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Sun H, Fu B, Qian X, Xu P, Qin W. Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction. Nat Commun 2024; 15:852. [PMID: 38286993 PMCID: PMC10825125 DOI: 10.1038/s41467-024-44987-9] [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: 06/21/2022] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs display enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of Tricarboxylic acid cycle in the translocation candidate RBPs may provide insights for investigating their possible roles in ferroptosis induced metabolism dysregulation.
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Affiliation(s)
- Haofan Sun
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Bin Fu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Ping Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Weijie Qin
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
- College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
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Zeng Y, Qian M, Yang X, Gao Q, Zhang C, Qi H. Electrochemiluminescence bioassay with anti-fouling ability for determination of matrix metalloproteinase 9 secreted from living cells under external stimulation. Mikrochim Acta 2023; 190:422. [PMID: 37775573 DOI: 10.1007/s00604-023-05996-5] [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: 05/01/2023] [Accepted: 09/13/2023] [Indexed: 10/01/2023]
Abstract
An electrochemiluminescence (ECL) bioassay with high sensitivity and anti-fouling ability was developed for determination of matrix metalloproteinase 9 (MMP-9) secreted from living cells under external stimulation. A peptide with sequence of CLGRMGLPGK and a new cyclometalated iridium(III) complex bearing carboxyl group, (pq)2Ir(dcbpy) (pq = 2-phenylquinoline, dcbpy = 2,2'-bipyridyl-4,4'-dicarboxyli acid, abbreviated as Ir) were employed as molecular recognition substrate and ECL emitter, respectively. The peptide was labelled with the Ir to form Ir-peptide as ECL probe. Ir-peptide was self-assembled onto Nafion and gold nanoparticles (AuNPs) modified glassy carbon electrode (AuNPs/Nafion/GCE) and then both of 6-mercapto-1-hexanol (MCH) and zwitterionic peptide as blocking reagents were co-assembled on Ir-peptide/AuNPs/Nafion/GCE to form an anti-fouling ECL peptide-based biosensor. MMP-9 can be quantified in the range 1.0-50 ng·mL-1 with a detection limit of 0.50 ng·mL-1 based on the decreased ECL intensity. Relative standard derivation was 2.3% for six fabricated anti-fouling ECL peptide-based biosensors after reaction with 50 ng·mL-1 MMP-9. The anti-fouling ECL peptide-based biosensor can be used to monitor MMP-9 secreted from living cells under external stimulation. 96.0%-108.0% of recoveries were obtained in 60-diluted cell culture media. This study demonstrates that the ECL biosensor by the combination of iridium(III) complex-based sensitive ECL method and the anti-fouling interface provides a promising way for the determination of MMP-9 in biological sample, which is viable in clinical diagnosis and point-of-care test of protease.
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Affiliation(s)
- Yu Zeng
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Manping Qian
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Xiaolin Yang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China.
| | - Qiang Gao
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Chengxiao Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Honglan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China.
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Huang H, Wu Y, Qian M, Yang X, Qi H. Iridium(III) solvent complex-based electrogenerated chemiluminescence and photoluminescence sensor array for the discrimination of bases in oligonucleotides. Bioelectrochemistry 2023; 150:108368. [PMID: 36634465 DOI: 10.1016/j.bioelechem.2023.108368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/24/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Development of rapid and sensitive method for the discrimination of bases in oligonucleotides is of great importance in clinical diagnosis. Here, we demonstrate the first case of single iridium(III) solvent complex-based electrogenerated chemiluminescence (ECL) and photoluminescence (PL) sensor array for the discrimination of bases in oligonucleotides. One iridium (III) solvent complex ([Ir(ppy)2(DMSO)Cl], ppy = 2-phenylpyridine, probe 1) was designed as both ECL and PL probe while five bases (guanine, adenine, cytosine, thymine and uracil) were chosen as analytes. Two-element sensor array was built for the discrimination of five bases based on the fingerprint response of probe 1 to bases via coordination interactions. The combination of unique ECL and PL variations with principal component analysis was applied for the quantitative analysis of five bases in a linear range of 1.0 μM-10 μM and for the effective discrimination of individual base, the mixture of bases and oligonucleotides. Moreover, the sensor array was successfully applied to discriminate different mismatched ss-DNAs from HIV gene (a fully-matched ss-DNA), even at single-base difference. This work demonstrates that the sensor array using single iridium (III) solvent complex is a promising approach for the discrimination of bases with good sensitivity and simpleness in clinical diagnosis.
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Affiliation(s)
- Hong Huang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China
| | - Yang Wu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China
| | - Manping Qian
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China
| | - Xiaolin Yang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China.
| | - Honglan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, PR China.
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Wei Y, Qi H, Zhang C. Recent advances and challenges in developing electrochemiluminescence biosensors for health analysis. Chem Commun (Camb) 2023; 59:3507-3522. [PMID: 36820650 DOI: 10.1039/d2cc06930j] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
This Feature Article simply introduces principles and mechanisms of electrochemiluminescence (ECL) biosensors for the determination of biomarkers and highlights recent advances of ECL biosensors on key aspects including new ECL reagents and materials, new biological recognition elements, and emerging construction biointerfacial strategies with illustrative examples and a critical eye on pitfalls and discusses challenges and perspectives of ECL biosensors for health analysis.
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Affiliation(s)
- Yuxi Wei
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, P. R. China.
| | - Honglan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, P. R. China.
| | - Chengxiao Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, P. R. China.
