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Zhang J, Bai D, Xie G, Xie Y, Lin Y, Hou Y, Yu Y, Zhang Y, Zhao R, Wang Z, Wang L, Chen H. A novel entropy-driven dual-output mode integrated with DNAzyme for enhanced microRNA detection. Talanta 2024; 275:126123. [PMID: 38663065 DOI: 10.1016/j.talanta.2024.126123] [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: 12/22/2023] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/30/2024]
Abstract
Accurate microRNA (miRNA) detection is pivotal in the diagnosis and monitoring of cancer. Entropy-driven catalysis (EDC) has attracted widespread attention as an enzyme-free, isothermal technique for miRNA detection owing to its inherent simplicity and reliability. However, conventional EDC is a single-output mode, limiting the efficiency of signal amplification. In this study, a novel EDC dual-output mode was employed in conjunction with DNAzyme, resulting in the development of an EDC dual-end DNAzyme (EDC-DED) approach for highly sensitive miRNA detection. In this system, miRNA-21 initiated the EDC reaction, producing a large amount of catalytically active dual-end Mg2+-dependent DNAzyme. The DNAzyme further cleaved the reporter cyclically, generating a notably amplified fluorescence signal. The proposed method achieved a low detection limit of 2 pM. Compared with the traditional EDC single-end DNAzyme (EDC-SED) strategy, the present method exhibited superior amplification efficiency, enhancing detection sensitivity by approximately 46.5-fold. Furthermore, this platform demonstrated ideal specificity, satisfactory reproducibility and acceptable detection capabilities in clinical serum samples. Therefore, the straightforward and convenient strategy is a potential tool for miRNA analysis, which may provide a new perspective for biological analysis and clinical application.
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Affiliation(s)
- Jianhong Zhang
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Dan Bai
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yaxing Xie
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yu Lin
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Yulei Hou
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Ying Yu
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Yaoyi Zhang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Luojia Wang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Hui Chen
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
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2
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Zhang C, Zhao X, Huang Z, Li Z, Hu J, Liu R, Lv Y. Highly sensitive detection of aflatoxin B1 byCRISPR/Cas12a-assisted single nanoparticle counting. Food Chem 2024; 443:138557. [PMID: 38280363 DOI: 10.1016/j.foodchem.2024.138557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/28/2023] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) and CRISPR-associated protein (Cas) have gained extensive applications in bioassays. However, CRISPR-based detection platforms are often hampered by limited analytical sensitivity, while nucleic acid-based amplification strategies are usually indispensable for additional signal enhancement with potential risks of amplification leakages. To address these challenges, an amplification-free CRISPR-based bioassay of aflatoxin B1 (AFB1) was proposed by applying single nanoparticle counting. Single-particle mode inductively coupled plasma mass spectrometry (Sp-ICPMS) has been regarded as a sensitive tool for nanoparticle counting since one nanoparticle can generate considerable signals above backgrounds. With AFB1, activator strands were introduced to initiate the trans-cleavage of CRISPR/Cas12a for cutting the nanoparticles-tagged-magnetic beads, which were transduced to nanoparticle count signals after separation. Finally, a pico-mole level limit-of-detections (LODs) with moderate selectivity was achieved. Certified reference materials (CRMs) analysis and recovery tests were conducted with promising results. To our best knowledge, this is the first report of the single particle counting-based CRISPR/Cas12a biosensing study.
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Affiliation(s)
- Chengchao Zhang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Xin Zhao
- Department of Clinical Laboratory, Chengdu Seventh People's Hospital, Chengdu, Sichuan 610041, PR China
| | - Zili Huang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Ziyan Li
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China.
| | - Yi Lv
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, PR China; Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, PR China
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3
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Liang P, Lv B, Chen K, Li D. Sensitive aptasensing of ATP based on a PAM site-regulated CRISPR/Cas12a activation. Mikrochim Acta 2024; 191:386. [PMID: 38867016 DOI: 10.1007/s00604-024-06477-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024]
Abstract
The combination of CRISPR/Cas12a and functional DNA provides the possibility of constructing biosensors for detecting non-nucleic-acid targets. In the current study, the duplex protospacer adjacent motif (PAM) in the activator of CRISPR/Cas12a was used as a molecular switch, and a sensitive adenosine triphosphate (ATP) detection biosensor was constructed using an allosteric probe-conjugated PAM site formation in hybridization chain reaction (HCR) integrated with the CRISPR/Cas12a system (APF-CRISPR). In the absence of ATP, an aptamer-containing probe (AP) is in a stem-loop structure, which blocks the initiation of HCR. In the presence of ATP, the structure of AP is changed upon ATP binding, resulting in the release of the HCR trigger strand and the production of long duplex DNA with many PAM sites. Since the presence of a duplex PAM site is crucial for triggering the cleavage activity of CRISPR/Cas12a, the ATP-dependent formation of the PAM site in HCR products can initiate the FQ-reporter cleavage, allowing ATP quantification by measuring the fluorescent signals. By optimizing the sequence elements and detection conditions, the aptasensor demonstrated superior detection performance. The limit of detection (LOD) of the assay was estimated to be 1.16 nM, where the standard deviation of the blank was calculated based on six repeated measurements. The dynamic range of the detection was 25-750 nM, and the whole workflow of the assay was approximately 60 min. In addition, the reliability and practicability of the aptasensor were validated by comparing it with a commercially available chemiluminescence kit for ATP detection in serum. Due to its high sensitivity, specificity, and reliable performance, the APF-CRISPR holds great potential in bioanalytical studies for ATP detection. In addition, we have provided a proof-of-principle for constructing a CRISPR/Cas12a-based aptasensor, in which the PAM is utilized to regulate Cas12a cleavage activity.
