xinjiang University of Science&Technology, Korla 841000, China
| | - Xiling Deng
- Key Laboratory of Xinjiang Phytomedicine Resources of Ministry of Education, School of Pharmacy/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832002, China
| | - Chenglin Hong
- Key Laboratory of Xinjiang Phytomedicine Resources of Ministry of Education, School of Pharmacy/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832002, China
| | - Shiguo Sun
- Key Laboratory of Xinjiang Phytomedicine Resources of Ministry of Education, School of Pharmacy/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832002, China
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, China
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8
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Pfeiffer P, Nilsson J, Gallud A, Baladi T, Le HN, Bood M, Lemurell M, Dahlén A, Grøtli M, Esbjörner E, Wilhelmsson L. Metabolic RNA labeling in non-engineered cells following spontaneous uptake of fluorescent nucleoside phosphate analogues. Nucleic Acids Res 2024; 52:10102-10118. [PMID: 39162218 PMCID: PMC11417403 DOI: 10.1093/nar/gkae722] [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] [Received: 05/16/2023] [Revised: 07/04/2024] [Accepted: 08/07/2024] [Indexed: 08/21/2024] Open
Abstract
RNA and its building blocks play central roles in biology and have become increasingly important as therapeutic agents and targets. Hence, probing and understanding their dynamics in cells is important. Fluorescence microscopy offers live-cell spatiotemporal monitoring but requires labels. We present two fluorescent adenine analogue nucleoside phosphates which show spontaneous uptake and accumulation in cultured human cells, likely via nucleoside transporters, and show their potential utilization as cellular RNA labels. Upon uptake, one nucleotide analogue, 2CNqAXP, localizes to the cytosol and the nucleus. We show that it could then be incorporated into de novo synthesized cellular RNA, i.e. it was possible to achieve metabolic fluorescence RNA labeling without using genetic engineering to enhance incorporation, uptake-promoting strategies, or post-labeling through bio-orthogonal chemistries. By contrast, another nucleotide analogue, pAXP, only accumulated outside of the nucleus and was rapidly excreted. Consequently, this analogue did not incorporate into RNA. This difference in subcellular accumulation and retention results from a minor change in nucleobase chemical structure. This demonstrates the importance of careful design of nucleoside-based drugs, e.g. antivirals to direct their subcellular localization, and shows the potential of fine-tuning fluorescent base analogue structures to enhance the understanding of the function of such drugs.
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Affiliation(s)
- Pauline Pfeiffer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- LanteRNA (Stealth Labels Biotech AB), c/o Chalmers Ventures AB, Vera Sandbergs allé 8, SE-41296 Gothenburg, Sweden
| | - Audrey Gallud
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-43181 Gothenburg, Sweden
| | - Tom Baladi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Hoang-Ngoan Le
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mattias Bood
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, P.O. Box 462, SE-40530 Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, P.O. Box 462, SE-40530 Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296 Gothenburg, Sweden
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9
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Jiang Y, Huang S, Ma H, Weng J, Du X, Lin Z, Kim J, You W, Zhang H, Wang D, Kim JS, Sun H. RNA-Activatable Near-Infrared Photosensitizer for Cancer Therapy. J Am Chem Soc 2024; 146:25270-25281. [PMID: 39215718 DOI: 10.1021/jacs.4c09470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Photodynamic therapy (PDT) has recently come to the forefront as an exceptionally powerful and promising method for the treatment of cancer. Existing photosensitizers are predominantly engineered to target diverse biomolecules, including proteins, DNA, lipids, and carbohydrates, and have proven to greatly enhance the efficacy or specificity of PDT. However, it is noteworthy that there exists a conspicuous scarcity of photosensitizers specifically designed to target RNAs. Recognizing the crucial and multifaceted roles played by RNAs in various cellular processes and disease states, we have ventured into the development of a novel RNA-targeting photosensitizer, named Se-718, designed specifically for PDT-based cancer therapy. Se-718 has been engineered to exhibit a high molar absorption coefficient in the NIR region, which is crucial for effective PDT. More importantly, Se-718 has demonstrated a distinct RNA-targeting capability, as evidenced through rigorous testing in both circular dichroism and fluorescence experiments. Furthermore, Se-718 has been shown to display both type I and type II photodynamic properties. This unique characteristic enables the efficient killing of cancer cells under a wide range of oxygen conditions, both normoxic (21% O2) and hypoxic (2% O2). The IC50 of Se-718 can be as low as 100 nM, and its light-to-dark toxicity ratio is an impressive 215 times higher, outperforming most photosensitizers currently available. Moreover, in vivo studies conducted with tumor-bearing mice have demonstrated the excellent antitumor effects and high safety profile of Se-718. Considering the outstanding PDT efficacy of Se-718, we are optimistic that the development of RNA-targeting photosensitizers may provide an innovative and highly effective option for cancer therapeutics in the near future.
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Affiliation(s)
- Yin Jiang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Shumei Huang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon ,Hong Kong999077, China
| | - Haiying Ma
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong510000, China
| | - Jintao Weng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaomeng Du
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Zhenxin Lin
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Jaewon Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Wenhui You
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Huatang Zhang
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
- Guangdong Laboratory of Chemistry and Fine Chemical Industry Jieyang Center, Jieyang ,Guangdong522000,China
| | - Dongqing Wang
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon ,Hong Kong999077, China
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon ,Hong Kong999077, China
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10
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Deng T, Shao J, Xie Z, Wang Q, Huang X, Zhou Z, Guo J, Li L, Liu F. Triphenylphosphine-bonded coumaranone dyes realize dual color imaging of mitochondria and nucleoli. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 317:124434. [PMID: 38735113 DOI: 10.1016/j.saa.2024.124434] [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: 03/28/2024] [Revised: 04/16/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Probing intracellular organelles with fluorescent dyes offers opportunities to understand the structures and functions of these cellular compartments, which is attracting increasing interests. Normally, the design principle varies for different organelle targets as they possess distinct structural and functional profiles against each other. Therefore, developing a probe with dual intracellular targets is of great challenge. In this work, a new sort of donor-π-bridge-acceptor (D-π-A) type coumaranone dyes (CMO-1/2/3/4) have been prepared. Four fluorescent probes (TPP@CMO-1/2/3/4) were then synthesized by linking these coumaranone dyes with an amphiphilic cation triphenylphosphonium (TPP). Interestingly, both TPP@CMO-1 and TPP@CMO-2 exhibited dual color emission upon targeting to two different organelles, respectively. The green emission is well localized in mitochondria, while, the red emission realizes nucleoli imaging. RNA is the target of TPP@CMOs, which was confirmed by spectroscopic analysis and computational calculation. More importantly, the number and morphology changes of nucleoli under drug stress have been successfully evaluated using TPP@CMO-1.
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Affiliation(s)
- Tao Deng
- Artemisinin Research Center, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China; School of Medicine, Foshan University, Foshan 528000, China
| | - Jinjin Shao
- Artemisinin Research Center, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Zhongguo Xie
- Artemisinin Research Center, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Qiling Wang
- Artemisinin Research Center, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xinxin Huang
- Artemisinin Research Center, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510120, China
| | - Jialiang Guo
- School of Medicine, Foshan University, Foshan 528000, China
| | - Lei Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China.
| | - Fang Liu
- Artemisinin Research Center, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
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11
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Hirata Y, Takemori H, Furuta K, Kamatari YO, Sawada M. Ferroptosis induces nucleolar stress as revealed by live-cell imaging using thioflavin T. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2024; 7:100196. [PMID: 39077682 PMCID: PMC11284673 DOI: 10.1016/j.crphar.2024.100196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/12/2024] [Accepted: 07/07/2024] [Indexed: 07/31/2024] Open
Abstract
Nucleolar stress induced by stressors like hypoxia, UV irradiation, and heat shock downregulates ribosomal RNA transcription, thereby impairing protein synthesis capacity and potentially contributing to cell senescence and various human diseases such as neurodegenerative disorders and cancer. Live-cell imaging of the nucleolus may be a feasible strategy for investigating nucleolar stress, but currently available nucleolar stains are limited for this application. In this study using mouse hippocampal HT22 cells, we demonstrate that thioflavin T (ThT), a benzothiazole dye that binds RNA with high affinity, is useful for nucleolar imaging in cells where RNAs predominate over protein aggregates. Nucleoli were stained with high intensity simply by adding ThT to the cell culture medium, making it suitable for use even in damaged cells. Further, ThT staining overlapped with specific nucleolar stains in both live and fixed cells, but did not overlap with markers for mitochondria, lysosomes, endoplasmic reticulum, and double-stranded DNA. Ferroptosis, an iron-dependent nonapoptotic cell death pathway characterized by lipid peroxide accumulation, reduced the number of ThT-positive puncta while endoplasmic reticulum stress did not. These findings suggest that ferroptosis is associated with oxidative damage to nucleolar RNA molecules and ensuing loss of nucleolar function.
