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Luo C, Yao W, Zhang H, Jia M, Lim CK, Hu W. Shedding light on imaging safety: Decoding the origin of photocytotoxicity in RhB-assisted fluorescence imaging. JOURNAL OF BIOPHOTONICS 2024; 17:e202400049. [PMID: 38634340 DOI: 10.1002/jbio.202400049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
Photocytotoxicity represents a significant limitation in the application of dye-assisted fluorescence imaging (FI), often resulting in undesirable cellular damage or even cell death, thereby restricting their practical utility. The prevalence of Rhodamine B (RhB) in FI underscores the importance of elucidating its photocytotoxicity effects to minimize photodamage. This study identifies the primary cause of photocytotoxicity stems from the generation of cytotoxic singlet oxygen in RhB, utilizing femtosecond transient absorption spectroscopy coupled with quantum chemical calculations. The Laser power-dependent cellular viability reveals a threshold at about 50 mW cm-2, surpassing which produces pronounced photocytotoxicity in vitro and in vivo. Notably, this threshold significantly falls below the safety limits (<200 mW cm-2) for laser use in health care, implying a huge risk of photodamage. This study provides valuable insights into the photocytotoxicity and offers essential guidelines for developing safer imaging protocols.
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Affiliation(s)
- Chaoqun Luo
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE), and Ningbo Institute of Northwestern Polytechnical University, Northwestern Polytechnical University, Xi'an, China
| | - Weiyun Yao
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE), and Ningbo Institute of Northwestern Polytechnical University, Northwestern Polytechnical University, Xi'an, China
| | - Haolin Zhang
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE), and Ningbo Institute of Northwestern Polytechnical University, Northwestern Polytechnical University, Xi'an, China
| | - Mingxuan Jia
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE), and Ningbo Institute of Northwestern Polytechnical University, Northwestern Polytechnical University, Xi'an, China
| | - Chang-Keun Lim
- School of Engineering and Digital Sciences, Department of Chemical and Materials Engineering, Nazarbayev University, Astana, Kazakhstan
| | - Wenbo Hu
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE), and Ningbo Institute of Northwestern Polytechnical University, Northwestern Polytechnical University, Xi'an, China
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2
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Zhao Z, Jiang M, He C, Yin W, Feng Y, Wang P, Ying L, Fu T, Su D, Peng R, Tan W. Enhancing Specific Fluorescence In Situ Hybridization with Quantum Dots for Single-Molecule RNA Imaging in Formalin-Fixed Paraffin-Embedded Tumor Tissues. ACS NANO 2024; 18:9958-9968. [PMID: 38547522 DOI: 10.1021/acsnano.3c10216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Single-molecule fluorescence in situ hybridization (smFISH) represents a promising approach for the quantitative analysis of nucleic acid biomarkers in clinical tissue samples. However, low signal intensity and high background noise are complications that arise from diagnostic pathology when performed with smFISH-based RNA imaging in formalin-fixed paraffin-embedded (FFPE) tissue specimens. Moreover, the associated complex procedures can produce uncertain results and poor image quality. Herein, by combining the high specificity of split DNA probes with the high signal readout of ZnCdSe/ZnS quantum dot (QD) labeling, we introduce QD split-FISH, a high-brightness smFISH technology, to quantify the expression of mRNA in both cell lines and clinical FFPE tissue samples of breast cancer and lung squamous carcinoma. Owing to its high signal-to-noise ratio, QD split-FISH is a fast, inexpensive, and sensitive method for quantifying mRNA expression in FFPE tumor tissues, making it suitable for biomarker imaging and diagnostic pathology.
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Affiliation(s)
- Zeyin Zhao
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Mengyuan Jiang
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chen He
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Wenjuan Yin
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yawei Feng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Peng Wang
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lisha Ying
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Dan Su
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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3
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Gu Y, Fan C, Yang H, Sun H, Wang X, Qiu X, Chen B, Li CM, Guo C. Fluorogenic RNA Aptamer-Based Amplification and Transcription Strategy for Label-free Sensing of Methyltransferase Activity in Complex Matrixes. Adv Biol (Weinh) 2024; 8:e2300668. [PMID: 38327153 DOI: 10.1002/adbi.202300668] [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: 12/29/2023] [Indexed: 02/09/2024]
Abstract
DNA methyltransferase is significant in cellular activities and gene expression, and its aberrant expression is closely linked to various cancers during initiation and progression. Currently, there is a great demand for reliable and label-free techniques for DNA methyltransferase evaluation in tumor diagnosis and cancer therapy. Herein, a low-background fluorescent RNA aptamer-based sensing approach for label-free quantification of cytosine-guanine (CpG) dinucleotides methyltransferase (M.SssI) is reported. The fluorogenic light-up RNA aptamers-based strategy exhibits high selectivity via restriction endonuclease, padlock-based recognition, and RNA transcription. By combining rolling circle amplification (RCA), and RNA transcription with fluorescence response of RNA aptamers of Spinach-dye compound, the proposed platform exhibited efficiently ultrahigh sensitivity toward M.SssI. Eventually, the detection can be achieved in a linear range of 0.02-100 U mL-1 with a detection limit of 1.6 × 10-3 U mL-1. Owing to these superior features, the method is further applied in serum samples spiked M.SssI, which delivers a recovery ranging from 92.0 to 107.0% and a relative standard deviation <7.0%, providing a promising and practical tool for determining M.SssI in complex biological matrices.
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Affiliation(s)
- Yu Gu
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Cunxia Fan
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Hongbin Yang
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Huiping Sun
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Xiaobao Wang
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Xingchen Qiu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Bo Chen
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
- Jiangsu Key Laboratory for Biomaterials and Devices, Department of Biological Science and Medical Engineering, Southeast University, Nanjing, 210009, P. R. China
| | - Chang-Ming Li
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
| | - Chunxian Guo
- Institute for Materials Science and Devices, School of Materials Science and Engineering, Suzhou University of Science and Technology, Kerui Road, Suzhou, 215009, P.R. China
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4
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Feng Y, Liu S, Yao Y, Chen M, Liu Q, Chen X. Endogenous mRNA-Powered and Spatial Confinement-Derived DNA Nanomachines for Ultrarapid and Sensitive Imaging of Let-7a. Anal Chem 2024; 96:564-571. [PMID: 38112715 DOI: 10.1021/acs.analchem.3c04837] [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: 12/21/2023]
Abstract
DNA nanostructure-based signal amplifiers offer new tools for imaging intracellular miRNA. However, the inadequate kinetics and susceptibility to enzymatic hydrolysis of these amplifiers, combined with a deficient cofactor concentration within the intracellular environment, significantly undermine their operational efficiency. In this study, we address these challenges by encapsulating a localized target strand displacement assembly (L-SD) and a toehold-exchange endogenous-powered component (R-mRNA) within a framework nucleic acid (FNA) structure─20 bp cubic DNA nanocage (termed RL-cube). This design enables the construction of an endogenous-powered and spatial-confinement DNA nanomachine for ratiometric fluorescence imaging of intracellular miRNA Let-7a. The R-mRNA is designed to be specifically triggered by glyceraldehyde 3-phosphate dehydrogenase (GAPDH), an abundant cellular enzyme, and concurrently releases a component that can recycle the target Let-7a. Meanwhile, L-SD reacts with Let-7a to release a stem-loop beacon, generating a FRET signal. The spatial confinement provided by the framework, combined with the ample intracellular supply of GAPDH, imparts remarkable sensitivity (7.57 pM), selectivity, stability, biocompatibility, and attractive dynamic performance (2240-fold local concentration, approximately four times reaction rate, and a response time of approximately 7 min) to the nanomachine-based biosensor. Consequently, this study introduces a potent sensing approach for detecting nucleic acid biomarkers with significant potential for application in clinical diagnostics and therapeutics.
