1
|
Tan P, Chen Y, Chang H, Liu T, Wang J, Lu Z, Sun M, Su G, Wang Y, Wang HD, Leung C, Rao H, Wu C. Deep learning assisted logic gates for real-time identification of natural tetracycline antibiotics. Food Chem 2024; 454:139705. [PMID: 38820637 DOI: 10.1016/j.foodchem.2024.139705] [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: 02/03/2024] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 06/02/2024]
Abstract
The overuse and misuse of tetracycline (TCs) antibiotics, including tetracycline (TTC), oxytetracycline (OTC), doxycycline (DC), and chlortetracycline (CTC), pose a serious threat to human health. However, current rapid sensing platforms for tetracyclines can only quantify the total amount of TCs mixture, lacking real-time identification of individual components. To address this challenge, we integrated a deep learning strategy with fluorescence and colorimetry-based multi-mode logic gates in our self-designed smartphone-integrated toolbox for the real-time identification of natural TCs. Our ratiometric fluorescent probe (CD-Au NCs@ZIF-8) encapsulated carbon dots and Au NCs in ZIF-8 to prevent false negative or positive results. Additionally, our independently developed WeChat app enabled linear quantification of the four natural TCs using the fluorescence channels. The colorimetric channels were also utilized as outputs of logic gates to achieve real-time identification of the four individual natural tetracyclines. We anticipate this strategy could provide a new perspective for effective control of antibiotics.
Collapse
Affiliation(s)
- Ping Tan
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Yuhui Chen
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Hongrong Chang
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Tao Liu
- College of Information Engineering, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Jian Wang
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China.
| | - Zhiwei Lu
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Mengmeng Sun
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Gehong Su
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Yanying Wang
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China
| | - Huimin David Wang
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Xingda Road, South District, Taichung 402, Taiwan, China
| | - Chunghang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa 999078, Macao
| | - Hanbing Rao
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China.
| | - Chun Wu
- College of Science, Sichuan Agricultural University, Xinkang Road, Yucheng District, Ya'an 625014, China.
| |
Collapse
|
2
|
Wang H, Li M, Zhang H, Yang L. A Tunable Threshold Colorimetric DNA Logic Gate for Intuitive Assessment of Chemical Contaminant Exceedance. Anal Chem 2024. [PMID: 38989925 DOI: 10.1021/acs.analchem.4c01529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Current molecular logic gates are predominantly focused on the qualitative assessment of target presence, which has certain limitations in scenarios requiring quantitative assessment, such as chemical contaminant monitoring. To bridge this gap, we have developed a novel DNA logic gate featuring a tunable threshold, specifically tailored to the limits of contaminants. At the core of this logic gate is a DNA-gold nanoparticle (AuNP) hybrid film that incorporates aptamer sequences to selectively bind to acetamiprid (ACE) and atrazine (ATR). Upon interaction with these contaminants, the film degrades, releasing AuNPs that, in the presence of Hg2+, catalyze the oxidation of TMB, resulting in a visible blue coloration on test paper. This aptamer-enabled process effectively establishes an OR logic gate, with ACE and ATR as inputs and the appearance of blue color as the output. A key innovation of our system is its tunable input threshold. By adjusting the concentration of Hg2+, we can fine-tune the color mutation points to match the input threshold to predefined limits, such as Maximum Residue Limits (MRLs). This alignment allows semiquantitative assessment of contaminant levels, providing intuitive visual feedback of contaminant exceedance. Validation experiments with spiked samples confirm its accuracy and reliability by closely matching HPLC results. Therefore, our colorimetric DNA logic gate is emerging as a promising tool for easy and semiquantitative monitoring of chemical contaminants across diverse applications.
Collapse
Affiliation(s)
- Hao Wang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Mingming Li
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Hanyang Zhang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Limin Yang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| |
Collapse
|
3
|
Zhang XW, Qi GX, Chen S, Yu YL, Wang JH. Ultrasensitive and Wash-Free Detection of Tumor Extracellular Vesicles by Aptamer-Proximity-Ligation-Activated Rolling Circle Amplification Coupled to Single Particle ICP-MS. Anal Chem 2024; 96:10800-10808. [PMID: 38904228 DOI: 10.1021/acs.analchem.4c02066] [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: 06/22/2024]
Abstract
Tumor-derived extracellular vesicles (TEVs) are rich in cellular information and hold great promise as a biomarker for noninvasive cancer diagnosis. However, accurate measurement of TEVs presents challenges due to their low abundance and potential interference from a high number of EVs derived from normal cells. Herein, an aptamer-proximity-ligation-activated rolling circle amplification (RCA) method for EV membrane recognition, coupled with single particle inductively coupled plasma mass spectrometry (sp-ICP-MS) for the quantification of TEVs, is developed. When DNA-labeled ultrasmall gold nanoparticle (AuNP) probes bind to the long chains formed by RCA, they aggregate to form large particles. Notably, small AuNPs scarcely produce pulse signals in sp-ICP-MS, thereby detecting TEVs in a wash-free manner. By leveraging the strong binding affinity of aptamers, dual aptamers for EpCAM and PD-L1 recognition, and the sp-ICP-MS technique, this method offers remarkable sensitivity and selectivity in tracing TEVs. Under optimized conditions, the present method shows a favorable linear relationship between the pulse signal frequency of sp-ICP-MS and TEV concentration within the range of 105-107 particles/mL, along with a detection limit of 1.1 × 104 particles/mL. The pulse signals from sp-ICP-MS combined with machine learning algorithms are used to discriminate cancer patients from healthy donors with 100% accuracy. Due to its simple and fast operation and excellent sensitivity and accuracy, this approach holds significant potential for diverse applications in life sciences and personalized medicine.
Collapse
Affiliation(s)
- Xue-Wei Zhang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Gong-Xiang Qi
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Shuai Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| |
Collapse
|
4
|
Gao L, Zhang Y, Chen L, Zhou Q, Zhou N, Xia X. Study of dual binding specificity of aptamer to ochratoxin A and norfloxacin and the development of fluorescent aptasensor in milk detection. Talanta 2024; 273:125935. [PMID: 38503123 DOI: 10.1016/j.talanta.2024.125935] [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: 07/06/2023] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
Target specificity, one of aptamer characteristics that determine recognition efficiency of biosensors, is generally considered to be an intrinsic property of aptamer. However, a high-affinity aptamer may have additional target binding specificity, little is known about the specificity of aptamer binding to multiple targets, which may result in false-positive results that hinder the accuracy of detection. Herein, an aptamer OBA3 with dual target ochratoxin A (OTA) and norfloxacin (NOR) was used as an example to explore the binding specificity mechanism and developed rapid fluorescent aptasensing methods. The nucleotide 15th T of aptamer OBA3 was demonstrated to be critical for specificity and affinity binding of target OTA via site-saturation mutagenesis. Substituting the 15th T base for C base could directly improve recognition specificity of aptamer for NOR and remove the binding affinity for OTA. The combination of π-π stacking interactions, salt bridges and hydrogen bonds between loop pocket of aptamer and quinolone skeleton, piperazinyl group may contributes to the fluoroquinolone antibiotics (NOR and difloxacin)-aptamer recognition interaction. Based on this understanding, a dual-aptamer fluorescent biosensor was fabricated for simultaneous detection of OTA and NOR, which has a linear detection range of 50-6000 nM with a detection limit of 31 nM for OTA and NOR. Combined with T15C biosensor for eliminating interference of OTA, the assay was applied to milk samples with satisfactory recovery (94.06-100.93%), which can achieve detection of OTA and NOR individually within 40 min.