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Affiliation(s)
- Yoko Hirata
- Life Science Research Center, Institute for Advanced Study, Gifu University, Gifu, 501-1193, Japan
| | - Hiroshi Takemori
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, 501-1193, Japan
- Graduate School of Natural Science and Technology, Gifu University, Gifu, 501-1193, Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, 501-1193, Japan
| | | | - Yuji O. Kamatari
- Life Science Research Center, Institute for Advanced Study, Gifu University, Gifu, 501-1193, Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, 501-1193, Japan
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, 501-1193, Japan
| | - Makoto Sawada
- Department of Brain Functions, Research Institute of Environmental Medicine, Nagoya University, Aichi, Japan
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12
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Li T, Dai C, Lu Q, Tian M. A polarity-responsive lysosomes-nucleus translocation probe for the dual-emissive visualization of cell apoptosis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 315:124272. [PMID: 38603960 DOI: 10.1016/j.saa.2024.124272] [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: 02/20/2024] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Visualization of cell apoptosis is a critical task playing central roles in the fundamental studies in biology, pathology, and biomedicine. Dual-emissive fluorescent probes are desired molecular tools for study on apoptosis, which however were rarely reported. Herein, utilizing the polarity differences between lysosomes and nucleus, a translocation type of fluorescent probe (NA-S) was developed for the dual-color visualization of cell apoptosis. NA-S was designed to be polarity sensitive, bearing alkalescence group, and with DNA affinity. In living cells, NA-S targeted the lysosomes to give blue fluorescence, which translocated into the nucleus during cell apoptosis to give green emission. Thereby, the cell apoptosis could be visualized with NA-S in dual-emissive manner. With the unique probe, the cell apoptosis induced by oxidative stress, UV irradiation, rotenone, colchicine, and paclitaxel have been successfully visualized.
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Affiliation(s)
- Tianyu Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China
| | - Chun Dai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China
| | - Qingqing Lu
- Engineering & Technology Center of Electrochemistry, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Minggang Tian
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China.
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13
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Liu J, Du W, Chen B, Tian Y, Tan J, Feng Z, Tian X. Correlative Super-resolution Optical and Electron Microscopic Imaging of Intracellular Ribosomal RNA by a Terpyridine Iridium(III) Complex. ACS Sens 2024; 9:3048-3056. [PMID: 38830243 DOI: 10.1021/acssensors.4c00232] [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] [Indexed: 06/05/2024]
Abstract
Ribosomal RNA (rRNA) plays a vital role in binding amino acids together, which dictates the primary structure of a protein. Visualization of its intracellular distribution and dynamics during protein synthesis enables a better understanding of the correlated biological essence. However, appropriate tools targeting live cell rRNA that are capable of multimodal imaging at the nanoscale are still lacking. Here, we rationally designed a series of terpyridine ammonium iridium(III) complexes, one of which is capable of selectively labeling rRNA in living cells. Its metal core and photostable nature allow further super-resolution STED imaging of rRNA found on the rough endoplasmic reticulum at a ∼40 nm resolution that is well correlated under correlative light and electron microscopy (CLEM). Interestingly, the Ir(III) complex demonstrated rRNA dynamics in living cells while boosting protein synthesis at the nanoscale. Our work offers a versatile tool to visualize rRNA synchronously under optical and electron microscopy, which provides a better understanding of rRNA evolution in living systems.
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Affiliation(s)
- Jia Liu
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology, Huaxi MR Research Centre (HMRRC), West China Hospital of Sichuan University, Chengdu 610000, P. R. China
- TCM Department, West China Second University Hospital, Chengdu 610000, P. R. China
| | - Wei Du
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), Nanjing 211816, P. R. China
| | - Bo Chen
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China
| | - Yupeng Tian
- College of Chemistry and Chemical Engineering, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei 230601, P. R. China
| | - Jing Tan
- Chinese Evidence-based Medicine Center, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu 610041, P. R. China
| | - Zhihui Feng
- School of Pharmacy, Anhui University of Traditional Chinese Medicine, Hefei 230012, P. R. China
| | - Xiaohe Tian
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology, Huaxi MR Research Centre (HMRRC), West China Hospital of Sichuan University, Chengdu 610000, P. R. China
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14
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Rubio V, McInchak N, Fernandez G, Benavides D, Herrera D, Jimenez C, Mesa H, Meade J, Zhang Q, Stawikowski MJ. Modular Fluorescent Cholesterol Naphthalimide Probes And Their Application For Cholesterol Trafficking Studies In Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600118. [PMID: 38979187 PMCID: PMC11230193 DOI: 10.1101/2024.06.24.600118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Development of fluorescent cholesterol analogs to better understand subcellular cholesterol trafficking is of great interest for cell biology and medicine. Our approach utilizes a bifunctional 1,8-naphthalimide scaffold with a push-pull character, modified on one side with a head group and a linker on the other side connecting it to cholesterol via an ester bond. Through structure-function studies, we've explored how different substituents-linkers and head groups-affect the ability of these fluorescent cholesterol naphthalimide analogs (CNDs) to mimic natural cholesterol behavior at both molecular and cellular levels. We categorized the resulting analogs into three groups: neutral, charged, and those featuring a hydroxyl group. Each compound was assessed for its solvatochromic behavior in organic solvents and model membranes. Extensive all-atom molecular dynamics simulations helped us examine how these analogs perform in model membranes compared to cholesterol. Additionally, we investigated the partitioning of these fluorescent probes in phase-separated giant unilamellar vesicles. We evaluated the uptake and distribution of these probes within mouse fibroblast cells and astrocytes, for their subcellular distributions in lysosomes and compared that to BODIPY-cholesterol, a well-regarded fluorescent cholesterol analog. The internalization efficiency of the fluorescent probes varies in different cell types and is affected mainly by the head groups. Our results demonstrate that the modular design significantly simplifies the creation of fluorescent cholesterol probes bearing distinct spectral, biophysical, and cellular targeting features, which makes it a valuable toolkit for the investigation of subcellular distribution and trafficking of cholesterol and its derivatives.
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15
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Jiang W, Qiao Q, Chen J, Bao P, Tao Y, Zhang Y, Xu Z. Rna Buffering Fluorogenic Probe for Nucleolar Morphology Stable Imaging And Nucleolar Stress-Generating Agents Screening. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309743. [PMID: 38326089 PMCID: PMC11022735 DOI: 10.1002/advs.202309743] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/22/2024] [Indexed: 02/09/2024]
Abstract
In the realm of cell research, membraneless organelles have become a subject of increasing interest. However, their ever-changing and amorphous morphological characteristics have long presented a formidable challenge when it comes to studying their structure and function. In this paper, a fluorescent probe Nu-AN is reported, which exhibits the remarkable capability to selectively bind to and visualize the nucleolus morphology, the largest membraneless organelle within the nucleus. Nu-AN demonstrates a significant enhancement in fluorescence upon its selective binding to nucleolar RNA, due to the inhibited twisted intramolecular charge-transfer (TICT) and reduced hydrogen bonding with water. What sets Nu-AN apart is its neutral charge and weak interaction with nucleolus RNA, enabling it to label the nucleolus selectively and reversibly. This not only reduces interference but also permits the replacement of photobleached probes with fresh ones outside the nucleolus, thereby preserving imaging photostability. By closely monitoring morphology-specific changes in the nucleolus with this buffering fluorogenic probe, screenings for agents are conducted that induce nucleolar stress within living cells.
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Affiliation(s)
- Wenchao Jiang
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences457 Zhongshan RoadDalian116023China
- University of Chinese Academy of SciencesBeijing100049China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences457 Zhongshan RoadDalian116023China
| | - Jie Chen
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences457 Zhongshan RoadDalian116023China
- University of Chinese Academy of SciencesBeijing100049China
| | - Pengjun Bao
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences457 Zhongshan RoadDalian116023China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yi Tao
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences457 Zhongshan RoadDalian116023China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yinchan Zhang
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences457 Zhongshan RoadDalian116023China
- University of Chinese Academy of SciencesBeijing100049China
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical ChemistryDalian Institute of Chemical PhysicsChinese Academy of Sciences457 Zhongshan RoadDalian116023China
- University of Chinese Academy of SciencesBeijing100049China
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16
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Luo JR, Long W, Chen ZX, Wang SM, Zeng YX, Lu YJ, Zheng BX, She MT, Wong WL. Live Cell Imaging and Real-Time Monitoring of Nucleolus Morphology and Mitophagy with a Red Fluorescent and Photostable rRNA-Specific Probe in Human Cancer Cells. ACS Sens 2024; 9:1545-1554. [PMID: 38450702 DOI: 10.1021/acssensors.3c02764] [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] [Indexed: 03/08/2024]
Abstract
rRNAs are prevalent in living organisms. They are produced in nucleolus and mitochondria and play essential cellular functions. In addition to the primary biofunction in protein synthesis, rRNAs have been recognized as the emerging signaling molecule and drug target for studies on nucleolus morphology, mitochondrial autophagy, and tumor cell malignancy. Currently, only a few rRNA-selective probes have been developed, and most of them encounter the drawbacks of low water solubility, poor nuclear membrane permeability, short emission wavelength, low stability against photobleaching, and high cytotoxicity. These unfavorable properties of rRNA probes limit their potential applications. In the present study, we reported a new rRNA-selective and near-infrared fluorescent turn-on probe, 4MPS-TO, capable of tracking rRNA in live human cancer cells. The real-time monitoring performance in nucleolus morphology and mitochondrial autophagy is demonstrated in HeLa cells. The probe shows great application potential for being used as a rRNA-selective, sensitive, and photostable imaging tool in chemical biology study and drug screening.