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Affiliation(s)
- Yinghui Feng
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Shenghong Liu
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Yao Yao
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Miao Chen
- College of Life Science, Central South University, Changsha 410083, Hunan, China
| | - Qi Liu
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Xiaoqing Chen
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
- Xiangjiang Laboratory, Changsha 410205, Hunan, China
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5
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Yin S, Zhao Y, Chen F, Zhong Z, Lu Q, Li H, Zhang Y. DNA Sensor-Based Strategy to Visualize the TRPM7 mRNA-Mg 2+ Signaling Pathway in Cancer Cells. Anal Chem 2023; 95:18107-18113. [PMID: 38019640 DOI: 10.1021/acs.analchem.3c03323] [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: 12/01/2023]
Abstract
Technological advances and methodological innovations in cell signaling pathway analysis will facilitate progress in understanding biological processes, intervening in diseases, and screening drugs. In this work, an elaborate strategy for visualizing and monitoring the transient receptor potential melastatin 7 (TRPM7)-Mg2+ signaling pathway in living cells was constructed through the logical analysis of upstream mRNA and downstream molecules by two individual DNA sensors. The DNA sensors are constructed by modifying the dye-labeled DNA sequences on the surface of gold nanoparticles. By hybridizing with upstream mRNA, Cy5-modified DNA sensor 1 can detect and silence it simultaneously, outputting a red fluorescence signal. When the upstream mRNA is silenced, the concentration of downstream molecules of Mg2+ will be affected and down-regulated. The FAM-modified DNA sensor 2 detects this change and emits a green fluorescence as a signal. Therefore, the dynamic information on TRPM7 mRNA and the Mg2+-mediated signaling pathway can be successfully obtained by fluorescence imaging methods. Furthermore, the TRPM7 mRNA-Mg2+ signaling pathway also affects cell activity and migratory function through cell scratching and other experiments. More importantly, the proposed sensor also shows potential for screening signaling pathway inhibitors. Our work provides a simple and general strategy for the visualization of signaling pathways, which helps to understand the changes in the physiological activities of cancer cells and the causes of carcinogenesis and is crucial for cancer diagnosis and prognosis.
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Affiliation(s)
- Shuhang Yin
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Yang Zhao
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Feng Chen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Zijie Zhong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Qiujun Lu
- College of Biological and Chemical Engineering, Changsha University, Changsha, Hunan 410022, China
| | - Haitao Li
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Youyu Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
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6
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Eguchi M, Yoshimura H, Ueda Y, Ozawa T. Split Luciferase-Fragment Reconstitution for Unveiling RNA Localization and Dynamics in Live Cells. ACS Sens 2023; 8:4055-4063. [PMID: 37889477 DOI: 10.1021/acssensors.3c01080] [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: 10/28/2023]
Abstract
The intracellular distribution and dynamics of RNAs play pivotal roles in various physiological phenomena. The ability to monitor the amount and localization of endogenous RNAs in living cells allows for elucidating the mechanisms of various intracellular events. Protein-based fluorescent RNA probes are now widely used to visualize and analyze RNAs in living cells. However, continuously monitoring the temporal changes in RNA localization and dynamics in living cells is challenging. In this study, we developed a bioluminescent probe for spatiotemporal monitoring of RNAs in living cells by using a split-luciferase reconstitution technique. The probe consists of split fragments of a bioluminescent protein, NanoLuc, connected with RNA-binding protein domains generated from a custom-made mutation of a PUM-HD. The probe showed rapid luminescence intensity changes in response to an increase or decrease in the amount of a target RNA in vitro. In live-cell imaging, temporal alteration of the intracellular distribution of endogenous β-actin mRNA was visualized in response to extracellular stimulation. Furthermore, the application of the probe to the visualization of the specific localization of β-actin mRNA in primary hippocampal neurons was conducted. These results demonstrate the capability of the bioluminescent RNA probe to monitor the changes in localization, dynamics, and the amount of target RNA in living cells.
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Affiliation(s)
- Masatoshi Eguchi
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshibumi Ueda
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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7
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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: 0] [Impact Index Per Article: 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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8
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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: 1.0] [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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9
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Feng X, Li L, Zhao Y, Li M. Enzyme and MicroRNA Dual-Regulated Photodynamic Molecular Beacons for Cell-Selective Amplification of Antitumor Efficacy. NANO LETTERS 2023; 23:7743-7749. [PMID: 37406355 DOI: 10.1021/acs.nanolett.3c01814] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Photodynamic molecular beacons (PMBs) are highly appealing for activatable photodynamic therapy (PDT), but their applications are hindered by limited therapeutic efficacy. Here, by molecular engineering of enzyme-responsive units in the loop region of DNA-based PMBs, we present for the first time the modular design of an enzyme/microRNA dual-regulated PMB (D-PMB) to achieve cancer-cell-selective amplification of PDT efficacy. In the design, the "inert" photosensitizers in D-PMB could be repeatedly activated in the presence of both tumor-specific enzyme and miRNA, leading to amplified generation of cytotoxic singlet oxygen species and therefore enhanced PDT efficacy in vitro and in vivo. By contrast, low photodynamic activity could be observed in healthy cells, as D-PMB activation has been largely avoided by the dual-regulatable design. This work presents a cooperatively activated PDT strategy, which enables enhanced therapeutic efficacy with improved tumor-specificity and thus conceptualizes an approach to expand the repertoire of designing smart tumor treatment modality.
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Affiliation(s)
- Xueyan Feng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Mengyuan Li
- School of Chemistry and Biological Engineering, Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing 100083, China
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10
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Yang F, Li S, Bi X, Yuan R, Xiang Y. Multicolor-Encoded DNA Framework Enables Specific and Amplified In Situ Detection of the Mitochondrial Apoptotic Signaling Pathway. Anal Chem 2023; 95:12514-12520. [PMID: 37553880 DOI: 10.1021/acs.analchem.3c02462] [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: 08/10/2023]
Abstract
Monitoring the molecular activation networks of cellular processes through fluorescence imaging to accurately elucidate the signaling pathways of mitochondrial apoptosis and the regulation of upstream and downstream molecules remains a current major challenge. In this work, a multicolor-encoded tetrahedral DNA framework (meTDF) carrying two pairs of catalytic hairpins is synthesized to monitor the intracellular upstream manganese superoxide dismutase (MnSOD) mRNA and the downstream cytochrome c (Cyt c) molecules for specific and sensitive detection of the mitochondrial apoptotic signaling pathway. These two types of molecules can trigger catalytic hairpin assembly (CHA) reactions with accelerated reaction kinetics for the hairpin pairs confined on meTDF to show highly amplified fluorescence for sensitive and simultaneous detection of MnSOD mRNA and Cyt c with detection limits of 3.7 pM and 0.23 nM in vitro, respectively. Moreover, the high stability and biocompatibility of the designed meTDF can facilitate efficient delivery of the probes into cells to monitor intracellular MnSOD mRNA and Cyt c for specific detection of the mitochondrial apoptosis pathway regulated by different drugs. With the successful demonstration of their robust capability, the meTDF nanoprobes can thus open new opportunities for detecting cell apoptotic mechanisms for studying the corresponding apoptotic signaling pathways and for screening potential therapeutic drugs.
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Affiliation(s)
- Fang Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Shunmei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xin Bi
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yun Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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11
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Sohrab SS, Raj R, Nagar A, Hawthorne S, Paiva-Santos AC, Kamal MA, El-Daly MM, Azhar EI, Sharma A. Chronic Inflammation's Transformation to Cancer: A Nanotherapeutic Paradigm. Molecules 2023; 28:molecules28114413. [PMID: 37298889 DOI: 10.3390/molecules28114413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
The body's normal immune response against any invading pathogen that causes infection in the body results in inflammation. The sudden transformation in inflammation leads to the rise of inflammatory diseases such as chronic inflammatory bowel disease, autoimmune disorders, and colorectal cancer (different types of cancer develop at the site of chronic infection and inflammation). Inflammation results in two ways: short-term inflammation i.e., non-specific, involves the action of various immune cells; the other results in long-term reactions lasting for months or years. It is specific and causes angiogenesis, fibrosis, tissue destruction, and cancer progression at the site of inflammation. Cancer progression relies on the interaction between the host microenvironment and tumor cells along with the inflammatory responses, fibroblast, and vascular cells. The two pathways that have been identified connecting inflammation and cancer are the extrinsic and intrinsic pathways. Both have their own specific role in linking inflammation to cancer, involving various transcription factors such as Nuclear factor kappa B, Activator of transcription, Single transducer, and Hypoxia-inducible factor, which in turn regulates the inflammatory responses via Soluble mediators cytokines (such as Interleukin-6, Hematopoietin-1/Erythropoietin, and tumor necrosis factor), chemokines (such as Cyclooxygenase-2, C-X-C Motif chemokines ligand-8, and IL-8), inflammatory cells, cellular components (such as suppressor cells derived from myeloid, tumor-associated macrophage, and acidophils), and promotes tumorigenesis. The treatment of these chronic inflammatory diseases is challenging and needs early detection and diagnosis. Nanotechnology is a booming field nowadays for its rapid action and easy penetration inside the infected destined cells. Nanoparticles are widely classified into different categories based on their different factors and properties such as size, shape, cytotoxicity, and others. Nanoparticles emerged as excellent with highly progressive medical inventions to cure diseases such as cancer, inflammatory diseases, and others. Nanoparticles have shown higher binding capacity with the biomolecules in inflammation reduction and lowers the oxidative stress inside tissue/cells. In this review, we have overall discussed inflammatory pathways that link inflammation to cancer, major inflammatory diseases, and the potent action of nanoparticles in chronic inflammation-related diseases.