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Affiliation(s)
- Pengda Liang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Bei Lv
- Key Lab of Innovative Applications of Bioresources and Functional Molecules of Jiangsu Province, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing, 210013, China
| | - Ke Chen
- Key Lab of Innovative Applications of Bioresources and Functional Molecules of Jiangsu Province, College of Life Science and Chemistry, Jiangsu Second Normal University, Nanjing, 210013, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
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Zhu L, Song L, Zheng C, Wang N, Xue C, Shen Z, Huang X. Intracellular nonenzymatic in situ growth of layered nanosheet DNA architectures based on palindrome-chained dumbbell probes for miRNA imaging. Talanta 2024; 277:126333. [PMID: 38850801 DOI: 10.1016/j.talanta.2024.126333] [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: 12/30/2023] [Revised: 05/07/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024]
Abstract
MicroRNA (miRNA) represents a class of important potential biomarkers, and their intracellular imaging is extremely useful for fundamental research and early diagnosis of human cancers. Hybridization chain reaction (HCR) has been shown to be effective in detecting miRNA in living cells. However, its practical applications are still hampered by inefficient reaction kinetics and poor biological stability under complex intracellular conditions. To address these issues, we report a palindrome-mediated multiple hybridization chain reaction (P-HCR) system to better visualize intracellular miRNAs. In the presence of the target miRNA, a layered nanosheet DNA architecture (LSDA) can be assembled in situ via the palindrome-mediated multiple HCR process. We demonstrate that the biological stability of this reaction system could be significantly improved by designing the probes to dumbbell-shaped structures and the distance of hairpins was effectively decreased due to palindrome-chained effect. Consequently, miRNA can be quantitatively identified even at extremely low concentrations of 4.7 pM. The P-HCR system can effectively differentiate the expression levels of miRNA in different tumor cells and normal cells, as demonstrated in live cell tests and the results were in agreement with the PCR, which is considered the gold standard. The new (P-HCR) system has the potential to revolutionize miRNA imaging in living cells.
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Affiliation(s)
- Lingye Zhu
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China; Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Lanlan Song
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China
| | - Cheng Zheng
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China
| | - Ning Wang
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China
| | - Chang Xue
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Xiaoying Huang
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China.
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5
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Yu J, Zhang J, Li M, You Y, Zhang C. CRISPR/Cas13a-triggered entropy-driven amplification for colorimetric and fluorescent dual-mode detection of microRNA. Anal Biochem 2024; 689:115499. [PMID: 38431141 DOI: 10.1016/j.ab.2024.115499] [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: 11/17/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
MicroRNAs (miRNAs) are crucial biomarkers for the early detection and monitoring of disease progression of chronic obstructive pulmonary disease (COPD). Herein, we have devised a method for detecting miRNA using a combination of colorimetric and graphene oxide-based fluorescent techniques. The target miRNA in our design could precisely activate the trans-cleavage activity of the CRISPR-Cas13a system. The activated Cas13a enzyme cuts the "rUrU" section in the P1 probe, generating a nicking site to induce entropy-driven amplification (EDA). One of the available EDA products has the capability to unfold the hairpin probe, thereby initiating the catalytic hairpin assembly, exposing the G-quadruplex structure, facilitating the subsequent color response. The fuel strand labeled with Cy3 successfully established a double-stranded DNA structure with DNA3, and consequently the Cy3 would not be quenched by graphene oxide (GO). The implementation of the dual-mode technique in this method yields greater benefits in terms of improving the precision and consistency of the miRNA measurements. The developed method has the capability to fluorescently measure miRNA-21 levels down to a concentration of 5.8 fM. In addition, the analysis of miRNA targets from clinical samples using this method demonstrates its promising utility in the fields of biomedical research of COPD.
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Affiliation(s)
- Juanchun Yu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Army Medical University, Chongqing, 400037, China
| | - Junhong Zhang
- Department of Geriatrics and Special Service Medicine, The First Affiliated Hospital of Army Medical University, Chongqing, 400038, China
| | - Meng Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Army Medical University, Chongqing, 400037, China
| | - Yiqin You
- Department of Clinical Laboratory, The Second Affiliated Hospital of Army Medical University, Chongqing, 400037, China
| | - Chenchen Zhang
- Department of Geriatrics and Special Service Medicine, The First Affiliated Hospital of Army Medical University, Chongqing, 400038, China.