Collapse
Affiliation(s)
- Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yue Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Lu Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qingtong Zhou
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Nandi Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
| |
Collapse
|
5
|
Deng J, Liu C, Sun J. DNA-Based Nanomaterials for Analysis of Extracellular Vesicles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2303092. [PMID: 38016069 DOI: 10.1002/adma.202303092] [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: 04/03/2023] [Revised: 07/21/2023] [Indexed: 11/30/2023]
Abstract
Extracellular vesicles (EVs) are cell-derived nanovesicles comprising a myriad of molecular cargo such as proteins and nucleic acids, playing essential roles in intercellular communication and physiological and pathological processes. EVs have received substantial attention as noninvasive biomarkers for disease diagnosis and prognosis. Owing to their ability to recognize protein and nucleic acid targets, DNA-based nanomaterials with excellent programmability and modifiability provide a promising tool for the sensitive and accurate detection of molecular cargo carried by EVs. In this perspective, recent advancements in EV analysis using a variety of DNA-based nanomaterials are summarized, which can be broadly classified into three categories: linear DNA probes, DNA nanostructures, and hybrid DNA nanomaterials. The design, construction, advantages, and disadvantages of different types of DNA nanomaterials, as well as their performance for detecting EVs are reviewed. The challenges and opportunities in the field of EV analysis by DNA nanomaterials are also discussed.
Collapse
Affiliation(s)
- Jinqi Deng
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Liu
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiashu Sun
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
6
|
Lu JY, Guo Z, Huang WT, Bao M, He B, Li G, Lei J, Li Y. Peptide-graphene logic sensing system for dual-mode detection of exosomes, molecular information processing and protection. Talanta 2024; 267:125261. [PMID: 37801930 DOI: 10.1016/j.talanta.2023.125261] [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: 07/01/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/08/2023]
Abstract
Peptides with highly sequence-dependent recognition, assembly, and encoding abilities can perform functions similar to DNA or even better, such as biosensing, molecular information processing, coding, or storage. However, the combination of versatile peptides and 2D materials are rarely used for multipurpose integrated applications, including biosensing, information processing and security. Herein, peptide-graphene sensing system was comprehensively used for dual-signal sensing of tumor-derived exosomes (TDEs), logic computing, and information protection. The system used fluorescent-labeled CD63-binding peptide CP05 and graphene oxide (GO) to selectively detect CD63 and TDEs by fluorescence and resonance light scattering. From three levels such as matter, energy, and information analysis, the matter and energy changes in GO-CP05 peptide sensing system were transformed into valuable information, which achieve the dual-mode quantitative detection of TDEs and its marker CD63, and the actual serum analysis. This matter-energy interaction network was also informationized, and utilized for parallel and batch logic computing, two kinds of molecular crypto-steganography (based on peptide sequence and Boolean logic relationships), which facilitates development of intelligent sensing and advanced information technology. This work not only provides a new method for sensitive detection of important disease markers, but also provides ideas for integrating molecular sensing and informatization to open molecular digitization.
Collapse
Affiliation(s)
- Jiao Yang Lu
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, "the 14th Five-Year Plan" Application Characteristic Discipline of Hunan Province (Clinical Medicine), Changsha Medical University, Changsha, 410219, PR China; Wuzhou Medical College, Wuzhou, 543100, PR China
| | - Zhen Guo
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, "the 14th Five-Year Plan" Application Characteristic Discipline of Hunan Province (Clinical Medicine), Changsha Medical University, Changsha, 410219, PR China
| | - Wei Tao Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, 410081, PR China
| | - Meihua Bao
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, "the 14th Five-Year Plan" Application Characteristic Discipline of Hunan Province (Clinical Medicine), Changsha Medical University, Changsha, 410219, PR China
| | - Binsheng He
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, "the 14th Five-Year Plan" Application Characteristic Discipline of Hunan Province (Clinical Medicine), Changsha Medical University, Changsha, 410219, PR China
| | - Guangyi Li
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, "the 14th Five-Year Plan" Application Characteristic Discipline of Hunan Province (Clinical Medicine), Changsha Medical University, Changsha, 410219, PR China
| | - Jieni Lei
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, "the 14th Five-Year Plan" Application Characteristic Discipline of Hunan Province (Clinical Medicine), Changsha Medical University, Changsha, 410219, PR China
| | - Yaqian Li
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, "the 14th Five-Year Plan" Application Characteristic Discipline of Hunan Province (Clinical Medicine), Changsha Medical University, Changsha, 410219, PR China.
| |
Collapse
|
7
|
Liu X, Cheng H, Zhao Y, Wang Y, Ge L, Huang Y, Li F. Immobilization-free dual-aptamer-based photoelectrochemical platform for ultrasensitive exosome assay. Talanta 2024; 266:125001. [PMID: 37517342 DOI: 10.1016/j.talanta.2023.125001] [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: 03/14/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
Exosomes, involved in cancer-specific biological processes, are promising noninvasive biomarkers for early diagnosis of cancer. Herein, an immobilization-free dual-aptamer-based photoelectrochemical (PEC) biosensor was proposed for the enrichment and quantification of cancer exosome based on photoactive bismuch oxyiodide/gold/cadmium sulfide (BiOI/Au/CdS) composites, nucleic acid-based recognition and signal amplification. In this biosensor, the recognition of exosome by two aptamers would trigger the deoxyribonucleotidyl transferase (TdT) enzyme-aided polymerization, leading to the enrichment of alkaline phosphatase (ALP) on Fe3O4 surface. After magnetic separation, ALP could catalyze the generation of ascorbic acid (AA) as electron donor and initiate the following redox cycle reaction for further signal amplification. Furthermore, all the above processes were performed in solution, the recognition and signal amplification efficiency would be superior than the heterogeneous strategy owing to the avoidance of steric hindrance effect. As a result, the proposed PEC biosensor was capable of enriching and detecting of cancer exosomes with high sensitivity and selectivity. The linear range of the biosensor was from 1.0 × 102 particles·μL-1 to 1.0 × 106 particles·μL-1 and the detection limit was estimated to be 21 particles·μL-1. Therefore, the proposed PEC biosensor holds great promise in quantifying tumor exosome for nondestructive early clinical cancer diagnosis and various other bioassay applications.