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Affiliation(s)
- Jun-Ren Luo
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Wei Long
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Ze-Xin Chen
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Shi-Min Wang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Yao-Xun Zeng
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Yu-Jing Lu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Bo-Xin Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Meng-Ting She
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
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17
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Groß P, Hoffmann RS, Müller M, Schönherr H, Ihmels H. Fluorimetric Cell Analysis with 9-Aryl-Substituted Berberine Derivatives as DNA-Targeting Fluorescent Probes. Chembiochem 2024; 25:e202300761. [PMID: 37934026 DOI: 10.1002/cbic.202300761] [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: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/08/2023]
Abstract
DNA-sensitive fluorescent light-up probes based on berberine are presented. This biogenic fluorophore was chosen as central unit to use its potential biocompatibility and its DNA-binding properties. To provide predictable fluorescence quenching in aqueous solution and a fluorescence light-up effect upon DNA binding, aryl substituents were attached at the 9-position by Suzuki-Miyaura coupling reactions. The 9-arylberberine derivatives have a very low fluorescence quantum yield (Φfl =<0.02), which is caused by the radiationless deactivation of the excited state by torsional relaxation about the biaryl axis. In addition, these berberine derivatives intercalate into DNA with high affinity (Kb =2.0-22×104 M-1 ). Except for the nitrophenyl- and hydroxyphenyl-substituted derivatives, all tested compounds exhibited a pronounced fluorescence light-up effect upon association with DNA, because the deactivation of the excited-state by torsional relaxation is suppressed in the DNA binding site. Most notably, it was shown exemplarily with the 9-(4-methoxyphenyl)- and the 9-(6-methoxynaphthyl)-substituted derivatives that these properties are suited for fluorimetric cell analysis. In particular, these probes generated distinct staining patterns in eukaryotic cells (NIH 3T3 mouse fibroblasts), which enabled the identification of nuclear substructures, most likely heterochromatin or nucleoli, respectively.
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Affiliation(s)
- Philipp Groß
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
| | - Renée S Hoffmann
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
| | - Mareike Müller
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
| | - Holger Schönherr
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
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18
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Yang Y, Yan DX, Rong RX, Shi BY, Zhang M, Liu J, Xin J, Xu T, Ma WJ, Li XL, Wang KR. Nucleolus imaging based on naphthalimide derivatives. Bioorg Chem 2024; 142:106969. [PMID: 37988784 DOI: 10.1016/j.bioorg.2023.106969] [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: 09/06/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]
Abstract
Nucleolus was an important cellular organelle. The abnormal morphology and number of the nucleolus have been considered as diagnostic biomarkers for some human diseases. However, the imaging agent based on nucleolus was limited. In this manuscript, a series of nucleolar fluorescent probes based on naphthalimide derivatives (NI-1 ∼ NI-5) had been designed and synthesized. NI-1 ∼ NI-5 could penetrate cell membranes and nuclear membranes, achieve clear nucleolar staining in living cells. These results suggested that the presence of amino groups on the side chains of naphthalimide backbone could enhance the targeting to the cell nucleolus. In addition, the molecular docking results showed that NI-1 ∼ NI-5 formed hydrogen bonds and hydrophobic interactions with RNA, and exhibited enhanced fluorescence upon binding with RNA. These results will provide favorable support for the diagnosis and treatment of nucleolus-related diseases in the future.
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Affiliation(s)
- Yan Yang
- Department of Immunology, School of Basic Medical Science, Hebei University, Baoding 071002, PR China
| | - Dong-Xiao Yan
- Department of Immunology, School of Basic Medical Science, Hebei University, Baoding 071002, PR China
| | - Rui-Xue Rong
- Department of Immunology, School of Basic Medical Science, Hebei University, Baoding 071002, PR China.
| | - Bing-Ye Shi
- Affiliated Hospital of Hebei University, Hebei University, Baoding 071002, PR China
| | - Man Zhang
- College of Chemistry and Materials Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), Key Laboratory of Chemical Biology of Hebei Province, Hebei University, Baoding 071002, PR China
| | - Jing Liu
- College of Chemistry and Materials Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), Key Laboratory of Chemical Biology of Hebei Province, Hebei University, Baoding 071002, PR China
| | - Jie Xin
- College of Chemistry and Materials Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), Key Laboratory of Chemical Biology of Hebei Province, Hebei University, Baoding 071002, PR China
| | - Tao Xu
- Department of Immunology, School of Basic Medical Science, Hebei University, Baoding 071002, PR China
| | - Wen-Jie Ma
- Department of Immunology, School of Basic Medical Science, Hebei University, Baoding 071002, PR China
| | - Xiao-Liu Li
- College of Chemistry and Materials Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), Key Laboratory of Chemical Biology of Hebei Province, Hebei University, Baoding 071002, PR China.
| | - Ke-Rang Wang
- College of Chemistry and Materials Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Ministry of Education), Key Laboratory of Chemical Biology of Hebei Province, Hebei University, Baoding 071002, PR China.
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19
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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: 3.0] [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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20
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Chan KH, Wang Y, Zheng BX, Long W, Feng X, Wong WL. RNA-Selective Small-Molecule Ligands: Recent Advances in Live-Cell Imaging and Drug Discovery. ChemMedChem 2023; 18:e202300271. [PMID: 37649155 DOI: 10.1002/cmdc.202300271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/13/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
RNA structures, including those formed from coding and noncoding RNAs, alternative to protein-based drug targets, could be a promising target of small molecules for drug discovery against various human diseases, particularly in anticancer, antibacterial and antivirus development. The normal cellular activity of cells is critically dependent on the function of various RNA molecules generated from DNA transcription. Moreover, many studies support that mRNA-targeting small molecules may regulate the synthesis of disease-related proteins via the non-covalent mRNA-ligand interactions that do not involve gene modification. RNA-ligand interaction is thus an attractive approach to address the challenge of "undruggable" proteins in drug discovery because the intracellular activity of these proteins is hard to be suppressed with small molecule ligands. We selectively surveyed a specific area of RNA structure-selective small molecule ligands in fluorescence live cell imaging and drug discovery because the area was currently underexplored. This state-of-the-art review thus mainly focuses on the research published within the past three years and aims to provide the most recent information on this research area; hopefully, it could be complementary to the previously reported reviews and give new insights into the future development on RNA-specific small molecule ligands for live cell imaging and drug discovery.
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Affiliation(s)
- Ka Hin Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Yakun Wang
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, P. R. China
| | - Bo-Xin Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Wei Long
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Xinxin Feng
- State Key Laboratory of Chem-/Bio-Sensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, P. R. China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, P. R. China
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21
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Mondal IC, Rawat P, Galkin M, Deka S, Karmakar A, Mondal P, Ghosh S. Julolidine-based small molecular probes for fluorescence imaging of RNA in live cells. Org Biomol Chem 2023; 21:7831-7840. [PMID: 37728395 DOI: 10.1039/d3ob01314f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Intracellular RNA imaging with organic small molecular probes has been an intense topic, although the number of such reported dyes, particularly dyes with high quantum yields and long wavelength excitation/emission, is quite limited. The present work reports the design and synthesis of three cationic julolidine-azolium conjugates (OX-JLD, BTZ-JLD and SEZ-JLD) as turn-on fluorescent probes with appreciably high quantum yields and brightness upon interaction with RNA. A structure-efficiency relationship has been established for their potential for the interaction and imaging of intracellular RNA. Given their chemical structure, the free rotation between the donor and the acceptor gets restricted when the probes bind with RNA resulting in strong fluorescence emission towards a higher wavelength upon photoexcitation. A detailed investigation revealed that the photophysical properties and the optical responses of two probes, viz. BTZ-JLD and SEZ-JLD, towards RNA are very promising and qualify them to be suitable candidates for biological studies, particularly for cellular imaging applications. The probes allow imaging of intracellular RNA with prominent staining of nucleoli in live cells under a range of physiological conditions. The results of the cellular digest test established the appreciable RNA selectivity of BTZ-JLD and SEZ-JLD inside the cellular environment. Moreover, a comparison between the relative intensity profile of SEZ-JLD before and after the RNA-digestion test inside the cellular environment indicated that the interference of cellular viscosity in fluorescence enhancement is insignificant, and hence, SEZ-JLD can be used as a cell membrane permeable cationic molecular probe for deep-red imaging of intracellular RNA with a good degree of selectivity.
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Affiliation(s)
- Iswar Chandra Mondal
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P-175005, India
| | - Priya Rawat
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, H.P-175005, India
| | - Maksym Galkin
- Laboratory of Chemical Biology, The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6 16610, Czech Republic
| | - Snata Deka
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P-175005, India
| | - Anirban Karmakar
- Centro de Química Estrutural, Instituto Superior Técnico, Avenida Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Prosenjit Mondal
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, H.P-175005, India
| | - Subrata Ghosh
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P-175005, India
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22
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Wu Y, Sun D, Han X, Zhao Z, Liang F, Liu S. Synthesis of Naphthalimide Derivatives and Their Luminescence upon Complexation with Cucurbit[ n]uril Hosts. J Org Chem 2023; 88:12376-12384. [PMID: 37610314 DOI: 10.1021/acs.joc.3c01111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
A series of naphthalimide derivatives are synthesized and their binding behavior upon complexation with cucurbit[n]urils (CB[n]s) has been investigated. With a heavy atom (bromine) on the naphthalimide core, 4-bromo-1,8-naphthalimide derivatives 1-4 show short room-temperature phosphorescence (RTP) lifetimes with low quantum yields. Their RTP properties are significantly enhanced in the presence of CB[8] or CB[10] both in aqueous solution and solid state owing to the efficient suppression of nonradiative decay and isolation of quenching factors by the rigid cavity of CB[n]. Without the bromine atom, 1,8-naphthalimide derivatives 5 and 6 show strong excimer emission upon complexation with CB[10] accompanied by fluorescence transition from blue to cyan. The fluorescence colors of 4-(dimethylamino)-1,8-naphthalimide derivatives 7 and 8 change from blue to white to yellow with the addition of CB[n]. This host-guest complexation strategy to modulate the luminescence of the luminophore would further broaden the application of luminescent materials.