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Affiliation(s)
- Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Riya Raj
- Department of Biochemistry, Bangalore University, Banglore 560056, India
| | - Amka Nagar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida 201310, India
| | - Susan Hawthorne
- School of Pharmacy and Pharmaceutical Sciences, Ulster University, Coleraine BT52 1SA, UK
| | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of University of Coimbra, University of Coimbra, 3000-548 Coimbra, Portugal
- LAQV, REQUIMTE, Department of Pharmaceutical Technology, Faculty of Pharmacy of University of Coimbra, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Mohammad Amjad Kamal
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Enzymoics Inc., Hebersham, NSW 2770, Australia
- Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | - Mai M El-Daly
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ankur Sharma
- Strathclyde Institute of Pharmaceutical and Biomedical Sciences, University of Strathclyde, Glasgow G1 0RE, UK
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12
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Thu M, Yanai K, Shigeto H, Yamamura S, Watanabe K, Ohtsuki T. FRET probe for detecting two mutations in one EGFR mRNA. Analyst 2023; 148:2626-2632. [PMID: 37191032 DOI: 10.1039/d3an00554b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Technologies for visualizing and tracking RNA are essential in molecular biology, including in disease-related fields. In this study, we propose a novel probe set (DAt-probe and T-probe) that simultaneously detects two mutations in the same RNA using fluorescence resonance energy transfer (FRET). The DAt-probe carrying the fluorophore Atto488 and the quencher Dabcyl were used to detect a cancer mutation (exon19del), and the T-probe carrying the fluorophore Tamra was used to detect drug resistance mutations (T790M) in epidermal growth factor receptor (EGFR) mRNA. These probes were designed to induce FRET when both mutations were present in the mRNA. Gel electrophoresis confirmed that the two probes could efficiently bind to the mutant mRNA. We measured the FRET ratios using wild-type and double-mutant RNAs and found a significant difference between them. Even in living cells, the FRET probe could visualize mutant RNA. As a result, we conclude that this probe set provides a method for detecting two mutations in the single EGFR mRNA via FRET.
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Affiliation(s)
- Myat Thu
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan.
| | - Kouta Yanai
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan.
| | - Hajime Shigeto
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Shohei Yamamura
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Kazunori Watanabe
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan.
| | - Takashi Ohtsuki
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan.
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13
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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: 0] [Impact Index Per Article: 0] [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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14
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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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15
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Zhan Y, Zhang R, Guo Y, Cao S, Chen G, Tian B. Recent advances in tumor biomarker detection by lanthanide upconversion nanoparticles. J Mater Chem B 2023; 11:755-771. [PMID: 36606393 DOI: 10.1039/d2tb02017c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Early tumor diagnosis could reliably predict the behavior of tumors and significantly reduce their mortality. Due to the response to early cancerous changes at the molecular or cellular level, tumor biomarkers, including small molecules, proteins, nucleic acids, exosomes, and circulating tumor cells, have been employed as powerful tools for early cancer diagnosis. Therefore, exploring new approaches to detect tumor biomarkers has attracted a great deal of research interest. Lanthanide upconversion nanoparticles (UCNPs) provide numerous opportunities for bioanalytical applications. When excited by low-energy near-infrared light, UCNPs exhibit several unique properties, such as large anti-Stoke shifts, sharp emission lines, long luminescence lifetimes, resistance to photobleaching, and the absence of autofluorescence. Based on these excellent properties, UCNPs have demonstrated great sensitivity and selectivity in detecting tumor biomarkers. In this review, an overview of recent advances in tumor biomarker detection using UCNPs has been presented. The key aspects of this review include detection mechanisms, applications in vitro and in vivo, challenges, and perspectives of UCNP-based tumor biomarker detection.
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Affiliation(s)
- Ying Zhan
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Runchi Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Yi Guo
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Siyu Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Bo Tian
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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16
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Dong Z, Xu X, Ni J, Li Y, An K, Meng L, Wu H. Cruciate DNA probes for amplified multiplexed imaging of microRNAs in living cells. J Mater Chem B 2022; 11:204-210. [PMID: 36504047 DOI: 10.1039/d2tb02027k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The real-time imaging of low-abundance tumor-related microRNAs (miRNAs) in living cells holds great potential for early clinical diagnosis of cancers. However, the relatively low detection sensitivity and possible false-positive signals of a probe in complex cellular matrices remain critical challenges for accurate RNA detection. Herein, we developed a novel aptamer-functionalized cruciate DNA probe that enabled amplified multiple miRNA imaging in living cells via catalytic hairpin assembly (CHA). The cross-shaped design of the cruciate DNA probe improved the stability against nucleases and acted as a modular scaffold for CHA circuits for efficient delivery into tumor cells. The cruciate DNA probe allowed self-assembly through thermal annealing and displayed excellent performance for sensitive miRNA detection in vitro. The cruciate DNA probe could be internalized into nucleolin-overexpressed cells specifically via cell-targeting of the AS1411 aptamer, achieving amplified fluorescence imaging and quantitative evaluation of the expression of miRNAs in living cells. Through the simultaneous detection of intracellular multiple miRNAs, the developed cruciate DNA probe could provide more accurate information and reduce the chances of false positive signals for cancer diagnosis. This approach offers a new opportunity for promoting the development of miRNA-related biomedical research and tumor diagnostic applications.
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Affiliation(s)
- Zhe Dong
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.,State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Xizhu Xu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Jing Ni
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Yuancheng Li
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Kang An
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Ling Meng
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Han Wu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
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17
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Chen L, Liu Y, Guo W, Liu Z. Light responsive nucleic acid for biomedical application. EXPLORATION 2022; 2:20210099. [PMCID: PMC10190984 DOI: 10.1002/exp.20210099] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/03/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Liwei Chen
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University Changsha Hunan Province P. R. China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University Changsha Hunan Province P. R. China
| | - Weisheng Guo
- Department of Minimally Invasive Interventional Radiology Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & The Second Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong Province P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics Xiangya School of Pharmaceutical Sciences Central South University Changsha Hunan Province P. R. China
- Molecular Imaging Research Center of Central South University Changsha Hunan Province P. R. China
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18
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Sheng J, Pi Y, Zhao S, Wang B, Chen M, Chang K. Novel DNA nanoflower biosensing technologies towards next-generation molecular diagnostics. Trends Biotechnol 2022; 41:653-668. [PMID: 36117022 DOI: 10.1016/j.tibtech.2022.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/29/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022]
Abstract
DNA nanoflowers (DNFs) are topological flower-like nanostructures based on ultralong-strand DNA and inorganic metal-ion frameworks. Because of their programmability, biocompatibility, and controllable assembly size for specific responses to molecular recognition stimuli, DNFs are powerful biosensing tools for detecting biomolecules. Here, we review the current state of DNF-based biosensing strategies for in vivo and in vitro detection, with a view of how the field has evolved towards molecular diagnostics. We also provide a detailed classification of DNF-based biosensing strategies and propose their future utility. Particularly as transduction elements, DNFs can accelerate biosensing engineering by signal amplification. Finally, we discuss the key challenges and further prospects of DNF-based biosensing technologies in developing applications of a broader scope.