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6
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Wang Q, He B, Liu Y, Wang Y, Jin H, Wei M, Zhao W, Xie D, Ren W, Suo Z, Xu Y. "Two-in-One" PtPdCu Trimetallic Multifunctional Nanoparticles-Mediated Dual-Signal-Integrated Aptasensor for Ultradetection of Enrofloxacin. ACS APPLIED MATERIALS & INTERFACES 2024; 16:22704-22714. [PMID: 38640487 DOI: 10.1021/acsami.4c02707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Balancing the accuracy and simplicity of aptasensors is a challenge in their construction. This study addresses this issue by leveraging the remarkable loading capacity and peroxidase-like catalytic activity of PtPdCu trimetallic nanoparticles, which reduces the reliance on precious metals. A dual-signal readout aptasensor for enrofloxacin (ENR) detection is designed, incorporating DNA dynamic network cascade reactions to further amplify the output signal. Exploiting the strong loading capacity of PtPdCu nanoparticles, they are self-assembled with thionine (Thi) to form a signal label capable of generating signals in two independent modes. The label exhibits excellent enzyme-like catalytic activity and enhances electron transfer capabilities. Differential pulse voltammetry (DPV) and square-wave voltammetry (SWV) are employed to independently read signals from the oxidation-reduction reaction of Thi and the catalytic oxidation of hydroquinone (HQ) to benzoquinone (BQ) by H2O2. The introduced DNA dynamic network cascade reaction modularizes sample processing and electrode surface signal generation, avoiding electrode contamination and efficiently increasing the output of the catalyzed hairpin assembly (CHA) cycle. Under optimized conditions, the developed aptasensor demonstrates detection limits of 0.112 (DPV mode) and 0.0203 pg/mL (SWV mode). Additionally, the sensor successfully detected enrofloxacin in real samples, expanding avenues for designing dual-mode signal amplification strategies.
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Affiliation(s)
- Qianqian Wang
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, P. R. China
| | - Baoshan He
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, P. R. China
| | - Yao Liu
- Henan Scientific Research Platform Service Center, Zhengzhou, Henan 450003, P. R. China
| | - Yuling Wang
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Huali Jin
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, P. R. China
| | - Min Wei
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, P. R. China
| | - Wenhong Zhao
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, P. R. China
| | - Dongdong Xie
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, P. R. China
| | - Wenjie Ren
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, P. R. China
| | - Zhiguang Suo
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, P. R. China
| | - Yiwei Xu
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan 450001, P. R. China
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7
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Fan Z, Zhou J, Shu Q, Dong Y, Li Y, Zhang T, Bai G, Yu H, Lu F, Li J, Zhao X. Aptamer-bivalent-cholesterol-mediated proximity entropy-driven exosomal protein reporter for tumor diagnosis. Biosens Bioelectron 2024; 251:116104. [PMID: 38368644 DOI: 10.1016/j.bios.2024.116104] [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: 11/19/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
Exosomal proteins from the parental cells are considered to be promising biomarker sets for precise tumor diagnostics and monitoring. However, the accurate quantitative analysis of low-abundance exosomal proteins remains challenging due to the heterogeneity of clinical samples. Here, we standardized the exosomal concentration with a fluorogenic membrane probe and developed an aptamer-bivalent-cholesterol-mediated Proximity Entropy-driven Exosomal Protein Reporter (PEEPR). The proposed PEEPR enables the in-situ analysis of multiple exosomal proteins by integrating bivalent cholesterol anchor (exosomal lipid bilayer) and aptamer (exosomal proteins) with a proximity entropy-driven circuit. Based on this strategy, we successfully achieved detection limits of 3.9 pg/mL exosomal GPC-3 and 3.4 pg/mL exosomal PD-L1. Notably, the standardization of exosome concentrations is designed to avoid errors due to biological heterogeneity. The results showed that evaluating the levels of exosomal GPC-3 and PD-L1 in clinical samples via this strategy could accurately differentiate healthy individuals, hepatitis B patients, and hepatocellular carcinoma patients. In summary, PEEPR is a promising clinical diagnostic strategy for the quantitative analysis of a variety of tumor-associated exosomal proteins for the precise diagnosis and personalized treatment monitoring of tumors.
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Affiliation(s)
- Zhichao Fan
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Jie Zhou
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China; Department of Laboratory Medicine, Xingcheng Special Service Sanatorium of Strategic Support Force, Huludao, 125100, China
| | - Qiuxia Shu
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yan Dong
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yingxue Li
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Tingrui Zhang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Gang Bai
- 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
| | - Hua Yu
- Department of General Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Fanghao Lu
- 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.
| | - Xiang Zhao
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
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Li Y, Li C, Zhang C, Zhao L, Huang Y. Triplex DNA-based aggregation-induced emission probe: A new platform for hybridization chain reaction-based fluorescence sensing assay. Anal Chim Acta 2024; 1299:342406. [PMID: 38499412 DOI: 10.1016/j.aca.2024.342406] [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: 12/09/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024]
Abstract
The hybridization chain reaction (HCR), as one of the nucleic acid amplification technologies, is combined with fluorescence signal output with excellent sensitivity, simplicity, and stability. However, current HCR-based fluorescence sensing methods still have some defects such as the blocking effect of the HCR combination with fluorophores and the aggregation-caused quenching (ACQ) phenomenon of traditional fluorophores. Herein, a triplex DNA-based aggregation-induced emission probe (AIE-P) was designed as the fluorescent signal transduction, which is able to provide a new platform for HCR-based sensing assay. The AIE-P was synthesized by attaching the AIE fluorophores to terminus of the oligonucleotide through amido bond, and captured the products of HCR to form triplex DNA. In this case, the AIE fluorophores were located in close proximity to generate fluorescence. This assay provided turn-on fluorescence efficiency with a high signal-to-noise ratio and excellent amplification capability to solve the shortcoming of HCR-based fluorescence sensing methods. It enabled sensitive detection of Vibrio parahaemolyticus in the range of 102-106 CFU mL-1, and with a low limit of detection down to 39 CFU mL-1. In addition, this assay expressed good specificity and practicability. The triplex DNA-based AIE probe forms a universal molecular tool for developing HCR-based fluorescence sensing methods.