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Affiliation(s)
- Yong Wu
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Dongdong Sun
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Xie Han
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
- The State Key Laboratory of Refractories and Metallurgy, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Zhiyong Zhao
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
- The State Key Laboratory of Refractories and Metallurgy, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Feng Liang
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
- The State Key Laboratory of Refractories and Metallurgy, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Simin Liu
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
- The State Key Laboratory of Refractories and Metallurgy, Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
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23
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Hawdon A, Geoghegan ND, Mohenska M, Elsenhans A, Ferguson C, Polo JM, Parton RG, Zenker J. Apicobasal RNA asymmetries regulate cell fate in the early mouse embryo. Nat Commun 2023; 14:2909. [PMID: 37253716 DOI: 10.1038/s41467-023-38436-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/03/2023] [Indexed: 06/01/2023] Open
Abstract
The spatial sorting of RNA transcripts is fundamental for the refinement of gene expression to distinct subcellular regions. Although, in non-mammalian early embryogenesis, differential RNA localisation presages cell fate determination, in mammals it remains unclear. Here, we uncover apical-to-basal RNA asymmetries in outer blastomeres of 16-cell stage mouse preimplantation embryos. Basally directed RNA transport is facilitated in a microtubule- and lysosome-mediated manner. Yet, despite an increased accumulation of RNA transcripts in basal regions, higher translation activity occurs at the more dispersed apical RNA foci, demonstrated by spatial heterogeneities in RNA subtypes, RNA-organelle interactions and translation events. During the transition to the 32-cell stage, the biased inheritance of RNA transcripts, coupled with differential translation capacity, regulates cell fate allocation of trophectoderm and cells destined to form the pluripotent inner cell mass. Our study identifies a paradigm for the spatiotemporal regulation of post-transcriptional gene expression governing mammalian preimplantation embryogenesis and cell fate.
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Affiliation(s)
- Azelle Hawdon
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Niall D Geoghegan
- Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Monika Mohenska
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, 3800, Australia
- Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Anja Elsenhans
- Department of Biology, University of Duisburg-Essen, Essen, Germany
| | - Charles Ferguson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jose M Polo
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, 3800, Australia
- Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Queensland, Australia
| | - Jennifer Zenker
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.
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24
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Xu X, Wang X, Cui X, Jia B, Xu B, Sun J. Dispersion Performances of Naphthalimides Doped in Dual Temperature- and pH-Sensitive Poly (N-Isopropylacrylamide-co-acrylic Acid) Shell Assembled with Vinyl-Modified Mesoporous SiO 2 Core for Fluorescence Cell Imaging. Polymers (Basel) 2023; 15:polym15102339. [PMID: 37242914 DOI: 10.3390/polym15102339] [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: 01/25/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/28/2023] Open
Abstract
Developing effective intelligent nanocarriers is highly desirable for fluorescence imaging and therapeutic applications but remains challenging. Using a vinyl-grafted BMMs (bimodal mesoporous SiO2 materials) as a core and PAN ((2-aminoethyl)-6-(dimethylamino)-1H-benzo[de]isoquinoline-1,3(2H)-dione))-dispersed dual pH/thermal-sensitive poly(N-isopropylacrylamide-co-acrylic acid) as a shell, PAN@BMMs with strong fluorescence and good dispersibility were prepared. Their mesoporous features and physicochemical properties were extensively characterized via XRD patterns, N2 adsorption-desorption analysis, SEM/TEM images, TGA profiles, and FT-IR spectra. In particular, their mass fractal dimension (dm) features based on SAXS patterns combined with fluorescence spectra were successfully obtained to evaluate the uniformity of the fluorescence dispersions, showing that the dm values increased from 2.49 to 2.70 with an increase of the AN-additive amount from 0.05 to 1%, along with the red shifting of their fluorescent emission wavelength from 471 to 488 nm. The composite (PAN@BMMs-I-0.1) presented a densification trend and a slight decrease in peak (490 nm) intensity during the shrinking process. Its fluorescent decay profiles confirmed two fluorescence lifetimes of 3.59 and 10.62 ns. The low cytotoxicity obtained via in vitro cell survival assay and the efficient green imaging performed via HeLa cell internalization suggested that the smart PAN@BMM composites are potential carriers for in vivo imaging and therapy.
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Affiliation(s)
- Xiaohuan Xu
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
| | - Xiaoli Wang
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
| | - Xueqing Cui
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
| | - Bingying Jia
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
| | - Bang Xu
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
| | - Jihong Sun
- Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, China
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25
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Jiang L, Cai H, Zhou W, Li Z, Zhang L, Bi H. RNA-Targeting Carbon Dots for Live-Cell Imaging of Granule Dynamics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210776. [PMID: 36645339 DOI: 10.1002/adma.202210776] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/02/2023] [Indexed: 05/26/2023]
Abstract
It is significant to monitor the different RNA granules dynamics and phase separation process inside cells under various stresses, for example, oxidative stress. The current small-molecule RNA probes work well only in fixed cells and usually encounter problems such as insufficient stability and biocompatibility, and thus a specific RNA-targeting fluorescent nanoprobe that can be used in the living cells is urgently desired. Here, the de novo design and microwave-assisted synthesis of a novel RNA-targeting, red-emissive carbon dots (named as M-CDs) are reported by choosing neutral red and levofloxacin as precursors. The as-synthesized M-CDs is water-soluble with a high fluorescence quantum yield of 22.83% and can selectively bind to RNA resulting in an enhanced red fluorescence. More interestingly, such an RNA-targeting, red-emissive M-CDs can be fast internalized into cells within 5 s and thus used for real-time imaging the dynamic process of intracellular stress granules under oxidative stress, revealing some characteristics of granules that have not been identified by previously reported RNA and protein biomarkers. This research paves a new pathway for visualizing bulk RNA dynamics and studying phase-separation behaviors in living cells by rational design of the fluorescent carbon dots in terms of structure and functionality.
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Affiliation(s)
- Lei Jiang
- School of Chemistry and Chemical Engineering, Anhui University, 111 Jiulong Road, Hefei, 230601, P. R. China
| | - Hao Cai
- School of Materials Science and Engineering, Anhui University, 111 Jiulong Road, Hefei, 23060, P. R. China
| | - Wanwan Zhou
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Huangshan Road, Hefei, Anhui, 230027, P. R. China
| | - Zijian Li
- School of Materials Science and Engineering, Anhui University, 111 Jiulong Road, Hefei, 23060, P. R. China
| | - Liang Zhang
- Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Huangshan Road, Hefei, Anhui, 230027, P. R. China
| | - Hong Bi
- School of Materials Science and Engineering, Anhui University, 111 Jiulong Road, Hefei, 23060, P. R. China
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26
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Kumar RR, Kumar A, Chuang CH, Shaikh MO. Recent Advances and Emerging Trends in Cancer Biomarker Detection Technologies. Ind Eng Chem Res 2023. [DOI: 10.1021/acs.iecr.2c04097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Rajkumar Rakesh Kumar
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Amit Kumar
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Cheng-Hsin Chuang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Muhammad Omar Shaikh
- Sustainability Science and Management, Tunghai University, Taichung 407224, Taiwan
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27
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Feng Z, Zhang D, Guo H, Su W, Tian Y, Tian X. Lighting up RNA-specific multi-photon and super-resolution imaging using a novel zinc complex. NANOSCALE 2023; 15:5486-5493. [PMID: 36852659 DOI: 10.1039/d2nr05392f] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ribonucleic acid (RNA) probes are critical for understanding the role of RNA dynamics in cellular function but are in short supply due to the lack of optimized imaging systems and excellent fluorescence emission performance. Here, the terpyridine Zn(II) complex (Zn-T) with D-π-A configuration and bright aggregation-induced fluorescence emission (AIE) has been fabricated for the selective detection and real-time monitoring of RNA. Impressively, Zn-T exhibits a large Stokes shift and three-photon absorption (3PA) activity and responds specifically through hydrophobic interactions with an RNA pocket. The combination of AIE-assisted two-photon fluorescence and stimulated emission depletion (STED) microscopy of Zn-T for imaging nuclear RNA has higher spatial resolution and brightness, thus providing an imaging platform for studying RNA-related physiological or pathological processes.
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Affiliation(s)
- Zhihui Feng
- Huaxi MR Research Centre (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology and National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610000, Sichuan Province, China.
| | - Dongxue Zhang
- Huaxi MR Research Centre (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology and National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610000, Sichuan Province, China.