Collapse
Affiliation(s)
- Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences, 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
| | - Yuecan Zhao
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Yue Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Lei Ge
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Yiping Huang
- College of Chemistry and Pharmaceutical Sciences, 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.
| |
Collapse
|
8
|
Liu X, Li B, Liu Q, Zhang L, Zhao R, Wu D, Wang L, Wang Z, Xie G, Feng W. Multifunctional dumbbell probes-based logic circuits: microRNAs logic detection and tumor cells identification. Anal Chim Acta 2023; 1280:341856. [PMID: 37858550 DOI: 10.1016/j.aca.2023.341856] [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: 08/16/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND The powerful logic processing capability of DNA logic circuits over multiple input signals perfectly meets the demands of multi-biomarker-based clinical diagnostics. As important biomarkers for cancer diagnosis and treatment, the orthogonal differential expression of microRNAs (miRNAs) in different diseases and different cancer cells makes the precise logical detection of multiple miRNAs particularly critical. RESULTS Therefore, we constructed two fundamental "AND" and "OR" logic gates and one "AND-OR" logic gate on the basis of our proposed multifunctional dumbbell probes. These logic gates allowed for the logical profiling of multiple cancer-associated miRNAs. In addition, by making simple adjustments to the functional modules of multifunctional dumbbell probes, the three logic gates we proposed could be easily transformed without the use of sophisticated probe design. Remarkably, these logic gates, in particular the "AND-OR" logic gate, were able to compute several miRNAs simultaneously, demonstrating excellent cell identification capabilities. SIGNIFICANCE Overall, this work provided a new idea for accurately distinguishing multiple cell types and showed great application prospects.
Collapse
Affiliation(s)
- Xin Liu
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Baiying Li
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Qian Liu
- Department of Nuclear Medicine, The Second Hospital of Chongqing Medical University, Chongqing 400010, PR China
| | - Li Zhang
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Di Wu
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Luojia Wang
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China.
| | - Wenli Feng
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China.
| |
Collapse
|
9
|
Zhu J, Sun W, Yao Y, Guo Z, Li Q, Li Z, Jiang L, Zuo S, Liu S, Huang J, Wang Y. Combination of specific proteins as markers for accurate detection of extracellular vesicles using proximity ligation-mediated bHCR amplification. Anal Chim Acta 2023; 1267:341322. [PMID: 37257980 DOI: 10.1016/j.aca.2023.341322] [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: 01/31/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 06/02/2023]
Abstract
As the molecular characteristics of extracellular vesicles (EVs) are closely related to the occurrence and progression of cancer, the detection of tumor-derived EVs provides a promising non-invasive tool for the early diagnosis and treatment of cancer. However, it would be difficult for most of the existing methods to avoid false positives because the obtained result declares the amounts of proteins, but cannot accurately reflect the protein sources, including EV proteins and interfering proteins, in the actual samples. In this manuscript, a robust, accurate, and sensitive fluorescent strategy for profiling EV proteins is developed by using the combination of specific proteins as markers (Co-marker). Our strategy relies on the Co-marker recognition-activated cascade bHCR amplification, which forms numerous G-quadruplex structures that are integrated with fluorescent dyes for signal transduction. Notably, the detection accuracy can be improved owing to the effective avoidance of false positives from interfering proteins or single protein markers. Moreover, by using the double-positive protein recognition mode, unpurified detection can be achieved that avoids time-consuming EVs purification procedures. With its capacities of accuracy, portability, sensitivity, high throughput, and non-purification, the developed strategy might provide a practical tool for EV identification and the related early diagnosis and treatment of cancer.
Collapse
Affiliation(s)
- Jingru Zhu
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Wenyu Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing, 210096, PR China
| | - Yuying Yao
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Zhiqiang Guo
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Qianru Li
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Zongqiang Li
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Long Jiang
- Qingdao Spring Water-treatment Co, Ltd, Qingdao, 266000, PR China
| | - Shangci Zuo
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Su Liu
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Jiadong Huang
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China; Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Yu Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China.
| |
Collapse
|
10
|
Deng F, Pan J, Chen M, Liu Z, Chen J, Liu C. Integrating CRISPR-Cas12a with catalytic hairpin assembly as a logic gate biosensing platform for the detection of polychlorinated biphenyls in water samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163465. [PMID: 37068691 DOI: 10.1016/j.scitotenv.2023.163465] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/23/2023] [Accepted: 04/08/2023] [Indexed: 06/01/2023]
Abstract
Polychlorinated biphenyls (PCBs) are ubiquitous persistent organic pollutants that cause harmful effects on environmental safety and human health. There is an urgent need to develop an intelligent method for PCBs sensing. In this work, we proposed a logic gate biosensing platform for simultaneous detection of multiple PCBs. 2,3',5,5'-tetrachlorobiphenyl (PCB72) and 3,3',4,4'-tetrachlorobiphenyl (PCB77) were used as the two inputs to construct biocomputing logic gates. We used 0 and 1 to encode the inputs and outputs. The aptamer was used to recognize the inputs and release the trigger DNA. A catalytic hairpin assembly (CHA) module is designed to convert and amplify each trigger DNA into multiple programmable DNA duplexes, which initiate the trans-cleavage activity of CRISPR/Cas12a for the signal output. The activated Cas12 cleaves the BHQ-Cy5 modified single-stranded DNA (ssDNA) to yield the fluorescence reporting signals. In the YES logic gate, PCB72 was used as the only input to carry out the logic operation. In the OR, AND, and INHIBIT logic gates, PCB72 and PCB77 were used as the two inputs. The output signals can be visualized by the naked eye under UV light transilluminators or quantified by a microplate reader. Our constructed biosensing platform possesses the merits of multiple combinations of inputs, intuitive digital output, and high flexibility and scalability, which holds great promise for the intelligent detection of different PCBs.
Collapse
Affiliation(s)
- Fang Deng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Manjia Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Chengshuai Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| |
Collapse
|
11
|
Hu X, Cheng S, Luo X, Xian Y, Zhang C. Polymerase-Driven Logic Signal Amplification for the Detection of Small Extracellular Vesicle Surface Proteins and the Identification of Breast Cancer. Anal Chem 2023. [PMID: 37366594 DOI: 10.1021/acs.analchem.3c01080] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Small extracellular vesicles (sEVs) derived from tumors contain a vast amount of cellular information and are regarded as a potential diagnostic biomarker for noninvasive cancer diagnosis. Nevertheless, it remains challenging to accurately measure sEVs from clinical samples due to the low abundance of these vesicles as well as their phenotypic heterogeneity. Herein, a polymerase-driven logic signal amplification system (PLSAS) was developed for the high-sensitivity detection of sEV surface proteins and breast cancer (BC) identification. Aptamers were introduced to serve as sensing modules to specifically recognize target proteins. By changing the input DNA sequences, two polymerase-driven primer exchange reaction systems were rationally designed for DNA logic computing. This allows for autonomous targeting of a limited number of targets using "OR" and "AND" logic, leading to a significant increase in fluorescence signals and enabling the specific and ultrasensitive detection of sEV surface proteins. In this work, we investigated surface proteins of mucin 1 (MUC1) and the epithelial cell adhesion molecule (EpCAM) as model proteins. When MUC1 or EpCAM proteins were used as single signal input in the "OR" DNA logic system, the detection limit of sEVs was 24 or 58 particles/μL, respectively. And MUC1 and EpCAM proteins of sEVs can be simultaneously detected in the AND logic method, which can significantly reduce the effect of phenotypic heterogeneity of sEVs to distinguish the source of sEVs derived from various mammary cell lines, such as MCF-7, MDA MB 231, SKBR3, and MCF-10A. The approach has achieved high discrimination in serologically tested positive BC samples (AUC 98.1%) and holds significant potential in advancing the early diagnosis and prognostic assessments of BC.