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Affiliation(s)
- Jing Sheng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Yan Pi
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, China
| | - Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Binpan Wang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China; College of Pharmacy and Laboratory Medicine, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China; State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
| | - Kai Chang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
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19
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Recent advance of RNA aptamers and DNAzymes for MicroRNA detection. Biosens Bioelectron 2022; 212:114423. [DOI: 10.1016/j.bios.2022.114423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 02/02/2023]
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20
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Liu X, Xiang J, Cheng H, Wang Y, Li F. Engineering Multipedal
DNA
Walker on Paper for Sensitive Electrochemical Detection of Plant
MicroRNA. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences Qingdao Agricultural University Qingdao 266109 People's Republic of China
| | - Junzhu Xiang
- College of plant health & medicine Qingdao Agricultural University Qingdao 266109 People's Republic of China
| | - Hao Cheng
- College of plant health & medicine Qingdao Agricultural University Qingdao 266109 People's Republic of China
| | - Yuying Wang
- College of plant health & medicine Qingdao Agricultural University Qingdao 266109 People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences Qingdao Agricultural University Qingdao 266109 People's Republic of China
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21
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Gebhard J, Hirsch L, Schwechheimer C, Wagenknecht HA. Hybridization-Sensitive Fluorescent Probes for DNA and RNA by a Modular "Click" Approach. Bioconjug Chem 2022; 33:1634-1642. [PMID: 35995426 PMCID: PMC9501807 DOI: 10.1021/acs.bioconjchem.2c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Fluorescent DNA probes were prepared in a modular approach
using
the “click” post-synthetic modification strategy. The
new glycol-based module and DNA building block place just two carbons
between the phosphodiester bridges and anchor the dye by an additional
alkyne group. This creates a stereocenter in the middle of this artificial
nucleoside substitute. Both enantiomers and a variety of photostable
cyanine–styryl dyes as well as thiazole orange derivatives
were screened as “clicked” conjugates in different surrounding
DNA sequences. The combination of the (S)-configured
DNA anchor and the cyanylated cyanine–styryl dye shows the
highest fluorescence light-up effect of 9.2 and a brightness of approximately
11,000 M–1 cm–1. This hybridization
sensitivity and fluorescence readout were further developed utilizing
electron transfer and energy transfer processes. The combination of
the hybridization-sensitive DNA building block with the nucleotide
of 5-nitroindole as an electron acceptor and a quencher increases
the light-up effect to 20 with the DNA target and to 15 with the RNA
target. The fluorescence readout could significantly be enhanced to
values between 50 and 360 by the use of energy transfer to a second
DNA probe with commercially available dyes, like Cy3.5, Cy5, and Atto590,
as energy acceptors at the 5′-end. The latter binary probes
shift the fluorescent readout from the range of 500–550 nm
to the range of 610–670 nm. The optical properties make these
fluorescent DNA probes potentially useful for RNA imaging. Due to
the strong light-up effect, they will not require washing procedures
and will thus be suitable for live-cell imaging.
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Affiliation(s)
- Julian Gebhard
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Lara Hirsch
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Christian Schwechheimer
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
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22
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Fluorescent Platforms for RNA Chemical Biology Research. Genes (Basel) 2022; 13:genes13081348. [PMID: 36011259 PMCID: PMC9407474 DOI: 10.3390/genes13081348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022] Open
Abstract
Efficient detection and observation of dynamic RNA changes remain a tremendous challenge. However, the continuous development of fluorescence applications in recent years enhances the efficacy of RNA imaging. Here we summarize some of these developments from different aspects. For example, single-molecule fluorescence in situ hybridization (smFISH) can detect low abundance RNA at the subcellular level. A relatively new aptamer, Mango, is widely applied to label and track RNA activities in living cells. Molecular beacons (MBs) are valid for quantifying both endogenous and exogenous mRNA and microRNA (miRNA). Covalent binding enzyme labeling fluorescent group with RNA of interest (ROI) partially overcomes the RNA length limitation associated with oligonucleotide synthesis. Forced intercalation (FIT) probes are resistant to nuclease degradation upon binding to target RNA and are used to visualize mRNA and messenger ribonucleoprotein (mRNP) activities. We also summarize the importance of some fluorescence spectroscopic techniques in exploring the function and movement of RNA. Single-molecule fluorescence resonance energy transfer (smFRET) has been employed to investigate the dynamic changes of biomolecules by covalently linking biotin to RNA, and a focus on dye selection increases FRET efficiency. Furthermore, the applications of fluorescence assays in drug discovery and drug delivery have been discussed. Fluorescence imaging can also combine with RNA nanotechnology to target tumors. The invention of novel antibacterial drugs targeting non-coding RNAs (ncRNAs) is also possible with steady-state fluorescence-monitored ligand-binding assay and the T-box riboswitch fluorescence anisotropy assay. More recently, COVID-19 tests using fluorescent clustered regularly interspaced short palindromic repeat (CRISPR) technology have been demonstrated to be efficient and clinically useful. In summary, fluorescence assays have significant applications in both fundamental and clinical research and will facilitate the process of RNA-targeted new drug discovery, therefore deserving further development and updating.
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23
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Zhao Y, Li X, Xiang MH, Gao F, Qu F, Li M, Lu L. Enzyme-free nucleic acid dual-amplification strategy combined with mimic enzyme catalytic precipitation reaction for the photoelectrochemical detection of microRNA-21. Mikrochim Acta 2022; 189:249. [PMID: 35680731 DOI: 10.1007/s00604-022-05345-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/27/2022] [Indexed: 11/28/2022]
Abstract
A novel photoelectrochemical (PEC) biosensor based on an enzyme-free nucleic acid dual-amplification strategy combined with a mimic enzyme to catalyze the deposition of a quencher is reported for the ultrasensitive detection of miRNA-21. A limited amount of target miRNA-21 can trigger the formation of long DNA duplexes on the electrode, owing to the synergistic effect of the enzyme-free nucleic acid dual-amplification strategy of entropy-driven strand displacement reaction (ESDR) amplification and hybridization chain reaction (HCR) amplification. The embedded manganese porphyrin (MnPP) in the long DNA duplexes acts as a horseradish peroxidase (HRP)-mimicking enzyme to catalyze the transformation of benzo-4-chlorohexadienone on the electrode surface, resulting in a significant reduction in photocurrent intensity. As a photosensitive material, BiOCl-BiOI is used as a tag to provide strong initial PEC signals. Based on the cascade integration of the enzyme-free nucleic acid dual-amplification strategy and the mimic enzyme-catalyzed precipitation reaction, the current PEC biosensor exhibits outstanding performance for miRNA-21 detection with an ultralow detection limit (33 aM) and a wide quantification range (from 100 aM to 1 nM). This work provides a new avenue toward the ultrasensitive detection of miRNAs, and is expected to be used for clinical and biochemical samples. A unique PEC biosensor with the BiOCl-BiOI composite, as the photosensitive material, has been developed for ultrasensitive miRNA-21 determination based on the combination of an enzyme-free nucleic acid dual-amplification strategy and mimic enzyme catalytic precipitation reaction.
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Affiliation(s)
- Yan Zhao
- Key Laboratory of Chemical Utilization of Plant Resources of Nanchang, College of Science, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.,College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Xiaomeng Li
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Mei-Hao Xiang
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Feng Gao
- Key Laboratory of Chemical Utilization of Plant Resources of Nanchang, College of Science, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Fengli Qu
- Key Laboratory of Chemical Utilization of Plant Resources of Nanchang, College of Science, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China. .,College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, 273165, Shandong, China.
| | - Mingfang Li
- Key Laboratory of Chemical Utilization of Plant Resources of Nanchang, College of Science, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Limin Lu
- Key Laboratory of Chemical Utilization of Plant Resources of Nanchang, College of Science, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
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Fam KT, Pelletier R, Bouhedda F, Ryckelynck M, Collot M, Klymchenko AS. Rational Design of Self-Quenched Rhodamine Dimers as Fluorogenic Aptamer Probes for Live-Cell RNA Imaging. Anal Chem 2022; 94:6657-6664. [PMID: 35486532 DOI: 10.1021/acs.analchem.1c04556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the growing interest in the understanding of the importance of RNAs in health and disease, detection of RNAs in living cells is of high importance. Fluorogenic dyes that light up specifically selected RNA aptamers constitute an attractive direction in the design of RNA imaging probes. In this work, based on our recently proposed concept of a fluorogenic dimer, we aim to develop a robust molecular tool for intracellular RNA imaging. We rationally designed a fluorogenic self-quenched dimer (orange Gemini, o-Gemini) based on rhodamine and evaluated its capacity to light up its cognate aptamer o-Coral in solution and live cells. We found that the removal of biotin from the dimer slightly improved the fluorogenic response without losing the affinity to the cognate aptamer (o-Coral). On the other hand, replacing sulforhodamine with a carboxyrhodamine produced drastic improvement of the affinity and the turn-on response to o-Coral and, thus, a better limit of detection. In live cells expressing o-Coral-tagged RNAs, the carboxyrhodamine analogue of o-Gemini without a biotin unit displayed a higher signal as well as faster internalization into the cells. We suppose that less hydrophilic carboxyrhodamine compared to sulforhodamine can more readily penetrate through the cell plasma membrane and, together with its higher affinity to o-Coral, provide the observed improvement in the imaging experiments. The promiscuity of the o-Coral RNA aptamer to the fluorogenic dimer allowed us to tune a fluorogen chemical structure and thus drastically improve the fluorescence response of the probe to o-Coral-tagged RNAs.