- Equipment and Material Department, West China Hospital, Sichuan University, Chengdu, China
| | - Hui Guo
- College of Chemistry and Chemical Engineering, Key Laboratory of Functional Inorganic Materials Chemistry of Anhui Province, Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University) Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P.R. China
| | - Wenqing Su
- College of Chemistry and Chemical Engineering, Key Laboratory of Functional Inorganic Materials Chemistry of Anhui Province, Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University) Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P.R. China
| | - Yupeng Tian
- College of Chemistry and Chemical Engineering, Key Laboratory of Functional Inorganic Materials Chemistry of Anhui Province, Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University) Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P.R. China
| | - Xiaohe Tian
- Huaxi MR Research Centre (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology and National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610000, Sichuan Province, China.
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28
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Suzuki M, Sato Y, Togashi N, Nishizawa S. Cationic Oligopeptides with Amino Groups as Synthetic Nucleolar Localization Signals for the Rational Design of Nucleolus-Staining Probes. ACS OMEGA 2023; 8:9592-9596. [PMID: 36936342 PMCID: PMC10018684 DOI: 10.1021/acsomega.3c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Cationic oligopeptides with amino groups were found to function as synthetic nucleolar localization signals for directing various fluorophores to the nucleolus with high selectivity in the cells with a view toward the development of nucleolus-staining probes.
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29
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Lin L, Bao Z, Jiang P, Xu Z, Shi B, Xu G, Wang D, Wei X, Gu B. Superior biocompatible carbon dots for dynamic fluorescence imaging of nucleoli in living cells. Biomater Sci 2023; 11:2935-2949. [PMID: 36912088 DOI: 10.1039/d2bm02139k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The nucleolus is a newly developed and promising target for cancer diagnosis and therapy, and its imaging is extremely significant for fundamental research and clinical applications. The unique feature, i.e., high resolution at the subcellular level, makes the fluorescence imaging method a powerful tool for nucleolus imaging. However, the fluorescence imaging of nucleoli in living cells is restricted by the limited availability of fluorescent agents with specific nucleolus-targeting capability and superior biocompatibility. Here, promising carbon dots (CDs) with intrinsic nucleolus-targeting capability were synthesized, characterized and employed for dynamic fluorescence imaging of nucleoli in living cells. The CDs exhibit a high fluorescence quantum yield of 0.2, excellent specificity and photostability, and superior biocompatibility, which were systematically demonstrated at the gene, cellular and animal levels and confirmed by their biological effects on embryonic development. All these features enabled CDs to light up the nucleoli for a long time with a high signal-to-noise ratio in living cells and monitor the nucleolar dynamics of malignant cells in camptothecin (CPT) based chemotherapy. Their excellent optical and biological features as well as general nucleolus-targeting capability endow CDs with great potential for future translational research.
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Affiliation(s)
- Liyun Lin
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Zhouzhou Bao
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pengfei Jiang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Zhourui Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518055, China.
| | - Bo Shi
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Gaixia Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518055, China.
| | - Dan Wang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Xunbin Wei
- Biomedical Engineering Department and International Cancer Institute, Peking University, Beijing 100081, China.
| | - Bobo Gu
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China.
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30
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Cesaretti A, Calzoni E, Montegiove N, Bianconi T, Alebardi M, La Serra MA, Consiglio G, Fortuna CG, Elisei F, Spalletti A. Lighting-Up the Far-Red Fluorescence of RNA-Selective Dyes by Switching from Ortho to Para Position. Int J Mol Sci 2023; 24:ijms24054812. [PMID: 36902248 PMCID: PMC10003335 DOI: 10.3390/ijms24054812] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
Fluorescence imaging is constantly searching for new far-red emitting probes whose turn-on response is selective upon the interaction with specific biological targets. Cationic push-pull dyes could indeed respond to these requirements due to their intramolecular charge transfer (ICT) character, by which their optical properties can be tuned, and their ability to interact strongly with nucleic acids. Starting from the intriguing results recently achieved with some push-pull dimethylamino-phenyl dyes, two isomers obtained by switching the cationic electron acceptor head (either a methylpyridinium or a methylquinolinium) from the ortho to the para position have been scrutinized for their ICT dynamics, their affinity towards DNA and RNA, and in vitro behavior. By exploiting the marked fluorescence enhancement observed upon complexation with polynucleotides, fluorimetric titrations were employed to evaluate the dyes' ability as efficient DNA/RNA binders. The studied compounds exhibited in vitro RNA-selectivity by localizing in the RNA-rich nucleoli and within the mitochondria, as demonstrated by fluorescence microscopy. The para-quinolinium derivative showed some modest antiproliferative effect on two tumor cell lines as well as improved properties as an RNA-selective far-red probe in terms of both turn-on response (100-fold fluorescence enhancement) and localized staining ability, attracting interest as a potential theranostic agent.
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Affiliation(s)
- Alessio Cesaretti
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Correspondence:
| | - Eleonora Calzoni
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Nicolò Montegiove
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Tommaso Bianconi
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Martina Alebardi
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Maria Antonietta La Serra
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Giuseppe Consiglio
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Cosimo Gianluca Fortuna
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Fausto Elisei
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Anna Spalletti
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
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31
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Wu S, Cui Y, Zhou M, Tao F, Wu W, Xing S, Sun R, Li X, Hu Q. pH-Triggered Charge Reversible Fluorescent Probe for Simultaneous Imaging of Lipid Droplets and Nucleoli in Living Cells. Anal Chem 2023; 95:4005-4014. [PMID: 36795765 DOI: 10.1021/acs.analchem.2c04230] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Cooperation between organelles is essential to maintain the normal functions of cells. Lipid droplets (LDs) and nucleoli, as important organelles, play an important role in the normal activities of cells. However, due to the lack of appropriate tools, in situ observation of the interaction between them has been rarely reported. In this work, taking into full consideration the pH and charge differences between LDs and nucleoli, a pH-triggered charge reversible fluorescent probe (LD-Nu) was constructed based on a cyclization-ring-opening mechanism. The in vitro pH titration experiment and 1H NMR showed that LD-Nu gradually transferred from the charged form to the electroneutral form with the increase of pH, and thus, the conjugate plane was reduced and its fluorescence blue-shifted. Most importantly, the physical contact between LDs and nucleoli was visualized for the first time. Meanwhile, the relationship between LDs and nucleoli was also further investigated, and the results showed that their interaction was more liable to be affected by the abnormality of LDs than those of nucleoli. Moreover, the cell imaging results displayed that the LDs both in the cytoplasm and nucleus were observed using the probe LD-Nu, and interestingly, the LDs in the cytoplasm were more susceptible to external stimuli than those in the nucleus. In a word, the probe LD-Nu can serve as a powerful tool for further exploration of the interaction mechanism between LDs and nucleoli in living cells.
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Affiliation(s)
- Shining Wu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Yuezhi Cui
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Mingyang Zhou
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Furong Tao
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Wenli Wu
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Shu Xing
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Rui Sun
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Xuechen Li
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Qiongzheng Hu
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
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32
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He M, Sato Y, Nishizawa S. Classical thiazole orange and its regioisomer as fluorogenic probes for nucleolar RNA imaging in living cells. Analyst 2023; 148:636-642. [PMID: 36602142 DOI: 10.1039/d2an01804g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In contrast to well-established DNA-selective dyes for live cell imaging, RNA-selective dyes have been less developed owing to the challenges of making small molecules have RNA selectivity over DNA. Two kinds of dyes are now commercially available for nucleolar RNA imaging in cells, but these two dyes do not apply to living cells and have limited use in fixed and permeabilized cells. Herein, we report on thiazole orange (TO), a well-known nucleic acid stain, as a promising fluorogenic dye for nucleolar RNA imaging in living cells. TO shows clear response selectivity for RNA over DNA with a significant light-up property upon binding to RNA (λem = 532 nm, I/I0 = 580-fold, and Φbound/Φfree = 380) and is even applicable to wash-free imaging of living cells. More interestingly, 2TO, a regioisomer of TO in which the benzothiazole unit is connected to position 2 in the quinoline ring, performs much better (λem = 532 nm, I/I0 = 430-fold, Φbound/Φfree = 1200), having superior selectivity for RNA in both solution and living cells. The comparison with TO derivatives carrying different substituents at N1 of the quinoline ring reveals that the slight change in the TO framework significantly affects RNA selectivity, photostability and membrane permeability.