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Electron transfer in protein modifications: from detection to imaging. Sci China Chem 2023. [DOI: 10.1007/s11426-022-1417-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Chen R, Wang X, Wu K, Liu S, Zhang Y. Voltammetric Study and Modeling of the Electrochemical Oxidation Process and the Adsorption Effects of Luminol and Luminol Derivatives on Glassy Carbon Electrodes. Anal Chem 2022; 94:17625-17633. [PMID: 36475634 DOI: 10.1021/acs.analchem.2c04297] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Luminol is one of the most widely used electrochemiluminescence (ECL) reagents, yet the detailed mechanism and kinetics of the electrochemical oxidation of luminol remain unclear. We propose a model that describes the electrochemical oxidation of luminol as multiple electron transfer reactions followed by an irreversible chemical reaction, and we applied a finite element method simulation to analyze the electron transfer kinetics in alkaline solutions. Although negligible at higher pH values, the adsorption of luminol on the glassy carbon electrode became noticeable in a solution with pH = 12. Additionally, various types of adsorption behaviors were observed for luminol derivatives and analogues, indicating that the molecular structure affected not only the oxidation but also the adsorption process. The adsorption effect was analyzed through a model with a Langmuir isotherm to show that the saturated surface concentration as well as the reaction kinetics increased with decreasing pH, suggesting a competition for the active sites between the molecule and OH-. Moreover, we show that the ECL intensity could be boosted through the adsorption effect by collecting the ECL intensity generated through the electrochemical oxidation of luminol and a luminol analogue, L012, in a solution with pH = 13. In contrast with luminol, a significant adsorption effect was observed for L012 at pH = 13, and the ECL intensity was enhanced by the adsorbed species, especially at higher scan rates. The magnitude of the enhancement of the ECL intensity matched well with the simulation using our model.
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Affiliation(s)
- Ran Chen
- Jiangsu Province Key Laboratory of Critical Care Medicine, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing211189, China
| | - Xin Wang
- Jiangsu Province Key Laboratory of Critical Care Medicine, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing211189, China
| | - Kaiqing Wu
- Jiangsu Province Key Laboratory of Critical Care Medicine, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing211189, China
| | - Songqin Liu
- Jiangsu Province Key Laboratory of Critical Care Medicine, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing211189, China
| | - Yuanjian Zhang
- Jiangsu Province Key Laboratory of Critical Care Medicine, Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing211189, China
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Advanced Pt hollow nanospheres/rubrene nanoleaves coupled with M-shaped DNA walker for ultrasensitive electrochemiluminescence bioassay. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Li R, Zhang D, Li X, Qi H. Sensitive and selective electrogenerated chemiluminescence aptasensing method for the determination of dopamine based on target-induced conformational displacement. Bioelectrochemistry 2022; 146:108148. [DOI: 10.1016/j.bioelechem.2022.108148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/25/2022] [Accepted: 04/26/2022] [Indexed: 11/02/2022]
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Li R, Li X, Su L, Qi H, Yue X, Qi H. Label‐free Electrochemical Aptasensor for the Determination of Serotonin. ELECTROANAL 2022. [DOI: 10.1002/elan.202100373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rong Li
- School of Chemistry and Chemical Engineering Yan'an University Yan'an 716000 P. R. China
| | - Xiaoxia Li
- School of Chemistry and Chemical Engineering Yan'an University Yan'an 716000 P. R. China
| | - Liu Su
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 P. R. China
| | - Hetong Qi
- School of Chemistry Xi'an Jiaotong University Xi'an 710049 P. R. China
| | - Xuanfeng Yue
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 P. R. China
| | - Honglan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710062 P. R. China
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Wang X, Liu H, Jiang J, Qian M, Qi H, Gao Q, Zhang C. Highly Efficient Aggregation-Induced Enhanced Electrochemiluminescence of Cyanophenyl-Functionalized Tetraphenylethene and Its Application in Biothiols Analysis. Anal Chem 2022; 94:5441-5449. [PMID: 35311260 DOI: 10.1021/acs.analchem.2c00631] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Exploring new electrochemiluminescence (ECL) luminophores with high ECL efficiency and good stability in aqueous solution is in great demand for biological sensing. In this work, highly efficient aggregation-induced enhanced ECL of cyanophenyl-functionalized tetraphenylethene (tetra[4-(4-cyanophenyl)phenyl]ethene, TCPPE) and its application in biothiols analysis were reported. TCPPE contains four 4-cyanophenyl groups covalently attached to the tetraphenylethene (TPE) core, generating a nonplanar three-dimensional twisted conformation structure. TCPPE nanoparticles (NPs) with an average size of 15.84 nm were prepared by a precipitation method. High ECL efficiency (593%, CdS as standard) and stable ECL emission (over one month) were obtained for TCPPE NPs in aqueous solution. The unique properties of TCPPE NPs could be ascribed to the efficient suppression of nonradiative transition, the decrease of the energy gap, and the increase of anionic radical stability, which were proved by theoretical calculation and electrochemical and fluorescence methods. Contrasting aggregation-induced ECL chromic emission was first observed for TCPPE NPs. As a proof-of-methodology, an ECL method was developed for three biothiol assays with detection limits of 6, 7, and 300 nM for cysteine, homocysteine, and glutathione, respectively. This work demonstrates that TCPPE NPs are promising ECL luminophores, and the incorporation of appropriate substituents into luminophores can improve ECL efficiency and radical stability.
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Affiliation(s)
- Xiaofei Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Huiwen Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Jiaxing Jiang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Materials Science and Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Manping Qian
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Honglan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Qiang Gao
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
| | - Chengxiao Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, People's Republic of China
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