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Affiliation(s)
- Kyong Tkhe Fam
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
| | - Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
| | - Farah Bouhedda
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, F-67000 Strasbourg, France
| | - Michael Ryckelynck
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, F-67000 Strasbourg, France
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Université de Strasbourg, 67401 Illkirch, France
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25
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Cao H, Wang Y, Zhang N, Xia S, Tian P, Lu L, Du J, Du Y. Progress of CRISPR-Cas13 Mediated Live-Cell RNA Imaging and Detection of RNA-Protein Interactions. Front Cell Dev Biol 2022; 10:866820. [PMID: 35356276 PMCID: PMC8959342 DOI: 10.3389/fcell.2022.866820] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/21/2022] [Indexed: 12/26/2022] Open
Abstract
Ribonucleic acid (RNA) and proteins play critical roles in gene expression and regulation. The relevant study increases the understanding of various life processes and contributes to the diagnosis and treatment of different diseases. RNA imaging and mapping RNA-protein interactions expand the understanding of RNA biology. However, the existing methods have some limitations. Recently, precise RNA targeting of CRISPR-Cas13 in cells has been reported, which is considered a new promising platform for RNA imaging in living cells and recognition of RNA-protein interactions. In this review, we first described the current findings on Cas13. Furthermore, we introduced current tools of RNA real-time imaging and mapping RNA-protein interactions and highlighted the latest advances in Cas13-mediated tools. Finally, we discussed the advantages and disadvantages of Cas13-based methods, providing a set of new ideas for the optimization of Cas13-mediated methods.
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Affiliation(s)
- Huake Cao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yuechen Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Second School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Ning Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
- First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Siyuan Xia
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Second School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Pengfei Tian
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
- First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li Lu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Juan Du
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, China
- Longgang District People’s Hospital of Shenzhen & The Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen, China
- *Correspondence: Yinan Du, ; Juan Du,
| | - Yinan Du
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- *Correspondence: Yinan Du, ; Juan Du,
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26
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Liu X, Wang Y, Effah CY, Wu L, Yu F, Wei J, Mao G, Xiong Y, He L. Endocytosis and intracellular RNAs imaging of nanomaterials-based fluorescence probes. Talanta 2022; 243:123377. [DOI: 10.1016/j.talanta.2022.123377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/12/2022]
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27
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Sun C, Gradzielski M. Advances in fluorescence sensing enabled by lanthanide-doped upconversion nanophosphors. Adv Colloid Interface Sci 2022; 300:102579. [PMID: 34924169 DOI: 10.1016/j.cis.2021.102579] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 01/02/2023]
Abstract
Lanthanide-doped upconversion nanoparticles (UCNPs), characterized by converting low-energy excitation to high-energy emission, have attracted considerable interest due to their inherent advantages of large anti-Stokes shifts, sharp and narrow multicolor emissions, negligible autofluorescence background interference, and excellent chemical- and photo-stability. These features make them promising luminophores for sensing applications. In this review, we give a comprehensive overview of lanthanide-doped upconversion nanophosphors including the fundamental principle for the construction of UCNPs with efficient upconversion luminescence (UCL), followed by state-of-the-art strategies for the synthesis and surface modification of UCNPs, and finally describing current advances in the sensing application of upconversion-based probes for the quantitative analysis of various analytes including pH, ions, molecules, bacteria, reactive species, temperature, and pressure. In addition, emerging sensing applications like photodetection, velocimetry, electromagnetic field, and voltage sensing are highlighted.
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Affiliation(s)
- Chunning Sun
- Stranski-Laboratorium für Physikalische und Theoretische Chemie, Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany.
| | - Michael Gradzielski
- Stranski-Laboratorium für Physikalische und Theoretische Chemie, Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany.
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28
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Egloff S, Melnychuk N, Cruz Da Silva E, Reisch A, Martin S, Klymchenko AS. Amplified Fluorescence in Situ Hybridization by Small and Bright Dye-Loaded Polymeric Nanoparticles. ACS NANO 2022; 16:1381-1394. [PMID: 34928570 DOI: 10.1021/acsnano.1c09409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Detection and imaging of RNA at the single-cell level is of utmost importance for fundamental research and clinical diagnostics. Current techniques of RNA analysis, including fluorescence in situ hybridization (FISH), are long, complex, and expensive. Here, we report a methodology of amplified FISH (AmpliFISH) that enables simpler and faster RNA imaging using small and ultrabright dye-loaded polymeric nanoparticles (NPs) functionalized with DNA. We found that the small size of NPs (below 20 nm) was essential for their access to the intracellular mRNA targets in fixed permeabilized cells. Moreover, proper selection of the polymer matrix of DNA-NPs minimized nonspecific intracellular interactions. Optimized DNA-NPs enabled sequence-specific imaging of different mRNA targets (survivin, actin, and polyA tails), using a simple 1 h staining protocol. Encapsulation of cyanine and rhodamine dyes with bulky counterions yielded green-, red-, and far-red-emitting NPs that were 2-100-fold brighter than corresponding quantum dots. These NPs enabled multiplexed detection of three mRNA targets simultaneously, showing distinctive mRNA expression profiles in three cancer cell lines. Image analysis confirmed the single-particle nature of the intracellular signal, suggesting single-molecule sensitivity of the method. AmpliFISH was found to be semiquantitative, correlating with RT-qPCR. In comparison with the commercial locked nucleic acid (LNA)-based FISH technique, AmpliFISH provides 8-200-fold stronger signal (dependent on the NP color) and requires only three steps vs ∼20 steps together with a much shorter time. Thus, combination of bright fluorescent polymeric NPs with FISH yields a fast and sensitive single-cell transcriptomic analysis method for RNA research and clinical diagnostics.
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Affiliation(s)
- Sylvie Egloff
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Nina Melnychuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Elisabete Cruz Da Silva
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Andreas Reisch
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Sophie Martin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
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29
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Xu H, Chen D, Jia L. Intelligent assembly of Y-shaped DNA nanostructures for intracellular microRNA imaging. Anal Chim Acta 2022; 1189:338701. [PMID: 34815048 DOI: 10.1016/j.aca.2021.338701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/14/2021] [Accepted: 05/25/2021] [Indexed: 11/26/2022]
Abstract
Highly sensitive and specific imaging of low-level microRNAs (miRNAs) in cytoplasm is vital for early diagnosis of cancers. In this work, we have developed the amplification strategies for miRNA-155 detection based on the combination the nicked rolling circle amplification (N-RCA) and catalyzed hairpin assembly (CHA). In this system, the target miRNA-155 acts as a polymerase primer to activate N-RCA to produce nicked fragment1 (NF1) and NF2. NF1 acted as new primer could further initiate a new N-RCA reaction over and over. Then, the NF2s could serve as triggers to induce the CHA reaction, and the Y-shaped DNA nanostructure (Y-SDN) was formed. Thus, an amplified fluorescence signal was obtained based on the multiple amplification. Under the optimized experimental conditions, a high sensitivity with a detection limit as low as 1.8 pM at 3σ miRNA-155 and excellent specificity in buffer condition have been achieved by applying this method. Meanwhile, the proposed method enables the application in miRNA-155 detection in human serum. Moreover, we have shown that the method performs well for the intracellular miRNA-155 imaging in cellular environments. Therefore, the present strategy was expected to apply into the clinical disease diagnosis effectively.
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Affiliation(s)
- Huo Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China.
| | - Danlong Chen
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China
| | - Lee Jia
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, China.