Collapse
Affiliation(s)
- Xinyu Hu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Shasha Cheng
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Xianzhu Luo
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Yuezhong Xian
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Cuiling Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| |
Collapse
|
12
|
Chao Q, Zhang Y, Li Q, Jiao L, Sun X, Chen X, Zhu L, Yang Q, Shang C, Kong RM, Fan GC, Song ZL, Luo X. Compute-and-Release Logic-Gated DNA Cascade Circuit for Accurate Cancer Cell Imaging. Anal Chem 2023; 95:7723-7734. [PMID: 37133978 DOI: 10.1021/acs.analchem.3c00898] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Accurate identification of cancer cells is an essential prerequisite for cancer diagnosis and subsequent effective curative interventions. The logic-gate-assisted cancer imaging system that allows a comparison of expression levels between biomarkers, rather than just reading biomarkers as inputs, returns a more comprehensive logical output, improving its accuracy for cell identification. To fulfill this key criterion, we develop a compute-and-release logic-gated double-amplified DNA cascade circuit. This novel system, CAR-CHA-HCR, consists of a compute-and-release (CAR) logic gate, a double-amplified DNA cascade circuit (termed CHA-HCR), and a MnO2 nanocarrier. CAR-CHA-HCR, a novel adaptive logic system, is designed to logically output the fluorescence signals after computing the expression levels of intracellular miR-21 and miR-892b. Only when miR-21 is present and its expression level is above the threshold CmiR-21 > CmiR-892b, the CAR-CHA-HCR circuit performs a compute-and-release operation on free miR-21, thereby outputting enhanced fluorescence signals to accurately image positive cells. It is capable of comparing the relative concentrations of two biomarkers while sensing them, thus allowing accurate identification of positive cancer cells, even in mixed cell populations. Such an intelligent system provides an avenue for highly accurate cancer imaging and is potentially envisioned to perform more complex tasks in biomedical studies.
Collapse
Affiliation(s)
- Qiqi Chao
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yuxi Zhang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qian Li
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Luzhen Jiao
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xufeng Sun
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xuxu Chen
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Lina Zhu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qian Yang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chengwen Shang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Rong-Mei Kong
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, China
| | - Gao-Chao Fan
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Zhi-Ling Song
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| |
Collapse
|
13
|
Khaksari S, Abnous K, Hadizadeh F, Ramezani M, Taghdisi SM, Mousavi Shaegh SA. Signal amplification strategies in biosensing of extracellular vesicles (EVs). Talanta 2023; 256:124244. [PMID: 36640707 DOI: 10.1016/j.talanta.2022.124244] [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: 09/17/2022] [Revised: 12/25/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
Extracellular vesicles (EVs) are membrane-enclosed vesicles secreted from mammalian cells. EVs act as multicomponent delivery vehicles to carry a wide variety of biological molecular information and participate in intercellular communications. Since elevated levels of EVs are associated with some pathological states such as inflammatory diseases and cancers, probing circulating EVs holds a great potential for early diagnostics. To this end, several detection methods have been developed in which biosensors have attracted great attentions in identification of EVs due to their simple instrumentation, versatile design and portability for point-of-care applications. The concentrations of EVs in bodily fluids are extremely low (i.e. 1-100 per μl) at early stages of a disease, which necessitates the use of signal amplification strategies for EVs detection. In this way, this review presents and discusses various amplification strategies for EVs biosensors based on detection modalities including surface plasmon resonance (SPR), calorimetry, fluorescence, electrochemical and electrochemiluminescence (ECL). In addition, microfluidic systems employed for signal amplification are reviewed and discussed in terms of their design and integration with the detection methods.
Collapse
Affiliation(s)
- Sedighe Khaksari
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Laboratory of Microfluidics and Medical Microsystems, Bu Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Khalil Abnous
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Farzin Hadizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Ali Mousavi Shaegh
- Orthopedic Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Clinical Research Unit, Mashhad University of Medical Sciences, Mashhad, Iran; Laboratory of Microfluidics and Medical Microsystems, Bu Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
14
|
Fan Z, Weng Q, Li Y, Zeng T, Wang J, Zhang H, Yu H, Dong Y, Zhao X, Li J. Accurate and rapid quantification of PD-L1 positive exosomes by a triple-helix molecular probe. Anal Chim Acta 2023; 1251:340984. [PMID: 36925282 DOI: 10.1016/j.aca.2023.340984] [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: 12/06/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
Programmed death ligand-1 (PD-L1) positive exosomes (P-Exo) have been widely used for tumor diagnosis. However, accurate and rapid quantification of P-Exo remains challenging due to the heterogeneity of clinical individuals and isolation techniques. In this study, the triple-helix molecular probe (THMP) coupled with high-affinity silica-based TiO2 magnetic beads was used to isolate exosomes and to analyze the relative abundance of P-Exo in total exosomes (T-Exo). By employing this strategy, the entire analysis was completed within 70 min and the detection limit for P-Exo was 880 particles μL-1. Additionally, the relative abundance of P-Exo in T-Exo (RAP-Exo/T-Exo) was calculated from their fluorescence ratio, which could avoid errors due to differences in samples and separation methods, and identify 1.5 × 103 P-Exo from 5 × 106 T-Exo per microliter. RAP-Exo/T-Exo values were not only effective in distinguishing healthy volunteers from breast cancer patients, but also highly positively correlated with the stage of breast carcinoma. Overall, this strategy opens a new avenue for rapid and quantitative analysis of P-Exo, providing an opportunity for precise diagnosis and prediction of treatment efficacy in cancer.
Collapse
Affiliation(s)
- Zhichao Fan
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China; School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Qin Weng
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China; School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yingxue Li
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Tian Zeng
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Junyi Wang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Honglan Zhang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Hua Yu
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Department of General Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Yan Dong
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
| | - Xiang Zhao
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
| | - Jianjun Li
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
| |
Collapse
|
15
|
Shen H, Li Z, Dou B, Feng Q, Wang P. An amplified logic gate driven by in situ synthesis of silver nanoclusters for identification of biomarkers. Chem Commun (Camb) 2023; 59:5705-5708. [PMID: 37083922 DOI: 10.1039/d3cc00643c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
An amplified DNA logic sensor was constructed for the identification of multiple biomarkers, in which the inputs of targets triggered the disassembly of a V-shaped probe (VSP) structure by a strand displacement reaction, leading to the synthesis of silver nanoclusters (AgNCs) for electrocatalytic reduction of H2O2. The sensing platform achieved sensitive detection of methylated DNA and microRNA 122 with detection limits down to 3.4 and 4.1 fM, respectively, and can be used for the assay of clinical serum samples from healthy volunteers and liver injury patients with satisfactory results. The DNA logic sensor exhibited the advantages of convenience, low cost, and versatility without the involvement of electroactive label modification, which is helpful for disease diagnosis as well as the fundamental investigation of interfacial electrochemistry and molecular biology.