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Affiliation(s)
- Yubin Li
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China; Research Center for Coastal Environmental Protection and Ecological Resilience, Guangdong Ocean University, Zhanjiang, 524088, China.
| | - Ciling Li
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chuangqiang Zhang
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Liting Zhao
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yaoyun Huang
- Faculty of Chemistry & Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, China
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9
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Yao Y, Liu Y, Liu X, Zhang X, Shi P, Zhang X, Zhang Q, Wei X. Bubble DNA tweezer: A triple-conformation sensor responsive to concentration-ratios. iScience 2024; 27:109074. [PMID: 38361618 PMCID: PMC10867447 DOI: 10.1016/j.isci.2024.109074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
DNA tweezers, with their elegant simplicity and flexibility, have been pivotal in biosensing and DNA computing. However, conventional tweezers are confined to a binary transformation pre/post target signal recognition, limiting them to presence/absence judgments. This study introduces bubble DNA tweezers (BDT), capable of three distinct conformations based on variable target signal ratios. In contrast to traditional compact tweezers, BDT features a looser structure centered around a non-complementary bubble domain located between the tweezer arms' connecting axis and target signal recognition jaws. This bubble triggers toehold-free DNA strand displacement, leading to three conformational changes at different target signal concentrations. BDT detects presence/absence and true concentration with remarkable specificity and sensitivity. This adaptability is not confined to ideal scenarios, proving valuable in complex, noisy environments. Our method facilitates target DNA/miRNA signal quantification within a specific length range, promising applications in clinical research and environmental detection, while inspiring future biological assay innovations.
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Affiliation(s)
- Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
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10
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Deng Z, Ding J, Bu J, Li J, Liu H, Gao P, Gong Z, Qin X, Yang Y, Zhong S. Fluorophore Label-Free Light-up Near Infrared Deoxyribonucleic Acid Nanosensor for Monitoring Extracellular Potassium Levels. Anal Chem 2024; 96:4023-4030. [PMID: 38412242 DOI: 10.1021/acs.analchem.3c03881] [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: 02/29/2024]
Abstract
Fluorescent DNA nanosensors have been widely used due to their unique advantages, among which the near-infrared (NIR) imaging mode can provide deeper penetration depth and lower biological background for the nanosensors. However, efficient NIR quenchers require ingenious design, complex synthesis, and modification, which severely limit the development of NIR DNA nanosensors. Label-free strategies based on G-quadruplex (G4) and NIR G4 dyes were first introduced into in situ extracellular imaging, and a novel NIR sensing strategy for the specific detection of extracellular targets is proposed. The strategy avoids complex synthesis and site-specific modification by controlling the change of the NIR signal through the formation of a G4 nanostructure. A light-up NIR DNA nanosensor based on potassium ion (K+)-sensitive G4 chain PS2.M was constructed to verify the strategy. PS2.M forms a stable G4 nanostructure in the presence of K+ and activates the NIR G4 dye CSTS, thus outputting NIR signals. The nanosensor can rapidly respond to K+ with a linear range of 5-50 mM and has good resistance to interference. The nanosensor with cholesterol can provide feedback on the changes in extracellular K+ concentration in many kinds of cells, serving as a potential tool for the study of diseases such as epilepsy and cancer, as well as the development of related drugs. The strategy can be potentially applied to the NIR detection of a variety of extracellular targets with the help of functional DNAs such as aptamer and DNAzyme.
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Affiliation(s)
- Zhiwei Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Jiacheng Ding
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Jiaqi Bu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Jiacheng Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Hui Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Peiru Gao
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Zan Gong
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Xiangxiang Qin
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Yanjing Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Shian Zhong
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
- Hunan Provincial Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, the "Double-First Class" Application Characteristic Discipline of Hunan Province (Pharmaceutical Science), Changsha Medical University, Changsha 410219, PR China
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11
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Chen J, Wang X, Guo J, Lv Y, Chen M, Tong H, Liu C. Heavy Metal-Induced Assembly of DNA Network Biosensor from Double-Loop Hairpin Probes for Ultrasensitive Detection of UO 22+ in Water and Soil Samples. Anal Chem 2024. [PMID: 38320403 DOI: 10.1021/acs.analchem.3c05526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The uranyl ion (UO22+) is the most stable form of uranium, which exhibits high toxicity and bioavailability posing a severe risk to human health. The construction of ultrasensitive, reliable, and robust sensing techniques for UO22+ detection in water and soil samples remains a challenge. Herein, a DNA network biosensor was fabricated for UO22+ detection using DNAzyme as the heavy metal recognition element and double-loop hairpin probes as DNA assembly materials. UO22+-activated specific cleavage of the DNAzyme will liberate the triggered DNA fragment, which can be utilized to launch a double-loop hairpin probe assembly among Hab, Hbc, and Hca. Through multiple cyclic cross-hybridization reactions, hexagonal DNA duplex nanostructures (n[Hab•Hbc•Hca]) were formed. This DNA network sensing system generates a high fluorescence response for UO22+ monitoring. The biosensor is ultrasensitive, with a detection limit of 2 pM. This sensing system also displays an excellent selectivity and robustness, enabling the DNA network biosensor to work even in complex water and soil samples with excellent accuracy and reliability. With the advantages of enzyme-free operation, outstanding specificity, and high sensitivity, our proposed DNA network biosensor provides a reliable, simple, and robust method for trace levels of UO22+ detection in environmental samples.