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30
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Xia LY, Tang YN, Zhang J, Dong TY, Zhou RX. Advances in the DNA Nanotechnology for the Cancer Biomarkers Analysis: Attributes and Applications. Semin Cancer Biol 2022; 86:1105-1119. [PMID: 34979273 DOI: 10.1016/j.semcancer.2021.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023]
Abstract
The most commonly used clinical methods are enzyme-linked immunosorbent assay (ELISA) and quantitative PCR (qPCR) in which ELISA was applied for the detection of protein biomarkers and qPCR was especially applied for nucleic acid biomarker analysis. Although these constructed methods have been applied in wide range, they also showed some inherent shortcomings such as low sensitivity, large sample volume and complex operations. At present, many methods have been successfully constructed on the basis of DNA nanotechnology with the merits of high accuracy, rapid and simple operation for cancer biomarkers assay. In this review, we summarized the bioassay strategies based on DNA nanotechnology from the perspective of the analytical attributes for the first time and discussed and the feasibility of the reported strategies for clinical application in the future.
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Affiliation(s)
- Ling-Ying Xia
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China; Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Ya-Nan Tang
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Jie Zhang
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Tian-Yu Dong
- College of Chemistry, Sichuan University Chengdu, Sichuan 610064, PR China
| | - Rong-Xing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan 610064, PR China.
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31
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Chen H, Liu Y, Feng S, Cao Y, Wu T, Liu Z. Cotton thread-based multi-channel photothermal biosensor for simultaneous detection of multiple microRNAs. Biosens Bioelectron 2021; 200:113913. [PMID: 34968855 DOI: 10.1016/j.bios.2021.113913] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023]
Abstract
The abnormal expression of microRNAs (miRNAs) is associated with various diseases. Developing simple and portable methods for sensitive, rapid and simultaneous detection of multiple miRNAs is critical to achieve accurate and timely diagnosis. Herein, a cotton thread-based multi-channel photothermal biosensor was proposed for simultaneous detection of three breast cancer-related miRNAs including miRNA-10b, miRNA-27a and miRNA-let-7a. Three cotton thread-based channels with one input were designed and the capture probes for detecting different miRNAs were immobilized on the test zones of the corresponding channels. Cu2-xS nanostrings prepared on the basis of hybridization chain reaction (HCR) were taken as the photothermal agents for signal transduction and amplification. The formation of a sandwich structure among the capture probe, target miRNA, and Cu2-xS nanostrings led to the accumulation of the Cu2-xS nanostrings on the test zones and transformed the concentration of miRNA into temperature signal under 808 nm laser irradiation. The temperature changes were quantified by a portable thermal camera and directly reflected the concentration of miRNAs. Under the optimal conditions, the developed multi-channel photothermal biosensor showed excellent specificity and sensitivity with the detection limits of 37 pM, 38 pM and 38 pM for miRNA-10b, miRNA-27a and miRNA-let-7a, respectively. Furthermore, a simultaneous detection of the three miRNAs in cell lysates were achieved and the results were in accordance with that obtained by the quantitative reverse transcription polymerase chain reaction (qRT-PCR), indicating its excellent capacity for practical applications. The developed biosensor provided an important tool for analysis of multiple targets and showed great potential in clinical diagnosis.
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Affiliation(s)
- Hanjun Chen
- College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Ying Liu
- College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Shaoqiong Feng
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Yu Cao
- College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China
| | - Tingting Wu
- College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China.
| | - Zhihong Liu
- College of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, PR China; College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
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32
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Tabara K, Watanabe K, Shigeto H, Yamamura S, Kishi T, Kitamatsu M, Ohtsuki T. Fluorophore-PNA-Quencher/Quencher-DNA probe for miRNA detection. Bioorg Med Chem Lett 2021; 51:128359. [PMID: 34534675 DOI: 10.1016/j.bmcl.2021.128359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/26/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
Micro RNAs (miRNAs) are involved in a variety of biological functions and are attracting attention as diagnostic and prognostic markers for various diseases. Highly sensitive RNA detection methods are required to determine miRNA expression levels and intracellular localization. In this study, we designed new double-stranded peptide nucleic acid (PNA)/DNA probes consisting of a fluorophore-PNA-quencher (fPq) and a quencher-DNA (qD) for miR-221 detection. We optimized the fPq structure, PNA-DNA hybrid length, and hybrid position. The resultant fPq-2/qD-6b probe was a 6-bp hybrid probe with a 10-base fPq and a 6-base qD. The signal-to-background ratios of the probes showed that fPq-2/qD-6b had a higher target sensitivity than fPq (PNA beacon)-type and fP/qD-type probes. The results of the detection limit and target specificity indicate that the fPq/qD probe is promising for RNA detection in both cells and cell extracts as well as for miRNA diagnosis.
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Affiliation(s)
- Kentaro Tabara
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Kazunori Watanabe
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Hajime Shigeto
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Shohei Yamamura
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Takamasa Kishi
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Mizuki Kitamatsu
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Takashi Ohtsuki
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan.
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33
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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: 1.0] [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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34
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Zhang J, Wang L, Jäschke A, Sunbul M. A Color‐Shifting Near‐Infrared Fluorescent Aptamer–Fluorophore Module for Live‐Cell RNA Imaging. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jingye Zhang
- Institute of Pharmacy and Molecular Biotechnology (IPMB) Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Lu Wang
- Department of Chemical Biology Max Planck Institute for Medical Research Jahnstraße 29 69120 Heidelberg Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB) Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB) Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
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35
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Depaix A, Mlynarska-Cieslak A, Warminski M, Sikorski PJ, Jemielity J, Kowalska J. RNA Ligation for Mono and Dually Labeled RNAs. Chemistry 2021; 27:12190-12197. [PMID: 34114681 DOI: 10.1002/chem.202101909] [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: 06/01/2021] [Indexed: 12/27/2022]
Abstract
Labeled RNAs are invaluable probes for investigation of RNA function and localization. However, mRNA labeling remains challenging. Here, we developed an improved method for 3'-end labeling of in vitro transcribed RNAs. We synthesized novel adenosine 3',5'-bisphosphate analogues modified at the N6 or C2 position of adenosine with an azide-containing linker, fluorescent label, or biotin and assessed these constructs as substrates for RNA labeling directly by T4 ligase or via postenzymatic strain-promoted alkyne-azide cycloaddition (SPAAC). All analogues were substrates for T4 RNA ligase. Analogues containing bulky fluorescent labels or biotin showed better overall labeling yields than postenzymatic SPAAC. We successfully labeled uncapped RNAs, NAD-capped RNAs, and 5'-fluorescently labeled m7 Gp3 Am -capped mRNAs. The obtained highly homogenous dually labeled mRNA was translationally active and enabled fluorescence-based monitoring of decapping. This method will facilitate the use of various functionalized mRNA-based probes.
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Affiliation(s)
- Anaïs Depaix
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Agnieszka Mlynarska-Cieslak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
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36
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Murayama K, Asanuma H. Design and Hybridization Properties of Acyclic Xeno Nucleic Acid Oligomers. Chembiochem 2021; 22:2507-2515. [PMID: 33998765 DOI: 10.1002/cbic.202100184] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/17/2021] [Indexed: 12/24/2022]
Abstract
Xeno nucleic acids (XNAs) are analogues of DNA and RNA that have a non-ribose artificial scaffold. XNAs are possible prebiotic genetic carriers as well as alternative genetic systems in artificial life. In addition, XNA oligomers can be used as biological tools. Acyclic XNAs, which do not have cyclic scaffolds, are attractive due to facile their synthesis and remarkably high nuclease resistance. To maximize the performance of XNAs, a negatively charged backbone is preferable to provide sufficient water solubility; however, acyclic XNAs containing polyanionic backbones suffer from high entropy cost upon duplex formation, because of the high flexibility of the acyclic nature. Herein, we review the relationships between the structure and duplex hybridization properties of various acyclic XNA oligomers with polyanion backbones.
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Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
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37
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Zhang J, Wang L, Jäschke A, Sunbul M. A Color-Shifting Near-Infrared Fluorescent Aptamer-Fluorophore Module for Live-Cell RNA Imaging. Angew Chem Int Ed Engl 2021; 60:21441-21448. [PMID: 34309994 PMCID: PMC8518806 DOI: 10.1002/anie.202107250] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Indexed: 11/07/2022]
Abstract
Fluorescent light‐up RNA aptamers (FLAPs) have become promising tools for visualizing RNAs in living cells. Specific binding of FLAPs to their non‐fluorescent cognate ligands results in a dramatic fluorescence increase, thereby allowing RNA imaging. Here, we present a color‐shifting aptamer‐fluorophore system, where the free dye is cyan fluorescent and the aptamer‐dye complex is near‐infrared (NIR) fluorescent. Unlike other reported FLAPs, this system enables ratiometric RNA imaging. To design the color‐shifting system, we synthesized a series of environmentally sensitive benzopyrylium‐coumarin hybrid fluorophores which exist in equilibrium between a cyan fluorescent spirocyclic form and a NIR fluorescent zwitterionic form. As an RNA tag, we evolved a 38‐nucleotide aptamer that selectively binds the zwitterionic forms with nanomolar affinity. We used this system as a light‐up RNA marker to image mRNAs in the NIR region and demonstrated its utility in ratiometric analysis of target RNAs expressed at different levels in single cells.
