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Jia D, Fan W, Ren W, Liu C. Click chemical ligation-enabled digital particle counting for multiplexed microRNA analysis. Biosens Bioelectron 2024; 261:116508. [PMID: 38896977 DOI: 10.1016/j.bios.2024.116508] [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: 04/29/2024] [Revised: 06/08/2024] [Accepted: 06/17/2024] [Indexed: 06/21/2024]
Abstract
Digital counting assays, that quantify targets by counting individual signal entities, provide a promising way for the sensitive analysis of biomarkers even at the single-molecule level. Considering the requirements of complex enzyme-catalyzed amplification techniques and specialized instruments in traditional digital counting biosensors, herein, a simple digital counting platform for microRNA (miRNA) analysis is developed by employing the miRNA-templated click chemical ligation to hinge ultrabright quantum dot-doped nanoparticles (QDNPs) on the bottom of microplate well. Compared with the traditional short miRNA-mediated sandwich hybridization mechanism, the click chemistry-mediated ligation featured enhanced stability, achieving higher sensitivity by directly counting the number of QDNPs with a common wide-field fluorescence microscope. Furthermore, enzyme-free cycling click ligation strategy is adopted to push the detection limit of miRNA down to a low level of 8 fM. What is more, taking advantages of the tunable emission wavelength and narrow emission spectra of fluorescent nanoparticles, the platform enables simultaneous detection of multiplex miRNA targets without cross interference. Benefiting from the simple operation, high sensitivity, and good generality, miRNA analysis in complex samples is successfully achieved. This method not only pioneers a new route for digital counting assays but also holds great potential in miRNA-related biological researches.
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Affiliation(s)
- Dailu Jia
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China.
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China.
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2
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Zhong J, Ge M, Gu T, Wang T, Liu Z, Bai P. Ultra-stable and highly-bright CsPbBr 3 perovskite/silica nanocomposites for miRNA detection based on digital single-nanoparticle counting. Talanta 2024; 273:125903. [PMID: 38503120 DOI: 10.1016/j.talanta.2024.125903] [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: 01/22/2024] [Revised: 02/21/2024] [Accepted: 03/09/2024] [Indexed: 03/21/2024]
Abstract
Single-nanoparticle counting (SNPC) based on fluorescent tag (FT) stands out for its capacity to achieve amplification-free and sensitive detection of biomarkers. The stability and luminescence of FT are important to the sensitivity and reliability of SPNC. In this work, we developed novel perovskite/silica nanocomposites by in-situ nanoconfined growth of CsPbBr3 nanocrystals inside mesoporous structure of silica nanoparticles. PbBr(OH) was formed in an alkaline-assisted reaction triggered by water on the surface of CsPbBr3 nanocrystals. The as-obtained nanocomposites, featuring dual protection from silica matrix and PbBr(OH), exhibited high absolute photoluminescence quantum yield (PLQY) of 86.5% and demonstrated outstanding PL stability confronting with water, heat, ultrasound and UV-irradiation, which is desired by SNPC-based biosensor. Thereafter, these nanocomposites were used to construct an operationally friendly SNPC assay for the amplification-free quantification of cancer-associated miRNA. Quantitative detection of miRNA could be accomplished by directly counting the number of nanocomposites using a flow cytometer in this assay. This strategy did not ask for multiple washing steps and demonstrated specific and sensitive detection of miRNA 21, which exhibited a dynamic range of 1-1000 pM and limit of detection of 79 amol. The employment of highly stable perovskite/silica nanocomposites improved the test reliability and stability of SNPC, revealing the vast potential of perovskites in biosensing.
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Affiliation(s)
- Jiajun Zhong
- Jihua Laboratory, No. 28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong, 528200, People's Republic of China
| | - Minghao Ge
- Jihua Laboratory, No. 28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong, 528200, People's Republic of China
| | - Tongxu Gu
- Jihua Laboratory, No. 28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong, 528200, People's Republic of China.
| | - Tong Wang
- Jihua Laboratory, No. 28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong, 528200, People's Republic of China; CAS Key Lab of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, People's Republic of China
| | - Zhizhou Liu
- CAS Key Lab of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, People's Republic of China
| | - Pengli Bai
- Jihua Laboratory, No. 28 Island Ring South Road, Guicheng Street, Nanhai District, Foshan, Guangdong, 528200, People's Republic of China; CAS Key Lab of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, People's Republic of China.