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Affiliation(s)
- Mengmeng He
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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Xiao L, Fang L, Chatterjee S, Kool ET. Diverse Reagent Scaffolds Provide Differential Selectivity of 2'-OH Acylation in RNA. J Am Chem Soc 2023; 145:143-151. [PMID: 36542611 DOI: 10.1021/jacs.2c09040] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RNA 2'-OH acylation is widely used both for mapping structure and for conjugating RNA, generally relying on selective reactions with unpaired nucleotides over paired ones. Common reagents for this acylation have been chiefly restricted to two similar aryl scaffolds, leaving open the question of how more broadly varied reagent structure might affect selectivity. Here, we prepared a set of 10 structurally diverse acylimidazole reagents and employed deep sequencing to profile their reactivity and selectivity in an RNA library of systematically varied structure. We show that structure-directed reactivity profiles vary significantly with the reagent scaffold, and we document new acylating agents that have altered selectivity profiles, including reagents that show elevated selectivity within loops, as well as compounds with reduced off-target reactivity in loop closing base pairs. Interestingly, we also show that the simplest reagent (acetylimidazole) is cell permeable and is small enough to map RNA structure in the presence of protein contacts that block other reagents. Finally, we describe reagents that show elevated selectivity within small loops, with applications in site-selective labeling. The results provide new tools for improved conjugation and mapping of RNA.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Sayantan Chatterjee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
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34
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Wu J, Lin Z, Zou Z, Liang S, Wu M, Hu TY, Zhang Y. Identifying the Phenotypes of Tumor-Derived Extracellular Vesicles Using Size-Coded Affinity Microbeads. J Am Chem Soc 2022; 144:23483-23491. [PMID: 36527408 DOI: 10.1021/jacs.2c10042] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tumor-derived extracellular vesicle (tEV) biomarkers can reflect cancer cell phenotypes and have great potential for cancer diagnosis and treatment. However, tEVs display high heterogeneity, and rapid and sensitive identification of EV biomarkers remains challenging due to their low expression. Spectral overlap also significantly limits the multiplex analysis of EV biomarkers by fluorescent probes. Herein, we developed a method for highly sensitive tEV phenotyping that uses size-coded microbeads that carry hairpin probes that can bind to aptamers targeting distinct tEV biomarkers. We also designed a microfluidic chip containing spacer arrays that segregate these microbeads in distinct chip regions according to their size to generate location-specific signals indicating the level of different EV biomarkers. The EV biomarker signal on these microbeads was amplified by in situ rolling cyclic amplification (RCA). This strategy permits the simultaneous detection of multiple tEV phenotypes by fluorescence spectroscopy without the limitations of spectral overlap. This study demonstrates that this tEV phenotyping method can rapidly and simultaneously detect six different tEV phenotypes with high sensitivity. Due to the programmability of the sensing platform, this method can be rapidly adapted to detect different tEV phenotype substitutions of the detected biomarkers. Notably, clinical cohort studies show that this strategy may provide new ideas for the precise diagnosis and personalized treatment of cancer patients.
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Affiliation(s)
- Jiacheng Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhun Lin
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhengyu Zou
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Siping Liang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Minhao Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Tony Y Hu
- Center of Cellular and Molecular Diagnosis, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Yuanqing Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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35
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Niu J, Meng F, Hao Q, Zong C, Fu J, Xue H, Tian M, Yu X. Ratiometric and Discriminative Visualization of Autophagy and Apoptosis with a Single Fluorescent Probe Based on the Aggregation/Monomer Principle. Anal Chem 2022; 94:17885-17894. [PMID: 36516436 DOI: 10.1021/acs.analchem.2c03815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Autophagy and apoptosis play a central role in maintaining homeostasis in mammals. Therefore, discriminative visualization of the two cellular processes is an important and challenging task. However, fluorescent probes enabling ratiometric visualization of both autophagy and apoptosis with different sets of fluorescence signals have not been developed yet. In this work, we constructed a versatile single fluorescent probe (NKLR) based on the aggregation/monomer principle for the ratiometric and discriminative visualization of autophagy and apoptosis. NKLR can simultaneously perform two-color imaging of RNA (deep red channel) and lysosomes (yellow channel) in aggregation and monomer states, respectively. During autophagy, NKLR migrated from cytoplasmic RNA and nuclear RNA to lysosomes, showing enhanced yellow emission and sharply decreased deep red fluorescence. Moreover, this migration process was reversible upon the recovery of autophagy. Comparatively, during apoptosis, NKLR immigrated from lysosomes to RNA, and the yellow emission decreased and even disappeared, while the fluorescence of the deep red channel slightly increased. Overall, autophagy and apoptosis could be discriminatively visualized via the fluorescence intensity ratios of the two channels. Meanwhile, the cells in three different states (healthy, autophagic, apoptotic) could be distinguished by three point-to-point fluorescence images via the localization and emission color of NKLR. Therefore, the probe NKLR can serve as a desirable molecular tool to reveal the in-depth relation between autophagy and apoptosis and facilitate the study on the two cellular processes.
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Affiliation(s)
- Jie Niu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Fangfang Meng
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Qiuhua Hao
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Chong Zong
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Jinyu Fu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Haiyan Xue
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Minggang Tian
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Xiaoqiang Yu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, P. R. China
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36
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Lau MHY, Wong CH, Chan HYE, Au-Yeung HY. Development of Fluorescent Turn-On Probes for CAG-RNA Repeats. BIOSENSORS 2022; 12:1080. [PMID: 36551047 PMCID: PMC9775061 DOI: 10.3390/bios12121080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Fluorescent sensing of nucleic acids is a highly sensitive and efficient bioanalytical method for their study in cellular processes, detection and diagnosis in related diseases. However, the design of small molecule fluorescent probes for the selective binding and detection of RNA of a specific sequence is very challenging because of their diverse, dynamic, and flexible structures. By modifying a bis(amidinium)-based small molecular binder that is known to selectively target RNA with CAG repeats using an environment-sensitive fluorophore, a turn-on fluorescent probe featuring aggregation-induced emission (AIE) is successfully developed in this proof-of-concept study. The probe (DB-TPE) exhibits a strong, 19-fold fluorescence enhancement upon binding to a short CAG RNA, and the binding and fluorescence response was found to be specific to the overall RNA secondary structure with A·A mismatches. These promising analytical performances suggest that the probe could be applied in pathological studies, disease progression monitoring, as well as diagnosis of related neurodegenerative diseases due to expanded CAG RNA repeats.
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Affiliation(s)
- Matthew Ho Yan Lau
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chun-Ho Wong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho Yin Edwin Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho Yu Au-Yeung
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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37
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Fu Y, Liu Y, Wen T, Fang J, Chen Y, Zhou Z, Gu X, Wu H, Sheng J, Xu Z, Zou W, Chen B. Real-time imaging of RNA polymerase I activity in living human cells. J Biophys Biochem Cytol 2022; 222:213608. [PMID: 36282216 PMCID: PMC9606689 DOI: 10.1083/jcb.202202110] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 08/19/2022] [Accepted: 09/27/2022] [Indexed: 11/22/2022] Open
Abstract
RNA polymerase I (Pol I) synthesizes about 60% of cellular RNA by transcribing multiple copies of the ribosomal RNA gene (rDNA). The transcriptional activity of Pol I controls the level of ribosome biogenesis and cell growth. However, there is currently a lack of methods for monitoring Pol I activity in real time. Here, we develop LiveArt (live imaging-based analysis of rDNA transcription) to visualize and quantify the spatiotemporal dynamics of endogenous ribosomal RNA (rRNA) synthesis. LiveArt reveals mitotic silencing and reactivation of rDNA transcription, as well as the transcriptional kinetics of interphase rDNA. Using LiveArt, we identify SRFBP1 as a potential regulator of rRNA synthesis. We show that rDNA transcription occurs in bursts and can be altered by modulating burst duration and amplitude. Importantly, LiveArt is highly effective in the screening application for anticancer drugs targeting Pol I transcription. These approaches pave the way for a deeper understanding of the mechanisms underlying nucleolar functions.
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Affiliation(s)
- Yujuan Fu
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Yaxin Liu
- Institute of Environmental Medicine, and Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tanye Wen
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Fang
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Yalong Chen
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ziying Zhou
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyi Gu
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Wu
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinghao Sheng
- Institute of Environmental Medicine, and Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengping Xu
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China,Institute of Environmental Medicine, and Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Zou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China,Insititute of Translational Medicine, Zhejiang University, Hangzhou, China,Wei Zou:
| | - Baohui Chen
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China,Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China,Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China,Correspondence to Baohui Chen:
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38
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Development of a Highly Selective and Sensitive Fluorescent Probe for Imaging RNA Dynamics in Live Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27206927. [PMID: 36296519 PMCID: PMC9607629 DOI: 10.3390/molecules27206927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
RNA imaging is of great importance for understanding its complex spatiotemporal dynamics and cellular functions. Considerable effort has been devoted to the development of small-molecule fluorescent probes for RNA imaging. However, most of the reported studies have mainly focused on improving the photostability, permeability, long emission wavelength, and compatibility with live-cell imaging of RNA probes. Less attention has been paid to the selectivity and detection limit of this class of probes. Highly selective and sensitive RNA probes are still rarely available. In this study, a new set of styryl probes were designed and synthesized, with the aim of upgrading the detection limit and maintaining the selectivity of a lead probe QUID−1 for RNA. Among these newly synthesized compounds, QUID−2 was the most promising candidate. The limit of detection (LOD) value of QUID−2 for the RNA was up to 1.8 ng/mL in solution. This property was significantly improved in comparison with that of QUID−1. Further spectroscopy and cell imaging studies demonstrated the advantages of QUID−2 over a commercially available RNA staining probe, SYTO RNASelect, for highly selective and sensitive RNA imaging. In addition, QUID−2 exhibited excellent photostability and low cytotoxicity. Using QUID−2, the global dynamics of RNA were revealed in live cells. More importantly, QUID−2 was found to be potentially applicable for detecting RNA granules in live cells. Collectively, our work provides an ideal probe for RNA imaging. We anticipate that this powerful tool may create new opportunities to investigate the underlying roles of RNA and RNA granules in live cells.