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Affiliation(s)
- Junhua Chen
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, 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
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Junhui Guo
- School of Material and Food, Jiangmen Polytechnic, Jiangmen 529000, China
| | - Yiwen Lv
- 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
| | - Hui Tong
- 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
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
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12
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Jiang J, Wang B, Luo L, Ying N, Shi G, Zhang M, Su H, Zeng D. A two-step electrochemical biosensor based on Tetrazyme for the detection of fibrin. Biotechnol Appl Biochem 2024; 71:193-201. [PMID: 37904286 DOI: 10.1002/bab.2531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023]
Abstract
In this study, an electrochemical biosensor was constructed for the detection of fibrin, specifically by a simple two-step approach, with a novel artificial enzyme (Tetrazyme) based on the DNA tetrahedral framework as signal probe. The multichannel screen-printed electrode with the activated surface cannot only remove some biological impurities, but also serve as a carrier to immobilize a large number of antigen proteins. The DNA tetrahedral nanostructure was employed to ensure the high sensitivity of the probe for biological analysis. The hemin was chimeric into the G-quadruplex to constitute the complex with peroxidase catalytic activity (hemin/G4-DNAzyme), subsequently, Tetrazyme was formed through combining of this complex and DNA tetrahedral nucleic acid framework. The artificial enzyme signal probe formed by the covalent combination of the homing peptide (Cys-Arg-Glu-Lys-Ala, CREKA), which is the aptamer of fibrin and the new artificial enzyme is fixed on the surface of the multichannel carbon electrode by CREKA-specific recognition, so as to realize the sensitive detection of fibrin. The feasibility of sensing platform was validated by cyclic voltammetry (CV) and amperometric i-t curve (IT) methods. Effects of Tetrazyme concentration, CREKA concentrations and hybridization time on the sensor were explored. Under the best optimal conditions of 0.6 μmol/L Tetrazyme, 80 μmol/L CREKA, and 2.5 h reaction time, the immunosensor had two linear detection ranges, 10-40 nmol/L, with linear regression equation Y = 0.01487X - 0.011 (R2 = 0.992), and 50-100 nmol/L, with linear regression equation Y = 0.00137X + 0.6405 (R2 = 0.998), the detection limit was 9.4 nmol/L, S/N ≥ 3. The biosensor could provide a new method with great potential for the detection of fibrin with good selectivity, stability, and reproducibility.
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Affiliation(s)
- Jiayi Jiang
- Department of Medical Devices, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Bin Wang
- Department of Medical Devices, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Linghuan Luo
- Department of Medical Devices, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Na Ying
- Department of Medical Devices, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Graduate, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Gaofan Shi
- Department of Medical Devices, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Mengmeng Zhang
- Department of Medical Devices, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Graduate, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Haoyuan Su
- Department of Medical Devices, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Dongdong Zeng
- Department of Medical Devices, Shanghai University of Medicine & Health Sciences, Shanghai, China
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13
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Yu Y, Li Q, Shi W, Yang Y, He H, Dai J, Mao G, Ma Y. Programmable Aptasensor for Regulating CRISPR/Cas12a Activity. ACS Sens 2024; 9:244-250. [PMID: 38085648 DOI: 10.1021/acssensors.3c01881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
CRISPR-mediated aptasensors have gained prevalence for detecting non-nucleic acid targets. However, there is an urgent need to develop an easily customizable design to improve the signal-to-noise ratio, enhance universality, and expand the detection range. In this article, we report a CRISPR-mediated programmable aptasensor (CPAS) platform. The platform includes single-stranded DNA comprising the aptamer sequence, locker DNA, and a crRNA recognition region, forming a hairpin structure through complementary hybridization. With T4 DNA polymerase, the crRNA recognition region was transformed into a complete double-stranded DNA through stem-loop extension, thereby activating the trans-cleavage activity of Cas 12a and generating fluorescence signals. The specific binding between the target molecule and aptamer disrupted the formation of the hairpin structure, altering the fluorescence signals. Notably, the CPAS platform allows for easy customization by simply changing the aptamer sequence and locker DNA, without entailing adjustments to the crRNA. The optimal number of bases in the locker DNA was determined to be seven nucleotides for the SARS-CoV-2 spike (S) protein and four nucleotides for ATP. The CPAS platform exhibited high sensitivity for S protein and ATP detection. Integration with a lateral flow assay enabled sensitive detection within 1 h, revealing its excellent potential for portable analysis.