Collapse
Affiliation(s)
- Hui Shen
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Zhimin Li
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Baoting Dou
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou 221116, China.
| |
Collapse
|
16
|
Cheng W, Sun Y, Zhao G, Khan A, Zhang J, Zhang Z, Yi Y, Kong D, Li J. A novel peptide-templated AgNPs nanoprobe for theranostics of prostate cancer. Biosens Bioelectron 2023; 223:114978. [PMID: 36586149 DOI: 10.1016/j.bios.2022.114978] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022]
Abstract
Prostate specific membrane antigen (PSMA)-positive exosomes have the potential to serve as highly sensitive biomarkers for prostate cancer detection. Herein, a sensitive electrochemical biosensor for the ultrasensitive detection of PSMA-positive exosomes has been constructed based on a peptide-templated AgNPs nanoprobe. In this work, PSMA-specific binding peptides immobilized on a gold electrode were responsible for prostate cancer-derived exosomes capturing. Well-designed peptide (CCY- LWYIKC) serves a dual role: as a signal probe and as a recognizer in the exosomes-identification process. Specifically, LWYIKC bind to cholesterol at the exosome membranes, and CCY function as peptide templates to host a large number of silver nanoparticles, leading to a strong electrochemical signal. Thus, the concentration of exosomes can be quantified via electrochemical signal. This innovative method displayed a wide detection range of 102 to 108 particles/μL and a detection limit as low as 37 particles/μL. Notably, the method has shown outstanding performance when validated using clinical samples, suggesting its potential for clinical applications.
Collapse
Affiliation(s)
- Wenting Cheng
- Department of Clinical Laboratory, Gaochun People's Hospital, Nanjing, 211300, China
| | - Ying Sun
- Department of Clinical Laboratory, Gaochun People's Hospital, Nanjing, 211300, China
| | - Guiping Zhao
- Department of Clinical Laboratory, Gaochun People's Hospital, Nanjing, 211300, China
| | - Adeel Khan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jianchun Zhang
- Department of Clinical Laboratory, Gaochun People's Hospital, Nanjing, 211300, China
| | - Zhaoli Zhang
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, China
| | - Yongxiang Yi
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, China.
| | - Dehua Kong
- Department of Clinical Laboratory, Gaochun People's Hospital, Nanjing, 211300, China.
| | - Jinlong Li
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, China.
| |
Collapse
|
17
|
He S, Ding L, Yuan H, Zhao G, Yang X, Wu Y. A review of sensors for classification and subtype discrimination of cancer: Insights into circulating tumor cells and tumor-derived extracellular vesicles. Anal Chim Acta 2023; 1244:340703. [PMID: 36737145 DOI: 10.1016/j.aca.2022.340703] [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: 07/23/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Liquid biopsy can reflect the state of tumors in vivo non-invasively, thus providing a strong basis for the early diagnosis, individualized treatment monitoring and prognosis of tumors. Circulating tumor cells (CTCs) and tumor-derived extracellular vesicles (tdEVs) contain information-rich components, such as nucleic acids and proteins, and they are essential markers for liquid biopsies. Their capture and analysis are of great importance for the study of disease occurrence and development and, consequently, have been the subject of many reviews. However, both CTCs and tdEVs carry the biological characteristics of their original tissue, and few reviews have focused on their function in the staging and classification of cancer. In this review, we focus on state-of-the-art sensors based on the simultaneous detection of multiple biomarkers within CTCs and tdEVs, with clinical applications centered on cancer classification and subtyping. We also provide a thorough discussion of the current challenges and prospects for novel sensors with the ultimate goal of cancer classification and staging. It is hoped that these most advanced technologies will bring new insights into the clinical practice of cancer screening and diagnosis.
Collapse
Affiliation(s)
- Sitian He
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Huijie Yuan
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Gaofeng Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China.
| | - Xiaonan Yang
- School of Information Engineering, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China.
| |
Collapse
|
18
|
Zhang Q, Ma R, Zhang Y, Zhao J, Wang Y, Xu Z. Dual-Aptamer-Assisted Ratiometric SERS Biosensor for Ultrasensitive and Precise Identification of Breast Cancer Exosomes. ACS Sens 2023; 8:875-883. [PMID: 36722734 DOI: 10.1021/acssensors.2c02587] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Due to the heterogeneity of breast cancer, its early accurate diagnosis remains a challenge. Exosomes carry abundant genetic materials and proteins and are ideal biomarkers for early cancer detection. Herein, a ratiometric surface-enhanced Raman scattering (SERS) biosensor for exosome detection was constructed using a regularly arranged Au@Ag nanoparticles/graphene oxide (Au@Ag NPs/GO) substrate with 4-nitrothiophenol (4-NTP) molecules as an internal standard. Aptamers of two overexpressed proteins (epithelial cell adhesion molecule and human epidermal growth factor receptor 2) were linked by a short complementary DNA with rhodamine X modified at the 3'-terminal to form V-shaped double-stranded DNA, which attached to the surface of Au@Ag NPs/GO substrate for the selective recognition of breast cancer cell-derived exosomes. In the presence of exosomes, a competitive reaction occurred, resulting in the formation of the V-shaped double-stranded DNA/exosomes complex, and the V-shaped double-stranded DNA separated from the SERS substrate. The SERS signal of rhodamine X on the V-shaped double-stranded DNA decreased with the concentration of exosomes increasing, whereas the SERS signal of 4-NTP on the substrate remained stable. The ratiometric SERS strategy provides huge electromagnetic enhancement and abundant DNA adsorbing sites on the GO layer, achieving a wide detection range of 2.7 × 102 to 2.7 × 108 particles/mL and an ultralow limit of detection down to 1.5 × 102 particles/mL, without the requirement of any nucleic acid amplification. Particularly, the proposed method has significant applications in early cancer diagnosis as it can accurately identify breast cancer cell-derived exosomes in clinical serum samples and can differentiate pancreatic cancer patients and healthy individuals.
Collapse
Affiliation(s)
- Qi Zhang
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Ruofei Ma
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Yingzhi Zhang
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Jing Zhao
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Yue Wang
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Zhangrun Xu
- Research Center for Analytical Sciences, Northeastern University, Shenyang 110819, P. R. China
| |
Collapse
|
19
|
Pan J, Xu W, Li W, Chen S, Dai Y, Yu S, Zhou Q, Xia F. Electrochemical Aptamer-Based Sensors with Tunable Detection Range. Anal Chem 2023; 95:420-432. [PMID: 36625123 DOI: 10.1021/acs.analchem.2c04498] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jing Pan
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Wenxia Xu
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Wanlu Li
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shuwen Chen
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yu Dai
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Shanwu Yu
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Qitao Zhou
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| |
Collapse
|
20
|
Sfragano PS, Pillozzi S, Condorelli G, Palchetti I. Practical tips and new trends in electrochemical biosensing of cancer-related extracellular vesicles. Anal Bioanal Chem 2023; 415:1087-1106. [PMID: 36683059 PMCID: PMC9867925 DOI: 10.1007/s00216-023-04530-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 01/24/2023]
Abstract
To tackle cancer and provide prompt diagnoses and prognoses, the constantly evolving biosensing field is continuously on the lookout for novel markers that can be non-invasively analysed. Extracellular vesicles (EVs) may represent a promising biomarker that also works as a source of biomarkers. The augmented cellular activity of cancerous cells leads to the production of higher numbers of EVs, which can give direct information on the disease due to the presence of general and cancer-specific surface-tethered molecules. Moreover, the intravesicular space is enriched with other molecules that can considerably help in the early detection of neoplasia. Even though EV-targeted research has indubitably received broad attention lately, there still is a wide lack of practical and effective quantitative procedures due to difficulties in pre-analytical and analytical phases. This review aims at providing an exhaustive outline of the recent progress in EV detection using electrochemical and photoelectrochemical biosensors, with a focus on handling approaches and trends in the selection of bioreceptors and molecular targets related to EVs that might guide researchers that are approaching such an unstandardised field.