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39
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Guan X, Wang B, Zhang Y, Qi G, Chen L, Jin Y. Monitoring Stress Response Difference in Nucleolus Morphology and ATP Content Changes during Hyperthermia Cell Apoptosis with Plasmonic Fluorescent Nanoprobes. Anal Chem 2022; 94:13842-13851. [PMID: 36174112 DOI: 10.1021/acs.analchem.2c02464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nucleolus, as a main "cellular stress receptor", is the hub of the stress response driving cancer development and has great research value in the field of organelle-targeting photothermal therapy. However, there are few studies focused on monitoring nucleolar stress response and revealing how the energy metabolism of cells regulates the nucleolar stress response during photothermal therapy. Herein, by designing a nucleolus-targeting and ATP- and photothermal-responsive plasmonic fluorescent nanoprobe (AuNRs-CDs) based on gold nanorods (AuNRs) and fluorescent carbon quantum dots (CDs), we achieved real-time fluorescence imaging of nucleus morphology while monitoring changes of ATP content at the subcellular level. We found that the green fluorescence diminished at 5 min of photothermal therapy, and the nucleolus morphology began to shrink and became smaller in cancerous HepG2 cells. In contrast, there is no significant change of green fluorescence in the nucleolar region of normal HL-7702 cells. ATP content monitoring also showed similar results. Apparently, in response to photothermal stimuli, cancerous cells produce more ATP (energy) along with obvious change in nucleolus morphology and state compared to normal cells under the hyperthermia-induced cell apoptosis. The developed AuNRs-CDs as a nucleolus imaging nanoprobe and effective photothermal agent present promising applications for nucleolar stress studies and targeted photothermal therapy.
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Affiliation(s)
- Xin Guan
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin P.R. China
| | - Bo Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P.R. China
| | - Ying Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P.R. China.,University of Science and Technology of China, Hefei 230026, Anhui, P.R. China
| | - Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P.R. China
| | - Limei Chen
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin P.R. China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P.R. China.,University of Science and Technology of China, Hefei 230026, Anhui, P.R. China
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40
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Wei C, Li H. Benzothiazole Derivatives Targeting G‐Quadruplex DNA: Synthesis, DNA Interaction and Living Cell Imaging. ChemistrySelect 2022. [DOI: 10.1002/slct.202202565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chunying Wei
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science Shanxi University Taiyuan 030006 P. R. China
| | - Haiying Li
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science Shanxi University Taiyuan 030006 P.R. China
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41
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Higuchi K, Sato Y, Togashi N, Suzuki M, Yoshino Y, Nishizawa S. Bright and Light-Up Sensing of Benzo[ c,d]indole-oxazolopyridine Cyanine Dye for RNA and Its Application to Highly Sensitive Imaging of Nucleolar RNA in Living Cells. ACS OMEGA 2022; 7:23744-23748. [PMID: 35847247 PMCID: PMC9280936 DOI: 10.1021/acsomega.2c02408] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Small molecular weight probes that can show a fluorescence signaling response upon binding to RNAs are promising for RNA imaging in living cells. Live-cell RNA imaging probes that can achieve a large light-up ability (>100-fold) and high Φbound value for RNA (>0.50) have been rarely reported to date. Here, benzo[c,d]indole-oxazolopyridine (BIOP), an unsymmetrical monomethine cyanine analogue, was newly developed as a bright and large light-up probe for imaging of nucleolar RNA in living cells. BIOP served as a yellow-emissive probe (λem = 570 nm) and exhibited a significant light-up response upon RNA binding (770-fold) with a high Φbound value (0.52). We demonstrated the advantages of BIOP over a commercially available RNA-staining probe, SYTO RNA select, for robust and sensitive RNA sensing by a systematic comparison of fluorescent properties for RNA. In addition, BIOP was found to possess high membrane permeability and low cytotoxicity in living cells. The examination of live-cell imaging revealed that BIOP exhibited emission in the nucleolus upon binding to nucleolar RNA much stronger than that of SYTO RNA select. Furthermore, BIOP facilitated the highly sensitive imaging of nucleolar RNA, in which 50 nM BIOP can stain nucleolar RNA in living cells with a 20 min incubation.
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42
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A highly sensitive strategy for glypican-3 detection based on aptamer/gold carbon dots/magnetic graphene oxide nanosheets as fluorescent biosensor. Anal Bioanal Chem 2022; 414:6441-6453. [PMID: 35788872 DOI: 10.1007/s00216-022-04201-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/30/2022] [Accepted: 06/24/2022] [Indexed: 11/01/2022]
Abstract
Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related deaths in China. Glypican-3 (GPC3) is a specific antigen related to HCC, which is widely used in clinical detection as a reliable marker of HCC. In this paper, a highly sensitive homogeneous apatasensor was designed for GPC3 detection based on fluorescence resonance energy transfer (FRET) where the GPC3 aptamer labelled gold carbon dots (AuCDs-GPC3Apt) are used as a donor and magnetic graphene oxide (Fe3O4/GO) nanosheets are used as an acceptor. A one-step hydrothermal method was used to synthesize AuCDs to provide sufficient fluorescence. The FRET phenomenon exists between AuCDs-GPC3Apt and Fe3O4/GO, which weakens the fluorescence intensity of the whole system. When the target GPC3 is added to the FRET system, the fluorescent AuCDs-GPC3Apt binds to the GPC3 and forms a folded structure, which leads to AuCDs-GPC3Apt separation from Fe3O4/GO nanosheets. The Fe3O4/GO is then magnetically separated so that the fluorescence of free labelled AuCDs-GPC3Apt is restored. Under the optimum conditions, the fluorescence recovery rate is linearly correlated with the concentration of GPC3 (5-100 ng·mL-1) and the detection limit is 3.01 ng·mL-1 (S/N = 3). This strategy shows recoveries from 98.76 to 101.29% in real human serum samples and provides an immediate and effective detection method for the quantification of GPC3 with great potential applications for early diagnosis of HCC. A sensitive homogeneous FRET-based apatasensor was designed for GPC3 detection where the AuCDs-GPC3Apt is a donor and Fe3O4/GO nanosheets are an acceptor. The GPC3 fluorescent aptasensor combines wider output range with low cost, high specificity, and good anti-interference.
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43
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Wu RS, Lin YS, Nain A, Unnikrishnan B, Lin YF, Yang CR, Chen TH, Huang YF, Huang CC, Chang HT. Evaluation of chemotherapeutic response in living cells using subcellular Organelle‒Selective amphipathic carbon dots. Biosens Bioelectron 2022; 211:114362. [PMID: 35617797 DOI: 10.1016/j.bios.2022.114362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/04/2022] [Accepted: 05/09/2022] [Indexed: 01/03/2023]
Abstract
Monitoring of structural changes in subcellular organelles is critical to evaluate the chemotherapeutic response of cells. However, commercial organelle selective fluorophores are easily photobleached, and thus are unsuitable for real-time and long-term observation. We have developed photostable carbon-dot liposomes (CDsomes)-based fluorophores for organellar and suborganellar imaging to circumvent these issues. The CDs synthesized through a mild pyrolysis/hydrolysis process exhibit amphipathic nature and underwent self-assembly to form liposome-like structures (CDsomes). The controlled hydrophilicity or hydrophobicity-guided preparation of CDsomes are used to selectively and rapidly (<1 min) stain nucleolus, cytoplasm, and membrane. In addition, the CDsomes offer universal high-contrast staining not only in fixed cells but also in living cells, allowing real-time observation and morphological identification in the specimen. The as-prepared CDsomes exhibit excitation-dependent fluorescence, and are much more stable under photoirradiation (e.g., ultraviolet light) than traditional subcellular dyes. Interestingly, the CDsomes can be transferred to daughter cells by diluting the particles, enabling multigenerational tracking of suborganelle for up to six generations, without interrupting the staining pattern. Therefore, we believe that the ultra-photostable CDsomes with high biocompatibility, and long-term suborganellar imaging capabilities, hold a great potential for screening and evaluating therapeutic performance of various chemotherapeutic drugs.
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Affiliation(s)
- Ren-Siang Wu
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Syuan Lin
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Amit Nain
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Binesh Unnikrishnan
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Yu-Feng Lin
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Cheng-Ruei Yang
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Heng Chen
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Fen Huang
- Institute of Analytical and Environmental Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
| | - Chih-Ching Huang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan; Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan.
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Hallaji Z, Bagheri Z, Oroujlo M, Nemati M, Tavassoli Z, Ranjbar B. An insight into the potentials of carbon dots for in vitro live-cell imaging: recent progress, challenges, and prospects. Mikrochim Acta 2022; 189:190. [PMID: 35419708 DOI: 10.1007/s00604-022-05259-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/03/2022] [Indexed: 12/11/2022]
Abstract
Carbon dots (CDs) are a strong alternative to conventional fluorescent probes for cell imaging due to their brightness, photostability, tunable fluorescence emission, low toxicity, inexpensive preparation, and chemical diversity. Improving the targeting efficiency by modulation of the surface functional groups and understanding the mechanisms of targeted imaging are the most challenging issues in cell imaging by CDs. Firstly, we briefly discuss important features of fluorescent CDs for live-cell imaging application in this review. Then, the newest modulated CDs for targeted live-cell imaging of whole-cell, cell organelles, pH, ions, small molecules, and proteins are elaborately discussed, and their challenges in these fields are explained.