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Affiliation(s)
- Yao Yu
- College of Chemistry & Pharmacy, Northwest A&F University Yangling, Shaanxi 712100, China
| | - Qiaoyu Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wen Shi
- College of Chemistry & Pharmacy, Northwest A&F University Yangling, Shaanxi 712100, China
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuxin Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hongpeng He
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Junbiao Dai
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Guobin Mao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingxin Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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14
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Yan H, Wu L, Wang J, Zheng Y, Zhao F, Bai Q, Hu H, Liang H, Niu X. Target-triggered dual signal amplification based on HCR-enhanced nanozyme activity for the sensitive visual detection of Escherichia coli. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:496-502. [PMID: 38078483 DOI: 10.1039/d3ay01824e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
The detection of foodborne pathogens is crucial for food hygiene regulation and disease diagnosis. Colorimetry has become one of the main analytical methods in studying foodborne pathogens due to its advantages of visualization, low cost, simple operation, and no complex instrument. However, the low sensitivity limits its applications in early identification and on-site detection for trace analytes. In order to overcome such a limitation, herein we propose a joint strategy featuring dual signal amplification based on the hybridization chain reaction (HCR) and DNA-enhanced peroxidase-like activity of gold nanoparticles (AuNPs) for the sensitive visual detection of Escherichia coli. Target bacteria bound specifically to the aptamer domain in the capture hairpin probe, exposing the trigger domain for HCR and forming the extended double-stranded DNA (dsDNA) structures. The peroxidase-like catalytic capacity of AuNPs can be enhanced significantly by dsDNAs with the sticky ends of dsDNAs being adsorbed on AuNPs and the rigidity of dsDNAs causing the spatial regulation of AuNP concentration. The intensity of the enhancement was linearly related to the number of target bacteria. With the above strategy, the detection limit of our colorimetric method for Escherichia coli was down to 28 CFU mL-1 within a short analytical time (50 min). This study provides a new perspective for the sensitive and visual detection of early bacterial contamination in foods.
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Affiliation(s)
- Hangli Yan
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China.
| | - Linghao Wu
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China.
| | - Jingyu Wang
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China.
| | - Yi Zheng
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China.
| | - Fengxia Zhao
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China.
| | - Qinqin Bai
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China.
| | - Hongmei Hu
- Hengyang Center for Disease Control and Prevention, Hengyang 421001, China
| | - Hao Liang
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China.
| | - Xiangheng Niu
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China.
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15
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Zhu F, Zhao Q. CRISPR/Cas12a linked sandwich aptamer assay for sensitive detection of thrombin. Anal Chim Acta 2024; 1287:342106. [PMID: 38182384 DOI: 10.1016/j.aca.2023.342106] [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: 08/25/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Thrombin is a serine protease and hemostasis regulator with multiple functions and recognized as an important biomarker for diseases, and sensitive detection of thrombin is of significance for clinical diagnostics and disease monitoring. Recently, the target-triggered nonspecific single-stranded deoxyribonuclease activity of CRISPR/Cas system is discovered, making it become a powerful tool in assay developments due to the ease of signal amplification. In the short period of development, many CRISPR based nucleic acid detection methods have already played a critical role in clinical diagnostics. However, the application of CRISPR/Cas system for protein biomarkers remains limited. RESULTS Here we describe a CRISPR/Cas12a linked sandwich aptamer assay for detection of thrombin, which was based on the formation of a sandwich complex of target by using a capture aptamer or antibody coated on the microplate and a well-designed detection DNA strand. The detection DNA strand contained an anti-thrombin aptamer and an active DNA of Cas12a, thus the sandwich complex was labeled with the active DNA. The active DNA triggered activity of Cas12a in indiscriminately cleaving fluorophore and quencher labeled DNA reporters, causing significant fluorescence increase. Our method enabled sensitive detection of thrombin down to 10 pM, and it showed high selectivity for thrombin. The assay exhibited good performance in diluted serum samples, demonstrating the applicability for thrombin analysis in the real media. SIGNIFICANCE This assay combines the merits of high affinity of aptamer, trans-cleavage activity of Cas12a, high selectivity of sandwich format analysis, and high-throughput detection of microplate assay, and it shows promise in applications.
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Affiliation(s)
- Fengxi Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China.