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3
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Jia D, Lei C, Ren W, Liu C. Augmented Fluorescence Signaling on a Single BaTiO 3 Microbead Optical Booster toward High-Sensitive Biosensing. Anal Chem 2024; 96:8560-8565. [PMID: 38720190 DOI: 10.1021/acs.analchem.4c00577] [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: 05/29/2024]
Abstract
In this work, we report a new generation of single microbead bioassay that employs a single BaTiO3 microbead as an optical booster for target biomarker enrichment and optical enhancement toward protein and nucleic acid analysis. The single BaTiO3 microbead can not only concentrate the target molecules by nearly 104-fold but also act as an optical booster to prominently enhance the target-induced fluorescence signal by the whispering gallery mode for improving the excitation efficiency and the microlens effect for promoting the signal collecting efficiency, respectively. Compared with using a conventional single microbead, this optical booster exhibits nearly 2 orders of magnitude higher sensitivity without the assistance of any signal amplification techniques or costly instruments. Moreover, this single microbead optical booster is capable of detecting different kinds of protein and nucleic acid biomarkers in a simple mix-and-read manner, holding great potential for early clinical diagnosis.
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Affiliation(s)
- Dailu Jia
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Chao Lei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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4
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Vanness BC, Linz TH. Multiplexed miRNA and Protein Analysis Using Digital Quantitative PCR in Microwell Arrays. Anal Chem 2024; 96:1371-1379. [PMID: 38183281 PMCID: PMC11168192 DOI: 10.1021/acs.analchem.3c05213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
Proteins and microRNAs (miRNAs) act in tandem within biological pathways to regulate cellular functions, and their misregulation has been correlated to numerous diseases. Because of their interconnectedness, both miRNAs and proteins must be evaluated together to obtain accurate insights into the molecular pathways of pathogenesis. However, few analytical techniques can measure both classes of biomolecules in parallel from a single biological sample. Here, microfluidic digital quantitative PCR (dqPCR) was developed to simultaneously quantify miRNA and protein targets in a multiplexed assay using a single detection chemistry. This streamlined analysis was achieved by integrating base-stacking PCR and immuno-PCR in a microfluidic array platform. Analyses of let-7a (miRNA) and IL-6 (protein) were first optimized separately to identify thermocycling and capture conditions amenable to both biomolecules. Singleplex dqPCR studies exhibited the expected digital signals and quantification cycles for both analytes over a range of concentrations. Multiplexed analyses were then conducted to quantify both let-7a and IL-6 with high sensitivity (LODs ∼ 3 fM) over a broad dynamic range (5-5000 fM) using only standard PCR reagents. This multiplexed dqPCR was then translated to the analysis of HEK293 cell lysate, where endogenous let-7a and IL-6 were measured simultaneously without sample purification or pretreatment. Collectively, these studies demonstrate that the integration of BS-PCR and immuno-PCR achieves a sensitive and streamlined approach for multiplexed analyses of miRNAs and proteins, which will enable researchers to gain better insights into disease pathogenesis in future applications.