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Affiliation(s)
- Zahra Hallaji
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, 14117-13116, Tehran, Iran
| | - Zeinab Bagheri
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983963113, Tehran, Iran.
| | - Mahdi Oroujlo
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983963113, Tehran, Iran
| | - Mehrnoosh Nemati
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, 1983963113, Tehran, Iran
| | - Zeinab Tavassoli
- Department of Biology, Islamic Azad University Central Tehran Branch, Tehran, Iran
| | - Bijan Ranjbar
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, 14117-13116, Tehran, Iran. .,Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 14117-13116, Tehran, Iran.
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45
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Xia T, Chen G, Zhou D, Liu W, Li X, Gu H, Ye Y, Du J, Fan J, Peng X. Nucleic Acid Probe-Based Difunctional Hematology Analysis Kit for Peripheral Blood Cell Analysis. ACS Sens 2022; 7:469-476. [PMID: 35129973 DOI: 10.1021/acssensors.1c02209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Traditional "one for one channel" long-wavelength probes in hematology analyzers limit their resolution and detection efficiency. In this study, we developed a "one for two channels" probe named NATO, which shows a short wavelength (λabs = 460 nm), good nucleus and nucleolus location, and a high signal-to-noise ratio to nucleic acids. When NATO was made into a hematology analysis kit and applied in an automated hematology analyzer, short-wavelength absorbance endows NATO with higher resolution, which in turn leads to better separation of red blood cells and platelets in the blood shadow of the differentiating (DIFF) channel. In addition, this kit showed terrific performance in both DIFF and reticulocytes channels. Our study sheds light on the development of hematology analysis in an automated hematology analyzer by proposing a nucleic acid probe with difunction and higher resolution.
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Affiliation(s)
- Tianping Xia
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Gengwen Chen
- Hematology Reagent R&D, Mindray Bio-medical Electronics Co. Ltd., Shenzhen 518132, China
| | - Danhong Zhou
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Weijian Liu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Xiaojing Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Hua Gu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Yi Ye
- Hematology Reagent R&D, Mindray Bio-medical Electronics Co. Ltd., Shenzhen 518132, China
| | - Jianjun Du
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Jiangli Fan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
- Ningbo Institute of Dalian University of Technology, Ningbo 315016, China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
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46
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Mondal IC, Galkin M, Sharma S, Murugan NA, Yushchenko DA, Girdhar K, Karmakar A, Mondal P, Gaur P, Ghosh S. Organosulfur/selenium-based Highly Fluorogenic Molecular Probes for Live-Cell Nucleolus Imaging. Chem Asian J 2022; 17:e202101281. [PMID: 35129298 DOI: 10.1002/asia.202101281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/16/2022] [Indexed: 11/10/2022]
Abstract
We present rationally designed cationic organochalcogens highly selective to RNA. We have demonstrated that the conformational dynamics and subsequently the optical properties of these dyes can be controlled to facilitate efficient bioimaging. We report organoselenium and organosulfur-based cell-permeable red-emissive probes bearing favorable cyclic sidearm with potential for selective and high contrast imaging of cell nucleoli. The probes exhibit high quantum yield upon interaction with RNA in an aqueous solution. An in-depth multiscale simulation study reveals that the prominent rotational freezing of the electron-donating sidearm of the probes in the microenvironment of RNA helps in attaining more planar conformation when compared to DNA. It exerts a greater extent of intramolecular charge transfer and hence leads to enhanced fluorescence emission. A systematic structure-interaction relationship study highlighted the impact of heavy-chalcogens toward the improved emissive properties of the probes.
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Affiliation(s)
| | - Maksym Galkin
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Laboratory of Chemical Biology, CZECH REPUBLIC
| | - Shubham Sharma
- IIT Mandi: Indian Institute of Technology Mandi, School of Basic Sciences, INDIA
| | - N Arul Murugan
- KTH Royal Institute of Technology, Department of Computer Science, SWEDEN
| | - Dmytro A Yushchenko
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Laboratory of Chemical Biology, CZECH REPUBLIC
| | - Khyati Girdhar
- IIT Mandi: Indian Institute of Technology Mandi, School of Basic Sciences, INDIA
| | - Anirban Karmakar
- Instituto Superior Tecnico Avenida Rovisco Pais, Centro de Quimica Estrutural, PORTUGAL
| | - Prosenjit Mondal
- IIT Mandi: Indian Institute of Technology Mandi, School of Basic Sciences, INDIA
| | - Pankaj Gaur
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Laboratory of Chemical Biology, CZECH REPUBLIC
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47
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Xue H, Lu J, Yan H, Huang J, Luo HB, Wong MS, Gao Y, Zhang X, Guo L. γ-Glutamyl transpeptidase-activated indole-quinolinium based cyanine as a fluorescence turn-on nucleolus-targeting probe for cancer cell detection and inhibition. Talanta 2022; 237:122898. [PMID: 34736714 DOI: 10.1016/j.talanta.2021.122898] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/10/2021] [Accepted: 09/19/2021] [Indexed: 01/02/2023]
Abstract
A nucleolus as a prominent sub-nuclear, membraneless organelle plays a crucial role in ribosome biogenesis, which is in the major metabolic demand in a proliferating cell, especially in aggressive malignancies. We develop a γ-glutamyltranspeptidase (GGT)-activatable indole-quinolinium (QI) based cyanine consisting of a novel tripeptide fragment (Pro-Gly-Glu), namely QI-PG-Glu as a turn-on red fluorescent probe for the rapid detection of GGT-overexpressed A549 cancer cells in vivo. QI-PG-Glu can be triggered by GGT to rapidly release an activated fluorophore, namely HQI, in two steps including the cleavage of the γ-glutamyl group recognized by GGT and the rapid self-driven cyclization of the Pro-Gly linker. HQI exhibits dramatically red fluorescence upon binding to rRNA for imaging of nucleolus in live A549 cells. HQI also intervenes in rRNA biogenesis by declining the RNA Polymerase I transcription, thus resulting in cell apoptosis via a p53 dependent signaling pathway. Our findings may provide an alternative avenue to develop multifunctional cancer cell-specific nucleolus-targeting fluorescent probes with potential anti-cancer effects.
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Affiliation(s)
- Huanxin Xue
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Jiaye Lu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Hongwei Yan
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Ju Huang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Man Shing Wong
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Yuqi Gao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
| | - Xiaolei Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
| | - Lei Guo
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
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48
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Sato Y, Igarashi Y, Suzuki M, Higuchi K, Nishizawa S. Deep-red fluorogenic cyanine dyes carrying an amino group-terminated side chain for improved RNA detection and nucleolar RNA imaging. RSC Adv 2021; 11:35436-35439. [PMID: 35493132 PMCID: PMC9042821 DOI: 10.1039/d1ra05872j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/22/2021] [Indexed: 01/01/2023] Open
Abstract
The introduction of an amino-group-terminated side chain into deep-red emissive benzo[c,d]indole–quinoline monomethine cyanine dye has led to the improved detection of RNAs as well as the imaging of nucleolar RNAs in cells. The introduction of an amino-group-terminated side chain into deep-red emissive benzo[c,d]indole–quinoline monomethine cyanine dye has led to the improved detection of RNAs as well as the imaging of nucleolar RNAs in cells.![]()
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku Sendai 980-8578 Japan +81-22-795-6552 +81-22-795-6549
| | - Yugo Igarashi
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku Sendai 980-8578 Japan +81-22-795-6552 +81-22-795-6549
| | - Michiyuki Suzuki
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku Sendai 980-8578 Japan +81-22-795-6552 +81-22-795-6549
| | - Kei Higuchi
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku Sendai 980-8578 Japan +81-22-795-6552 +81-22-795-6549
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku Sendai 980-8578 Japan +81-22-795-6552 +81-22-795-6549
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49
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Yu H, Guo Y, Zhu W, Havener K, Zheng X. Recent advances in 1,8-naphthalimide-based small-molecule fluorescent probes for organelles imaging and tracking in living cells. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214019] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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50
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He H, Chen X, Feng Z, Liu L, Wang Q, Bi S. Nanoscopic Imaging of Nucleolar Stress Enabled by Protein-Mimicking Carbon Dots. NANO LETTERS 2021; 21:5689-5696. [PMID: 34181434 DOI: 10.1021/acs.nanolett.1c01420] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The nucleolus is a central hub for coordinating cellular stress responses during cancer development and treatment. Accurate identification of nucleolar stress response is crucially desired for nucleolus-based diagnostics and therapeutics but technically challenging due to the need to address the ultrastructural analysis. Here, we report a protein-like CD with the integration of fluorescent blinking domains and RNA-binding motifs, which offers the ability to perform enhanced super-resolution imaging of the nucleolar ultrastructure. This image allows extraction of multidimensional information from the nucleolus for accurate distinguishment of different cells from the same cell types. Furthermore, we demonstrate for the first time this CD-depicted nucleolar ultrastructure as a sensitive hallmark to identify and discriminate subtle responses to various stressors as well as to afford RNA-related information that has been inaccessible by conventional immunofluorescence methods. This protein-mimicking CD could become a broadly useful probe for nucleolar stress studies in cell diagnostics and therapeutics.
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Affiliation(s)
- Hua He
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaoliang Chen
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Zhenzhen Feng
- Technical Center of Qingdao Customs District, Qingdao 266500, China
| | - Lihua Liu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Qian Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Simin Bi
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
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