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16
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Liu J, Cui L, Shi X, Yan J, Wang Y, Ni Y, He J, Wang X. Generation of DNAzyme in Bacterial Cells by a Bacterial Retron System. ACS Synth Biol 2024; 13:300-309. [PMID: 38171507 DOI: 10.1021/acssynbio.3c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
DNAzymes are catalytically active single-stranded DNAs in which DNAzyme 10-23 (Dz 10-23) consists of a catalytic core and a substrate-binding arm that reduces gene expression through sequence-specific mRNA cleavage. However, the in vivo application of Dz 10-23 depends on exogenous delivery, which leads to its inability to be synthesized and stabilized in vivo, thus limiting its application. As a unique reverse transcription system, the bacterial retron system can synthesize single-stranded DNA in vivo using ncRNA msr/msd as a template. The objective of this work is to reduce target gene expression using Dz 10-23 generated in vivo by the retron system. In this regard, we successfully generated Dz 10-23 by cloning the Dz 10-23 coding sequence into the retron msd gene and tested its ability to reduce specific gene expression by examining the mRNA levels of cfp encoding cyan fluorescence protein and other functional genes such as mreB and ftsZ. We found that Dz had different repressive effects when targeting different mRNA regions, and in general, the repressive effect was stronger when targeting downstream of mRNAs. Our results also suggested that the reduction effect was due to cleavage of the substrate mRNA by Dz 10-23 rather than the antisense effect of the substrate-binding arm. Therefore, this study not only provided a retron-based method for the intracellular generation of Dz 10-23 but also demonstrated that Dz 10-23 could reduce gene expression by cleaving target mRNAs in cells. We believe that this new strategy would have great potential in the regulation of gene expression.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lina Cui
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xinyu Shi
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jiahao Yan
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yifei Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuyang Ni
- College of Life Sciences, Shangrao Normal University, Shangrao 334001, PR China
| | - Jin He
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xun Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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17
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Wu J, Lin X, Li J, Lv Z, Duan N, Wang Z, Wu S. Dual-color nanospheres based on aggregation-induced emission and catalytic hairpin assembly for simultaneous imaging of acrylamide and miR-21 in living cells. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132815. [PMID: 37879280 DOI: 10.1016/j.jhazmat.2023.132815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023]
Abstract
Acrylamide (AA) is a heat-processed potent food carcinogen that is widely used in industry, posing a significant risk to human health. Therefore, it is necessary to investigate the toxic effects and mechanism of AA. miR-21 is a representative biomarker during AA-induced carcinogenesis. Here, dual-color aggregation-induced emission nanoparticles (AIENPs) were developed for the detection and simultaneous imaging of AA and miR-21. AIENPs were synthesized by combining aggregation-induced emission (AIE) dyes and a poly (styrene-co-maleic anhydride) (PSMA) amphiphilic polymer modified with hairpin DNA. Upon AA intervention and aptamer recognition, cDNA was dissociated, leading to miR-21 overexpression and initiating the catalytic hairpin assembly cycle. Consequently, fluorescence quenching was observed due to FRET between AIENPs and labeled quenchers. The relative fluorescence intensities of dual-color AIENPs displayed good linear relationships with logarithmic AA and miR-21 concentrations. Moreover, there was a gradual decrease in dual-color AIENP fluorescence as the HepG2 cell concentration of AA (0-500 μM) and stimulation time (0-12 h) increased, making it possible to simultaneously image AA and AA-induced miR-21. The findings of this work are valuable for revealing the cytotoxic mechanism of AA.
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Affiliation(s)
- Jiajun Wu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xianfeng Lin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jin Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ziyu Lv
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Shijia Wu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
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18
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Yu X, Pu H, Sun DW. Developments in food neonicotinoids detection: novel recognition strategies, advanced chemical sensing techniques, and recent applications. Crit Rev Food Sci Nutr 2023:1-19. [PMID: 38149655 DOI: 10.1080/10408398.2023.2290698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Neonicotinoid insecticides (NEOs) are a new class of neurotoxic pesticides primarily used for pest control on fruits and vegetables, cereals, and other crops after organophosphorus pesticides (OPPs), carbamate pesticides (CBPs), and pyrethroid pesticides. However, chronic abuse and illegal use have led to the contamination of food and water sources as well as damage to ecological and environmental systems. Long-term exposure to NEOs may pose potential risks to animals (especially bees) and even human health. Consequently, it is necessary to develop effective, robust, and rapid methods for NEOs detection. Specific recognition-based chemical sensing has been regarded as one of the most promising detection tools for NEOs due to their excellent selectivity, sensitivity, and robust interference resistance. In this review, we introduce the novel recognition strategies-enabled chemical sensing in food neonicotinoids detection in the past years (2017-2023). The properties and advantages of molecular imprinting recognition (MIR), host-guest recognition (HGR), electron-catalyzed recognition (ECR), immune recognition (IR), aptamer recognition (AR), and enzyme inhibition recognition (EIR) in the development of NEOs sensing platforms are discussed in detail. Recent applications of chemical sensing platforms in various food products, including fruits and vegetables, cereals, teas, honey, aquatic products, and others are highlighted. In addition, the future trends of applying chemical sensing with specific recognition strategies for NEOs analysis are discussed.