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Affiliation(s)
- Brice C. Vanness
- Department of Chemistry, Wayne State University, Detroit, MI 48202
| | - Thomas H. Linz
- Department of Chemistry, Wayne State University, Detroit, MI 48202
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Klebes A, Ates HC, Verboket RD, Urban GA, von Stetten F, Dincer C, Früh SM. Emerging multianalyte biosensors for the simultaneous detection of protein and nucleic acid biomarkers. Biosens Bioelectron 2024; 244:115800. [PMID: 37925943 DOI: 10.1016/j.bios.2023.115800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/17/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
Traditionally, biosensors are designed to detect one specific analyte. Nevertheless, disease progression is regulated in a highly interactive way by different classes of biomolecules like proteins and nucleic acids. Therefore, a more comprehensive analysis of biomarkers from a single sample is of utmost importance to further improve both, the accuracy of diagnosis as well as the therapeutic success. This review summarizes fundamentals like biorecognition and sensing strategies for the simultaneous detection of proteins and nucleic acids and discusses challenges related to multianalyte biosensor development. We present an overview of the current state of biosensors for the combined detection of protein and nucleic acid biomarkers associated with widespread diseases, among them cancer and infectious diseases. Furthermore, we outline the multianalyte analysis in the rapidly evolving field of single-cell multiomics, to stress its significance for the future discovery and validation of biomarkers. Finally, we provide a critical perspective on the performance and translation potential of multianalyte biosensors for medical diagnostics.
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Affiliation(s)
- Anna Klebes
- Hahn-Schickard, 79110, Freiburg, Germany; University of Freiburg, IMTEK - Department of Microsystems Engineering, Laboratory for MEMS Applications, 79110, Freiburg, Germany
| | - H Ceren Ates
- University of Freiburg, IMTEK - Department of Microsystems Engineering, Disposable Microsystems Group, 79110, Freiburg, Germany; University of Freiburg, FIT Freiburg Centre for Interactive Materials and Bioinspired Technology, 79110, Freiburg, Germany
| | - René D Verboket
- Department of Trauma-, Hand- and Reconstructive Surgery, University Hospital Frankfurt, Johann Wolfgang Goethe University, 60590, Frankfurt am Main, Germany
| | - Gerald A Urban
- University of Freiburg, IMTEK - Department of Microsystems Engineering, Laboratory for Sensors, 79110, Freiburg, Germany; University of Freiburg, Freiburg Materials Research Centre - FMF, 79104, Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, 79110, Freiburg, Germany; University of Freiburg, IMTEK - Department of Microsystems Engineering, Laboratory for MEMS Applications, 79110, Freiburg, Germany
| | - Can Dincer
- University of Freiburg, IMTEK - Department of Microsystems Engineering, Disposable Microsystems Group, 79110, Freiburg, Germany; University of Freiburg, FIT Freiburg Centre for Interactive Materials and Bioinspired Technology, 79110, Freiburg, Germany
| | - Susanna M Früh
- Hahn-Schickard, 79110, Freiburg, Germany; University of Freiburg, IMTEK - Department of Microsystems Engineering, Laboratory for MEMS Applications, 79110, Freiburg, Germany
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6
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Zhang S, Yao L, Lv X, Lu M, Gao F, Zhang L, Zhao S, Hu S. Engineered Cancer Cells as Signal Probes for Fluorescence-Assisted Digital Counting Analysis. Anal Chem 2023; 95:4227-4234. [PMID: 36795965 DOI: 10.1021/acs.analchem.2c05684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Fluorescence-assisted digital counting analysis allowed sensitive quantification of targets by measuring individual fluorescent labels. However, traditional fluorescent labels suffered from low brightness, small size, and sophisticated preparation procedures. Herein, engineering fluorescent dye-stained cancer cells with magnetic nanoparticles were proposed to construct single-cell probes for fluorescence-assisted digital counting analysis by quantifying the target-dependent binding or cleaving events. Various engineering strategies of cancer cells including biological recognition and chemical modification were developed for rationally designing single-cell probes. Introduction of suitable recognition elements into single-cell probes allowed digital quantification of each target-dependent event via counting the colored single-cell probes in the representative image taken using a confocal microscope. The reliability of the proposed digital counting strategy was corroborated by traditional optical microscopy- and flow cytometry-dependent counting technologies. The advantages of single-cell probes, including high brightness, big size, ease of preparation, and magnetic separation, contributed to the sensitive and selective analysis of targets of interest. As proof-to-concept assays, indirect analysis of exonuclease III (Exo III) activity, as well as direct quantitation of cancer cells, were investigated, and the potential in biological sample analysis was also assessed. This sensing strategy will open a new avenue for the development of biosensors.