Collapse
Affiliation(s)
- Patrick Severin Sfragano
- grid.8404.80000 0004 1757 2304Department of Chemistry Ugo Schiff, University of Florence, Via Della Lastruccia 3, 50019 Sesto, Fiorentino, Italy
| | - Serena Pillozzi
- grid.24704.350000 0004 1759 9494Medical Oncology Unit, Careggi University Hospital, Largo Brambilla 3, 50134 Florence, Italy
| | - Gerolama Condorelli
- grid.4691.a0000 0001 0790 385XDepartment of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Via Pansini, 5, 80131 Naples, Italy ,grid.419543.e0000 0004 1760 3561IRCCS Istituto Neurologico Mediterraneo (INM) Neuromed, Via Atinense 18, 86077 Pozzilli, Italy
| | - Ilaria Palchetti
- grid.8404.80000 0004 1757 2304Department of Chemistry Ugo Schiff, University of Florence, Via Della Lastruccia 3, 50019 Sesto, Fiorentino, Italy
| |
Collapse
|
21
|
Qi M, Shi P, Zhang X, Cui S, Liu Y, Zhou S, Zhang Q. Reconfigurable DNA triplex structure for pH responsive logic gates †. RSC Adv 2023; 13:9864-9870. [PMID: 36998523 PMCID: PMC10043996 DOI: 10.1039/d3ra00536d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The DNA triplex is a special DNA structure often used as a logic gate substrate due to its high stability, programmability, and pH responsiveness. However, multiple triplex structures with different C−G−C+ proportions must be introduced into existing triplex logic gates due to the numerous logic calculations involved. This requirement complicates circuit design and results in many reaction by-products, greatly restricting the construction of large-scale logic circuits. Thus, we designed a new reconfigurable DNA triplex structure (RDTS) and constructed the pH-responsive logic gates through its conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. The use of these logic calculations necessitates fewer substrates, further enhancing the extensibility of the logic circuit. This result is expected to promote the development of the triplex in molecular computing and facilitate the completion of large-scale computing networks. We constructed pH-responsive logic gates through substrate conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. Our logic gates necessitate fewer substrates when two types of logic calculations are needed.![]()
Collapse
Affiliation(s)
- Mingxuan Qi
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Shuang Cui
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of TechnologyDalian 116024China
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian UniversityDalian 116622China
| |
Collapse
|
22
|
Yan C, Shi G, Chen J. Fluorescent Detection of Two Pesticides Based on CRISPR-Cas12a and Its Application for the Construction of Four Molecular Logic Gates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12700-12707. [PMID: 36128975 DOI: 10.1021/acs.jafc.2c04548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An intelligent detection platform was developed through molecular logic gate operation based on CRISPR-Cas12a and signal amplification circuits using two kinds of pesticides [acetamiprid (ACE) and atrazine (ATR)] as inputs. The pesticide-aptamer bindings activate the signal amplification process to produce numerous double-stranded DNA, which can be identified by CRISPR-Cas12a. Under the optimal assay conditions, the sensor exhibits excellent analytical performance, with the detection limits for ACE and ATR of 2.5 and 0.2 pM, respectively. The practicality of the platform was verified by testing pesticide concentrations in food samples. Several molecular logic gates (OR, AND, XOR, and INHIBIT) were constructed using "0" and "1" to encode the target pesticides and the fluorescence readout. The logic detection platform with simple operation, high sensitivity, and multiple logic functions is promising to become a powerful sensing system for the intelligent assay of different pesticides in food samples.
Collapse
Affiliation(s)
- Chong Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, People's Republic of China
| | - Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, People's Republic of China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, People's Republic of China
| |
Collapse
|
23
|
Huang R, He L, Jin L, Li Z, He N, Miao W. Recent advancements in DNA nanotechnology-enabled extracellular vesicles detection and diagnosis: A mini review. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
24
|
Deng J, Zhao S, Li J, Cheng Y, Liu C, Liu Z, Li L, Tian F, Dai B, Sun J. One-Step Thermophoretic AND Gate Operation on Extracellular Vesicles Improves Diagnosis of Prostate Cancer. Angew Chem Int Ed Engl 2022; 61:e202207037. [PMID: 35749531 DOI: 10.1002/anie.202207037] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Indexed: 01/19/2023]
Abstract
Circulating extracellular vesicles (EVs) have emerged as a valuable source of cancer biomarkers. However, the high degree of EV heterogeneity and the complexity of clinical samples pose a challenge in the sensitive identification of tumor-derived EVs. Here we introduce a one-step thermophoretic AND gate operation (Tango) assay that integrates polyethylene glycol (PEG)-enhanced thermophoretic accumulation of EVs and simultaneous AND gate operation on EV membranes by dual-aptamers recognition. By using the Tango assay to detect tumor-derived EVs with co-presence of EpCAM and PSMA directly from serum in a homogeneous, separation-free format, we can discriminate prostate cancer (PCa) patients from benign prostatic hyperplasia (BPH) patients in the diagnostic gray zone with an accuracy of 91 % in 15 min. Our approach streamlines EV enrichment and AND gate operation on EVs in a single assay, providing a rapid, straightforward, and powerful method for precise and non-invasive diagnosis of cancer.
Collapse
Affiliation(s)
- Jinqi Deng
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Zhao
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junhong Li
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yangchang Cheng
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Liu
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheng Liu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lele Li
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Tian
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Dai
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jiashu Sun
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, Beijing, 100190, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
25
|
Liu J, Wang R, Zhou H, Mathesh M, Dubey M, Zhang W, Wang B, Yang W. Nucleic acid isothermal amplification-based soft nanoarchitectonics as an emerging electrochemical biosensing platform. NANOSCALE 2022; 14:10286-10298. [PMID: 35791765 DOI: 10.1039/d2nr02031a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The emergence of nucleic acid isothermal amplification strategies based on soft nanoarchitectonics offers a new dimension to the traditional electrochemical technique, particularly because of its flexibility, high efficiency, and increased sensitivity for analytical applications. Various DNA/RNA isothermal amplification strategies have been developed for the design and fabrication of new electrochemical biosensors for efficient and important biomolecular detection. Herein, we provide an overview of recent efforts in this research field and the strategies for signal-amplified sensing systems, with their biological applications, current challenges and prospects in this promising new area.