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Affiliation(s)
- Jingye Zhang
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Lu Wang
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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38
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Miao P, Tang Y. Cascade Strand Displacement and Bipedal Walking Based DNA Logic System for miRNA Diagnostics. ACS CENTRAL SCIENCE 2021; 7:1036-1044. [PMID: 34235264 PMCID: PMC8228592 DOI: 10.1021/acscentsci.1c00277] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 05/05/2023]
Abstract
DNA logic gated operations empower the highly efficient analysis of multiplex nucleic acid inputs, which have attracted extensive attention. However, the integration of DNA logic gates with abundant computational functions and signal amplification for biomedical diagnosis is far from being fully achieved. Herein, we develop a bipedal DNA walker based amplified electrochemical method for miRNA detection, which is then used as the basic unit for the construction of various logic circuits, enabling the analysis of multiplex miRNAs. In the bipedal walking process, target triggered strand displacement polymerization is able to produce a large number of strands for the fabrication of three-way junction-structured bipedal walkers. The following catalytic hairpin assembly ensures the walking event and the immobilization of signal probes for output. Ultrahigh sensitivity is realized due to the integration of dual signal amplification. In addition, under logic function controls by input triggered cascade strand displacement reactions, NOT, AND, OR, NAND, NOR, XOR, and XNOR logic gates are successfully established. The as-developed DNA logic system can also be extended to multi-input modes, which holds great promise in the fields of DNA computing, multiplex analysis, and clinical diagnosis.
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Affiliation(s)
- Peng Miao
- Suzhou
Institute of Biomedical Engineering and Technology, Chinese Academy
of Sciences, Suzhou 215163, People’s Republic
of China
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Yuguo Tang
- Suzhou
Institute of Biomedical Engineering and Technology, Chinese Academy
of Sciences, Suzhou 215163, People’s Republic
of China
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39
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Poly(A)+ Sensing of Hybridization-Sensitive Fluorescent Oligonucleotide Probe Characterized by Fluorescence Correlation Methods. Int J Mol Sci 2021; 22:ijms22126433. [PMID: 34208525 PMCID: PMC8234900 DOI: 10.3390/ijms22126433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022] Open
Abstract
Ribonucleic acid (RNA) plays an important role in many cellular processes. Thus, visualizing and quantifying the molecular dynamics of RNA directly in living cells is essential to uncovering their role in RNA metabolism. Among the wide variety of fluorescent probes available for RNA visualization, exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probes are useful because of their low fluorescence background. In this study, we apply fluorescence correlation methods to ECHO probes targeting the poly(A) tail of mRNA. In this way, we demonstrate not only the visualization but also the quantification of the interaction between the probe and the target, as well as of the change in the fluorescence brightness and the diffusion coefficient caused by the binding. In particular, the uptake of ECHO probes to detect mRNA is demonstrated in HeLa cells. These results are expected to provide new insights that help us better understand the metabolism of intracellular mRNA.
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40
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Dong Z, Yan S, Liu B, Hao Y, Lin L, Chang T, Sun H, Wang Y, Li H, Wu H, Hang X, He S, Hu J, Xue X, Wu N, Chang L. Single Living Cell Analysis Nanoplatform for High-Throughput Interrogation of Gene Mutation and Cellular Behavior. NANO LETTERS 2021; 21:4878-4886. [PMID: 33830766 DOI: 10.1021/acs.nanolett.1c00199] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The genetic heterogeneities in cancer cells pose challenges to achieving precise drug treatment in a widely applicable manner. Most single-cell gene analysis methods rely on cell lysis for gene extraction and identification, showing limited capacity to provide the correlation of genetic properties and real-time cellular behaviors. Here, we report a single living cell analysis nanoplatform that enables interrogating gene properties and drug resistance in millions of single cells. We designed a Domino-probe to identify intracellular target RNAs while releasing 10-fold amplified fluorescence signals. An on-chip addressable microwell-nanopore array was developed for enhanced electro-delivery of the Domino-probe and in situ observation of cell behaviors. The proof-of-concept of the system was validated in primary lung cancer cell samples, revealing the positive-correlation of the ratio of EGFR mutant cells with their drug susceptibilities. This platform provides a high-throughput yet precise tool for exploring the relationship between intracellular genes and cell behaviors at the single-cell level.
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Affiliation(s)
- Zaizai Dong
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Shi Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Bing Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yongcun Hao
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, Northwestern Polytechnical University, Xi'an 710072, China
| | - Long Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Tianrui Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Hong Sun
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yusen Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Hu Li
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Han Wu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xinxin Hang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Shiqi He
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Jiaming Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Xinying Xue
- Department of Respiratory and Critical Care, Beijing Shijitan Hospital, Capital Medical University, Peking University Ninth School of Clinical Medicine, Beijing 100038, China
- Department of Respiratory and Critical Care, Chinese PLA General Hospital, Beijing 100853, China
- Affiliated Hospital of Weifang Medical University, Shandong 261031, China
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
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41
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Li Z, Zhang P, Zhang R, Wang X, Tse YC, Zhang H. A collection of toolkit strains reveals distinct localization and dynamics of membrane-associated transcripts in epithelia. Cell Rep 2021; 35:109072. [PMID: 33951426 DOI: 10.1016/j.celrep.2021.109072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/10/2021] [Accepted: 04/11/2021] [Indexed: 01/10/2023] Open
Abstract
Visualizing mRNA in real time in vivo at high resolution is critical for a full understanding of the spatiotemporal dynamics of gene regulation and function. Here, using a PP7/PCP-based mRNA-tagging approach, we construct a collection of tissue-specific and differentially expressed toolkit strains for visualizing mRNAs encoding apical, basolateral, and junctional proteins in Caenorhabditis elegans epithelia. We precisely delineate the spatiotemporal organization and dynamics of these transcripts across multiple subcellular compartments and tissues. Remarkably, all the transcripts exhibit an asymmetric, membrane-associated localization during epithelial polarization and maturation, which suggests that mRNA localization is a prerequisite for epithelial polarization and function. Single-particle tracking reveals striking features of the transport dynamics of the mRNAs in a gene-specific, compartment-linked, and time-resolved manner. The toolkit can be used to identify the cis-regulatory elements and trans-acting factors for mRNA localization. This study provides a valuable resource to investigate complex RNA dynamics in epithelial polarity and morphogenesis.
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Affiliation(s)
- Zhimin Li
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR 999078, China
| | - Pei Zhang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR 999078, China
| | - Ruotong Zhang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR 999078, China
| | - Xinyan Wang
- Core Research Facilities, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yu Chung Tse
- Core Research Facilities, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongjie Zhang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR 999078, China.
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42
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Chang J, Zhang Y, Li Y, Han Z, Tian F, Liu C, Feng Q, Wang Y, Sun J, Zhang L. Multilayer Ratiometric Fluorescent Nanomachines for Imaging mRNA in Live Cells. SMALL METHODS 2021; 5:e2001047. [PMID: 34927842 DOI: 10.1002/smtd.202001047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/15/2020] [Indexed: 06/14/2023]
Abstract
Detection of mRNA expression in live cells during treatment is a challenging task, despite its importance in tumor biology and potential therapeutic leads. Here a multilayer ratiometric fluorescent nanomachine for live-cell perturbation and imaging of mRNA at single cell resolution is reported. The nanomachines fabricated by microfluidic approaches consist of fluorescent polymeric cores and multiple lipid layers, which can efficiently deliver siRNA and molecular beacons (MBs) to cytosol and then release the cargo in a sequential way. The siRNA molecules released from the outer lipid layers lead to silencing of multidrug resistance 1 (MDR1) gene, and the MBs from the middle lipid layers detect the presence of MDR1 mRNA. The fluorescent ratio of MBs to fluorescent polymeric cores positively correlates with the expression level of MDR1 mRNA in MCF-7/ADR cells during siRNA treatment. The nanomachines provide comparable results with traditional qPCR for quantifying mRNA, showing great potential for modulation and imaging of intratumoral mRNA in vitro and in vivo.