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Affiliation(s)
- Shengkai Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Lijia Yao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Xiaofei Lv
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Meijun Lu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Fengli Gao
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, P. R. China
| | - Liangliang Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Shengqiang Hu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
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Wang X, Zhu X, Shi X, Zhou Y, Chai Y, Yuan R. Electrostatic Interaction-Induced Aggregation-Induced Emission-Type AgAu Bimetallic Nanoclusters as a Highly Efficient Electrochemiluminescence Emitter for Ultrasensitive Detection of Glial Fibrillary Acidic Protein. Anal Chem 2023; 95:3452-3459. [PMID: 36719845 DOI: 10.1021/acs.analchem.2c05209] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Herein, the aggregation-induced emission (AIE)-type carboxymethyl chitosan (CMCS)@6-aza-2-thiothymine (ATT) templated AgAu bimetallic nanoclusters (CMCS@ATT-AgAu BMNCs) with superior electrochemiluminescence (ECL) emission were first synthesized to construct a biosensor for the ultrasensitive detection of glial fibrillary acidic protein (GFAP). Impressively, unlike the traditional AIE-type bimetallic nanoclusters (BMNCs) obtained by complicated multi-step synthesis, the AIE-type CMCS@ATT-AgAu BMNCs were prepared by the electrostatic interaction between the negatively charged ATT and positively charged CMCS, in which the molecule ATT was served as a capping and reducing agent of bimetal ions. In addition, a rapidly moving cholesterol labeled DNA walker was constructed to move freely on the lipid bilayer to increase its moving efficiency, and the well-regulated DNA was intelligently designed to further improve its walking efficiency for rapid and ultrasensitive detection of GFAP with a limit of detection (LOD) as low as 73 ag/mL. This strategy proposed an avenue to synthesize highly efficient BMNCs-based ECL emitters, which have great potential in ultrasensitive biosensing for early diagnosis of diseases.
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Affiliation(s)
- Xiaofeng Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing400715, P. R China
| | - Xiaochun Zhu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing400715, P. R China
| | - Xiaoyu Shi
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing400715, P. R China
| | - Ying Zhou
- College of Food Science, Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Southwest University, Chongqing400715, P. R. China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing400715, P. R China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing400715, P. R China
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8
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Li Y, Huang Z, Li Z, Li C, Liu R, Lv Y. Mass Spectrometric Multiplex Detection of MicroRNA and Protein Biomarkers for Liver Cancer. Anal Chem 2022; 94:17248-17254. [PMID: 36448711 DOI: 10.1021/acs.analchem.2c04171] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The occurrence of cancers is often accompanied by the abnormal expression of several sorts of biomarkers (e.g., nucleic acids and proteins). The multiplex assessment of them would substantially aid in the early detection and precise diagnosis, which is often hampered by their different detection schemes, different reaction matrix and reagents, and spectral overlapping. Herein, we propose a simple and sensitive mass spectrometric method for the multiplex detection of nucleic acid and protein, in which liver cancer-related biomarkers miRNA 223 and alpha-fetoprotein (AFP) were selected as model analytes. The self-amplification effect of metal atom-based nanoparticle probes can provide high sensitivity in complex serum samples without any additional amplification procedure. The detection limits for the simultaneous detection of miRNA 223 and AFP were 103 (2.1 pM) and 219 amol (0.15 ng/mL), respectively, with high specificity and selectivity. The proposed method is potentially useful for the rapid screening of cancers.
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Affiliation(s)
- Yan Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 Sichuan, China
| | - Zili Huang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 Sichuan, China
| | - Ziyan Li
- Analytical & Testing Center, Sichuan University, Chengdu 610064 Sichuan, China
| | - Caixia Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 Sichuan, China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 Sichuan, China
| | - Yi Lv
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064 Sichuan, China.,Analytical & Testing Center, Sichuan University, Chengdu 610064 Sichuan, China
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