Collapse
Affiliation(s)
- Jing Liu
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China.
| | - Ruke Wang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China.
| | - Hong Zhou
- Shandong Key Laboratory of Biochemical Analysis; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Motilal Mathesh
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, 3217, Australia.
| | - Mukul Dubey
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
| | - Wengan Zhang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China.
| | - Bo Wang
- College of Chemical and Biological Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China.
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, 3217, Australia.
| |
Collapse
|
26
|
Bioprobes-regulated precision biosensing of exosomes: From the nanovesicle surface to the inside. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214538] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
27
|
Abstract
Regulatory processes in biology can be re-conceptualized in terms of logic gates, analogous to those in computer science. Frequently, biological systems need to respond to multiple, sometimes conflicting, inputs to provide the correct output. The language of logic gates can then be used to model complex signal transduction and metabolic processes. Advances in synthetic biology in turn can be used to construct new logic gates, which find a variety of biotechnology applications including in the production of high value chemicals, biosensing, and drug delivery. In this review, we focus on advances in the construction of logic gates that take advantage of biological catalysts, including both protein-based and nucleic acid-based enzymes. These catalyst-based biomolecular logic gates can read a variety of molecular inputs and provide chemical, optical, and electrical outputs, allowing them to interface with other types of biomolecular logic gates or even extend to inorganic systems. Continued advances in molecular modeling and engineering will facilitate the construction of new logic gates, further expanding the utility of biomolecular computing.
Collapse
|
28
|
Deng J, Zhao S, Li J, Cheng Y, Liu C, Liu Z, Li L, Tian F, Dai B, Sun J. One‐Step Thermophoretic AND Gate Operation on Extracellular Vesicles Improves Diagnosis of Prostate Cancer. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jinqi Deng
- National Center for Nanoscience and Technology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CHINA
| | - Shuai Zhao
- National Center for Nanoscience and Technology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CHINA
| | - Junhong Li
- Fudan University Shanghai Cancer Center Department of Urology CHINA
| | - Yangchang Cheng
- National Center for Nanoscience and Technology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CHINA
| | - Chao Liu
- National Center for Nanoscience and Technology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CHINA
| | - Zheng Liu
- Fudan University Shanghai Cancer Center Department of Urology CHINA
| | - Lele Li
- National Center for Nanoscience and Technology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CHINA
| | - Fei Tian
- National Center for Nanoscience and Technology CAS Key Laboratory of Standardization and Measurement for Nanotechnology CHINA
| | - Bo Dai
- Fudan University Shanghai Cancer Center Department of Urology CHINA
| | - Jiashu Sun
- National Center for Nanoscience and Technology No.11 Beiyitiao, Zhongguancun Beijing CHINA
| |
Collapse
|
29
|
Hao P, Niu L, Luo Y, Wu N, Zhao Y. Surface Engineering of Lipid Vesicles Based on DNA Nanotechnology. Chempluschem 2022; 87:e202200074. [PMID: 35604011 DOI: 10.1002/cplu.202200074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/01/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Pengyan Hao
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Liqiong Niu
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Yuanyuan Luo
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Na Wu
- Xi'an Jiaotong University School of Life Science and Technology No.28, West Xianning Road 710049 Xi'an CHINA
| | - Yongxi Zhao
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| |
Collapse
|
30
|
Chen J, Fu S, Zhang C, Liu H, Su X. DNA Logic Circuits for Cancer Theranostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2108008. [PMID: 35254723 DOI: 10.1002/smll.202108008] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Cancer diagnosis and therapeutics (theranostics) based on the tumor microenvironment (TME) and biomarkers has been an emerging approach for precision medicine. DNA nanotechnology dynamically controls the self-assembly of DNA molecules at the nanometer scale to construct intelligent DNA chemical reaction systems. The DNA logic circuit is a particularly emerging approach for computing within the DNA chemical systems. DNA logic circuits can sensitively respond to tumor-specific markers and the TME through logic operations and signal amplification, to generate detectable signals or to release anti-cancer agents. In this review, the fundamental concepts of DNA logic circuits are clarified, the basic modules in the circuit are summarized, and how this advanced nano-assembly circuit responds to tumor-related molecules, how to perform logic operations, to realize signal amplification, and selectively release drugs through discussing over 30 application examples, are demonstrated. This review shows that DNA logic circuits have powerful logic judgment and signal amplification functions in improving the specificity and sensitivity of cancer diagnosis and making cancer treatment controllable. In the future, researchers are expected to overcome the existing shortcomings of DNA logic circuits and design smarter DNA devices with better biocompatibility and stability, which will further promote the development of cancer theranostics.
Collapse
Affiliation(s)
- Jing Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Chunyi Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huiyu Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| |
Collapse
|
31
|
Biorecognition Engineering Technologies for Cancer Diagnosis: A Systematic Literature Review of Non-Conventional and Plausible Sensor Development Methods. Cancers (Basel) 2022; 14:cancers14081867. [PMID: 35454775 PMCID: PMC9030888 DOI: 10.3390/cancers14081867] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/14/2022] [Accepted: 03/22/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Approximately 70% of patients with cancer are diagnosed at late stages of the disease in developing countries. This is partly owed to the restricted access to cost-effective and accurate diagnostic tools in healthcare systems. Biosensor diagnostic tools based on conventional antibodies have been a valuable option for creating accessible detection systems for cancer. However, antibodies have certain limitations related to cost, stability, and applicability. The latter promoted the research and development of alternative approaches to generating molecules and molecule-based scaffolds with similar biorecognition properties to antibodies (non-conventional technologies). This review aimed to present and analyze the current trends of three of these emerging non-conventional technologies for biorecognition engineering in cancer diagnostics, named: molecularly imprinted polymers, recombinant antibodies, and antibody mimetic molecules. These non-conventional technologies are promising, relevant, and more accessible alternatives to conventional antibodies in developing cancer biosensors and worthy of being acknowledged by the scientific community, especially for their use in point-of-care cancer diagnostics in developing countries. Abstract Cancer is the second cause of mortality worldwide. Early diagnosis of this multifactorial disease is challenging, especially in populations with limited access to healthcare services. A vast repertoire of cancer biomarkers has been studied to facilitate early diagnosis; particularly, the use of antibodies against these biomarkers has been of interest to detect them through biorecognition. However, there are certain limitations to this approach. Emerging biorecognition engineering technologies are alternative methods to generate molecules and molecule-based scaffolds with similar properties to those presented by antibodies. Molecularly imprinted polymers, recombinant antibodies, and antibody mimetic molecules are three novel technologies commonly used in scientific studies. This review aimed to present the fundamentals of these technologies and address questions about how they are implemented for cancer detection in recent scientific studies. A systematic analysis of the scientific peer-reviewed literature regarding the use of these technologies on cancer detection was carried out starting from the year 2000 up to 2021 to answer these questions. In total, 131 scientific articles indexed in the Web of Science from the last three years were included in this analysis. The results showed that antibody mimetic molecules technology was the biorecognition technology with the highest number of reports. The most studied cancer types were: multiple, breast, leukemia, colorectal, and lung. Electrochemical and optical detection methods were the most frequently used. Finally, the most analyzed biomarkers and cancer entities in the studies were carcinoembryonic antigen, MCF-7 cells, and exosomes. These technologies are emerging tools with adequate performance for developing biosensors useful in cancer detection, which can be used to improve cancer diagnosis in developing countries.