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Affiliation(s)
- Jianqiao Chang
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100149, China
| | - Yu Zhang
- Department of Medical Oncology and Radiation Sickness, Peking University Third Hospital, Peking University, Beijing, 100191, China
| | - Yike Li
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100149, China
| | - Ziwei Han
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100149, China
| | - Fei Tian
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100149, China
| | - Chao Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100149, China
| | - Qiang Feng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100149, China
| | - Yuguang Wang
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Center of Digital Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100149, China
| | - Lu Zhang
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
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43
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Chen J, Zhang Y, Chen D, Wang T, Yin W, Yang HH, Xu Y, Chen JX, Dai Z, Zou X. Toehold-mediated ligation-free rolling circle amplification enables sensitive and rapid imaging of messenger RNAs in situ in cells. Anal Chim Acta 2021; 1160:338463. [PMID: 33894961 DOI: 10.1016/j.aca.2021.338463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 11/27/2022]
Abstract
In situ analysis of tumor-related messenger RNAs (mRNAs) is significant in identifying cancer cells at the genetic level in the early stage. Rolling circle amplification (RCA)-based methods are primary tools for in situ mRNA assay, however, the necessary ligation reaction not only shows low ligation efficiency, but also greatly prolongs the assay time that increases the risk of cells losing and mRNAs leakage. In this work, we propose a novel toehold-mediated ligation-free RCA (TMLFRCA) on a designed structure-switchable dumbbell-shaped probe (SDP). Target mRNA can specifically activate SDP from its circular form by toehold strand displacement, thereby initiates in situ RCA for mRNA imaging with the help of a short DNA primer. For the proof-of-concept demonstration, the TK1 mRNA was sensitively detected by TMLFRCA in less than 3.5 h with a limit of detection (LOD) of 0.39 fM (corresponds to 2.39×108copiesL-1), and significantly improved specificity capable for distinguishing single base difference. The sensitivity of the TMLFRCA for TK1 mRNA in situ assay is ∼29-fold and ∼7-fold higher than that of FISH and ligase-assisted RCA method, respectively, which enables the TMLFRCA method capability of highly sensitive and specific distinction mRNA expression levels between cancer cells and normal cells. We believe this TMLFRCA strategy would be of great value in both basic research and clinical diagnosis.
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Affiliation(s)
- Jun Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Yanfei Zhang
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou, 510275, PR China
| | - Danping Chen
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou, 510275, PR China
| | - Tianchen Wang
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou, 510275, PR China
| | - Wen Yin
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou, 510275, PR China
| | - Hui-Hui Yang
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou, 510275, PR China
| | - Yuzhi Xu
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou, 510275, PR China
| | - Jin-Xiang Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China
| | - Zong Dai
- School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 511400, PR China.
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, 135 Xingang West Road, Guangzhou, 510275, PR China
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44
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Gao P, Lou R, Liu X, Cui B, Pan W, Li N, Tang B. Rational Design of a Dual-Layered Metal–Organic Framework Nanostructure for Enhancing the Cell Imaging of Molecular Beacons. Anal Chem 2021; 93:5437-5441. [DOI: 10.1021/acs.analchem.0c05060] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Peng Gao
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Ruxin Lou
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Xiaohan Liu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Bingjie Cui
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
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45
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Wu H, Zhou WJ, Liu L, Fan Z, Tang H, Yu RQ, Jiang JH. In vivo mRNA imaging based on tripartite DNA probe mediated catalyzed hairpin assembly. Chem Commun (Camb) 2021; 56:8782-8785. [PMID: 32618290 DOI: 10.1039/d0cc03596c] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Herein, we develop a novel tripartite DNA probe to transport phosphorothioated substrate hairpins and an aptamer for the intramolecular CHA circuit, which achieves detection of a low amount of specific mRNA in living cells and mice. Our study provides an improved strategy to promote in vivo fluorescence imaging applications in early-stage clinical diagnosis.
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Affiliation(s)
- Han Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Wen-Jing Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Lan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Ze Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Hao Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
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46
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Chang J, Lv W, Wu J, Li H, Li F. Simultaneous photoelectrochemical detection of dual microRNAs by capturing CdS quantum dots and methylene blue based on target-initiated strand displaced amplification. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.05.041] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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47
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Gao L, Wang W, Wang X, Yang F, Xie L, Shen J, Brimble MA, Xiao Q, Yao SQ. Fluorescent probes for bioimaging of potential biomarkers in Parkinson's disease. Chem Soc Rev 2021; 50:1219-1250. [DOI: 10.1039/d0cs00115e] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review comprehensively summarizes various types of fluorescent probes for PD and their applications for detection of various PD biomarkers.
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Affiliation(s)
- Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
- Department of Chemistry
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
- Department of Chemistry
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
| | - Fen Yang
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
| | - Liuxing Xie
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
| | - Jun Shen
- Department of Radiology
- Sun Yat-Sen Memorial Hospital
- Sun Yat-Sen University
- Guangzhou
- P. R. China
| | - Margaret A. Brimble
- School of Chemical Sciences
- The University of Auckland
- Auckland 1010
- New Zealand
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
- Department of Chemistry
| | - Shao Q. Yao
- Department of Chemistry
- National University of Singapore
- Singapore
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48
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Jiang M, Mu J, Jacobson O, Wang Z, He L, Zhang F, Yang W, Lin Q, Zhou Z, Ma Y, Lin J, Qu J, Huang P, Chen X. Reactive Oxygen Species Activatable Heterodimeric Prodrug as Tumor-Selective Nanotheranostics. ACS NANO 2020; 14:16875-16886. [PMID: 33206522 DOI: 10.1021/acsnano.0c05722] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanotheranostics based on tumor-selective small molecular prodrugs could be more advantageous in clinical translation for cancer treatment, given its defined chemical structure, high drug loading efficiency, controlled drug release, and reduced side effects. To this end, we have designed and synthesized a reactive oxygen species (ROS)-activatable heterodimeric prodrug, namely, HRC, and nanoformulated it for tumor-selective imaging and synergistic chemo- and photodynamic therapy. The prodrug consists of the chemodrug camptothecin (CPT), the photosensitizer 2-(1-hexyloxyethyl)-2-devinyl pyropheophorbide-a (HPPH), and a thioketal linker. Compared to CPT- or HPPH-loaded polymeric nanoparticles (NPs), HRC-loaded NPs possess higher drug loading capacity, better colloidal stability, and less premature drug leakage. Interestingly, HRC NPs were almost nonfluorescent due to the strong π-π stacking and could be effectively activated by endogenous ROS once entering cells. Thanks to the higher ROS levels in cancer cells than normal cells, HRC NPs could selectively light up the cancer cells and exhibit much more potent cytotoxicity to cancer cells. Moreover, HRC NPs demonstrated highly effective tumor accumulation and synergistic tumor inhibition with reduced side effects on mice.
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Affiliation(s)
- Meijuan Jiang
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jing Mu
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Orit Jacobson
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zhantong Wang
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Liangcan He
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Fuwu Zhang
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Weijing Yang
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Qiaoya Lin
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zijian Zhou
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ying Ma
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jing Lin
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Peng Huang
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, Maryland 20892, United States
- Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 117597, Singapore
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Dong Z, Xue X, Liang H, Guan J, Chang L. DNA Nanomachines for Identifying Cancer Biomarkers in Body Fluids and Cells. Anal Chem 2020; 93:1855-1865. [PMID: 33325676 DOI: 10.1021/acs.analchem.0c03518] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Identifying molecular biomarkers promises to significantly improve the accuracy in cancer diagnosis at its early stage. DNA nanomachines, which are designable and switchable nanostructures made of DNA, show broad potential to detect tumor biomarkers with noninvasive, inexpensive, highly sensitive, and highly specific advantages. This Feature summarizes the recent DNA nanomachine-based platforms for the early detection of cancer biomarkers, both from body fluids and in cells.
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Affiliation(s)
- Zaizai Dong
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xinying Xue
- Department of Respiratory and Critical Care, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China.,Department of Respiratory and Critical Care, Chinese PLA General Hospital, Beijing 100853, China
| | - Hailun Liang
- School of Public Administration and Policy, Renmin University of China, Beijing 100872, China
| | - Jingjiao Guan
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China.,School of Biomedical Engineering, Research and Engineering Center of Biomedical Materials, Anhui Medical University, Hefei 230032, China
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Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
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Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
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