Collapse
|
32
|
Zhou J, Lin Q, Huang Z, Xiong H, Yang B, Chen H, Kong J. Aptamer-Initiated Catalytic Hairpin Assembly Fluorescence Assay for Universal, Sensitive Exosome Detection. Anal Chem 2022; 94:5723-5728. [PMID: 35377617 DOI: 10.1021/acs.analchem.2c00231] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cancer-cell-derived exosomes are regarded as noninvasive biomarkers for early cancer diagnosis because of their critical roles in intercellular communication and molecular exchange. A robust aptamer-initiated catalytic hairpin assembly (AICHA) fluorescence assay is proposed for universal, sensitive detection of cancer-derived exosomes. The AICHA was verified with the specific detection of MCF-7 cell-derived exosomes with a wide calibration range of 8.4 particles/μL to 8.4 × 105 particles/μL and a low detection limit (LOD) of 0.5 particles/μL. The universality of the AICHA method was verified for PANC-1 cell-derived exosomes, the LOD of which was determined to be 0.1 particles/μL. The performances in serum samples were detected with a recovery rate range of 95.45-106.2%, which demonstrates its significant potential for protein biomarker analysis and cancer diagnosis.
Collapse
Affiliation(s)
- Jiaqi Zhou
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Qiuyuan Lin
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Zhipeng Huang
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Huiwen Xiong
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Bin Yang
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai 200438, China
| |
Collapse
|
33
|
Liang TT, Qin X, Xiang Y, Tang Y, Yang F. Advances in nucleic acids-scaffolded electrical sensing of extracellular vesicle biomarkers. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
34
|
Pan J, Deng F, Liu Z, Shi G, Chen J. Toehold-Mediated Cascade Catalytic Assembly for Mycotoxin Detection and Its Logic Applications. Anal Chem 2022; 94:3693-3700. [PMID: 35176850 DOI: 10.1021/acs.analchem.1c05485] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this work, an enzyme-free biosensor is reported for mycotoxin detection based on a toehold-mediated catalytic hairpin assembly (CHA) and a DNAzyme-cascaded hydrolysis reaction. In the presence of a mycotoxin, the recognition between an aptamer and the mycotoxin releases the trigger DNA. The trigger DNA initiates the toehold-mediated CHA, generating large amounts of partial duplex B/C with four toeholds, which can be used to assemble the DNAzyme-cascaded hydrolysis reaction. Furthermore, through a collaborative autoassembly reaction among the B/C duplex, DNA1, and DNA2, supramolecular nanostructures corresponding to Mg2+-dependent DNAzymes can be formed. With the incubation of Mg2+, the dual-modified (TAMRA/BHQ2) substrate strand DNA2 will be cleaved into two fragments, yielding a high TAMRA fluorescence signal for mycotoxin testing. Under optimal conditions, the sensing system was ultrasensitive and showed low detection limits of 0.2 pM for ochratoxin A (OTA), 0.13 pM for aflatoxin B1 (AFB1), and 0.17 pM for zearalenone (ZEN). The mycotoxin aptasensor also exhibited high selectivity and was successfully applied for the quantitative analysis of OTA, AFB1, and ZEN in wine samples. Due to the advantages of flexibility and versatility, this mycotoxin platform was used to fabricate several concatenated logic gates including "AND-INHIBIT", "INHIBIT-OR", "OR-AND", and "OR-INHIBIT" logic biocomputings. Such multiple functions of the logic system provided a universal sensing strategy for the intelligent detection of multiplex mycotoxins, demonstrating considerable potential in food safety and environmental monitoring.
Collapse
Affiliation(s)
- Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Fang Deng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Zhi Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Gu Shi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
35
|
Yang L, Jia J, Li S. Advances in the Application of Exosomes Identification Using Surface-Enhanced Raman Spectroscopy for the Early Detection of Cancers. Front Bioeng Biotechnol 2022; 9:808933. [PMID: 35087806 PMCID: PMC8786808 DOI: 10.3389/fbioe.2021.808933] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022] Open
Abstract
Exosomes are small nanoscale vesicles with a double-layered lipid membrane structure secreted by cells, and almost all types of cells can secrete exosomes. Exosomes carry a variety of biologically active contents such as nucleic acids and proteins, and play an important role not only in intercellular information exchange and signal transduction, but also in various pathophysiological processes in the human body. Surface-enhanced Raman Spectroscopy (SERS) uses light to interact with nanostructured materials such as gold and silver to produce a strong surface plasmon resonance effect, which can significantly enhance the Raman signal of molecules adsorbed on the surface of nanostructures to obtain a rich fingerprint of the sample itself or Raman probe molecules with ultra-sensitivity. The unique advantages of SERS, such as non-invasive and high sensitivity, good selectivity, fast analysis speed, and low water interference, make it a promising technology for life science and clinical testing applications. In this paper, we briefly introduce exosomes and the current main detection methods. We also describe the basic principles of SERS and the progress of the application of unlabeled and labeled SERS in exosome detection. This paper also summarizes the value of SERS-based exosome assays for early tumor diagnosis.
Collapse
Affiliation(s)
- Lu Yang
- Department of Internal Medicine, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital and Institute), Shenyang, China
| | - Jingyuan Jia
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, China
- *Correspondence: Jingyuan Jia, ; Shenglong Li,
| | - Shenglong Li
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital and Institute), Shenyang, China
- *Correspondence: Jingyuan Jia, ; Shenglong Li,
| |
Collapse
|
36
|
Cheng S, Kong Q, Hu X, Zhang C, Xian Y. An Ultrasensitive Strand Displacement Signal Amplification-Assisted Synchronous Fluorescence Assay for Surface Proteins of Small Extracellular Vesicle Analysis and Cancer Identification. Anal Chem 2022; 94:1085-1091. [DOI: 10.1021/acs.analchem.1c04122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shasha Cheng
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Qianqian Kong
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Xinyu Hu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Cuiling Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Yuezhong Xian
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| |
Collapse
|
37
|
Kong Q, Cheng S, Hu X, You J, Zhang C, Xian Y. Ultrasensitive detection of tumor-derived small extracellular vesicles based on nonlinear hybridization chain reaction fluorescence signal amplification and immunomagnetic separation. Analyst 2022; 147:1859-1865. [DOI: 10.1039/d2an00242f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An ultrasensitive nonlinear hybridization chain reaction signal amplification fluorescence assay for the detection of small extracellular vesicles.
Collapse
Affiliation(s)
- Qianqian Kong
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Shasha Cheng
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Xinyu Hu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Jia You
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Cuiling Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Yuezhong Xian
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| |
Collapse
|