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Affiliation(s)
- Xinru Yu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
- Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Hongbin Pu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
- Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
- Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
- Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
- Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Belfield, Dublin 4, Ireland
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19
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Wang W, Geng L, Zhang Y, Shen W, Bi M, Gong T, Hu Z, Guo C, Wang T, Sun T. Development of antibody-aptamer sandwich-like immunosensor based on RCA and Nicked-PAM CRISPR/Cas12a system for the ultra-sensitive detection of a biomarker. Anal Chim Acta 2023; 1283:341849. [PMID: 37977804 DOI: 10.1016/j.aca.2023.341849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 11/19/2023]
Abstract
Biomarkers are the most sensitive reactants and early indicators of many kinds of diseases. The development of highly sensitive and simple techniques to quantify them is challenging. In this study, based on rolling cycle amplification (RCA) and the Nicked PAM/CRISPR-Cas12a system (RNPC) as a signal reporter, a sandwich-type method was developed using antibody@magnetic beads and aptamer for the high-sensitive detection of the C-reactive protein (CRP). The antibody-antigen (target)-aptamer sandwich-like reaction was coupled to RCA, which can produce hundreds of similar binding sites and are discriminated by CRISPR/Cas12a for signal amplification. The ultrasensitivity is achieved based on the dual-signal enhancing strategy, which involves the special recognition of aptamers, RCA, and trans-cleavage of CRISPR/Cas12a. By incorporating the CRISPR/Cas12a system with cleaved PAM, the nonspecific amplification of the RCA reaction alone was greatly reduced, and the dual signal output of RCA and Cas12a improved the detection sensitivity. Our assay can be performed only in two steps. The first step takes only 20 min of target capture, followed by a one-pot reaction, where the target concentration can be obtained by fluorescence values as long as there are 37 °C reaction conditions. Under optimal conditions, this system detected CRP with high sensitivity. The fabricated biosensor showed detection limits of 0.40 pg/mL in phosphate-buffered saline and 0.73 pg/mL in diluted human serum and a broad linear dynamic range of 1.28 pg/mL to 100 ng/mL within a total readout time of 90 min. The method could be used to perform multi-step signal amplification, which can help in the ultrasensitive detection of other proteins. Overall, the proposed biosensor might be used as an immunosensor biosensor platform.
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Affiliation(s)
- Wen Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China; School of Public Health and Management, Binzhou Medical College, Shandong, 264003, PR China
| | - Lu Geng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China
| | - Yiyang Zhang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China
| | - Weili Shen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China
| | - Meng Bi
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China
| | - Tingting Gong
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China
| | - Zhiyong Hu
- School of Public Health and Management, Binzhou Medical College, Shandong, 264003, PR China
| | - Changjiang Guo
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China; School of Public Health and Management, Binzhou Medical College, Shandong, 264003, PR China.
| | - Tianhui Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China.
| | - Tieqiang Sun
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China.
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20
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Xiao Y, Zhang T, Zhang H. Recent advances in the peptide-based biosensor designs. Colloids Surf B Biointerfaces 2023; 231:113559. [PMID: 37738870 DOI: 10.1016/j.colsurfb.2023.113559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/09/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023]
Abstract
Biosensors have rapidly emerged as a high-sensitivity and convenient detection method. Among various types of biosensors, optical and electrochemical are the most commonly used. Conventionally, antibodies have been employed to ensure specific interaction between the transmission material and analytes. However, there has been increasing recognition of peptides as a promising recognition element for biosensor development in recent years. The use of peptides as recognition elements provides high level of specificity, sensitivity, and stability for the detection process. The combination of peptide designs and optical or electrochemical detection methods has significantly improved biosensor efficacy. These advancements present opportunities for developing biosensors with diverse functions that can be used to lay a strong scientific foundation for the development of personalized medicine and various other fields. This paper reviews the recent advancements in the development and application of peptide-based optical and electrochemical biosensors, as well as their prospects as a sensor type.
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Affiliation(s)
- Yue Xiao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Ting Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Houjin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China.
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21
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Zhu L, Zhu L, Zhang X, Yang L, Liu G, Xiong X. Programmable electrochemical biosensing platform based on catalytic hairpin assembly and entropy-driven catalytic cascade amplification circuit. Anal Chim Acta 2023; 1278:341715. [PMID: 37709458 DOI: 10.1016/j.aca.2023.341715] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 09/16/2023]
Abstract
Herein, powerful DNA strand displacement reaction and sensitive electrochemical analysis method were ingeniously integrated to develop a programmable biosensing platform. Using DNA as the detection model, a cascade amplification system based on catalytic hairpin assembly and entropy-driven catalytic was constructed, and the reaction rate and signal amplification effect were significantly improved. The product of the cascade amplification circuit could undergo strand displacement reaction with the signal probe on the electrode surface to obtain sensitive electrochemical signal changes and realize highly sensitive detection of the target. In addition, without redesigning the DNA sequences in the cascade amplification circuit, the by-product strand typically wasted in traditional entropy-driven catalytic reactions can be fully utilized to construct a single-signal output biosensing system and even a dual-signal output ratiometric biosensing platform, improving the detection repeatability and reliability of the system, and expanding the application of DNA strand displacement reaction in electrochemical biosensing. Furthermore, benefiting from the design flexibility of the DNA molecules, the constructed biosensing platform realized the sensitive detection of aptamer substrate (kanamycin as an example) and certain metal ion (mercury as an example) by simply recoding the corresponding recognition sequence, demonstrating the good versatility of the biosensing platform.
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Affiliation(s)
- Liping Zhu
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Sichuan Normal University), Ministry of Education, College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, 610066, China.
| | - Li Zhu
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Sichuan Normal University), Ministry of Education, College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, 610066, China
| | - Xuemei Zhang
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Sichuan Normal University), Ministry of Education, College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, 610066, China
| | - Li Yang
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Sichuan Normal University), Ministry of Education, College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, 610066, China
| | - Guoyu Liu
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Sichuan Normal University), Ministry of Education, College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, 610066, China
| | - Xiaoli Xiong
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Sichuan Normal University), Ministry of Education, College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, 610066, China.
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22
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Li Y, Zhao Z, Liu Y, Wang N, Man S, Ma L, Wang S. CRISPR/Cas System: The Accelerator for the Development of Non-nucleic Acid Target Detection in Food Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13577-13594. [PMID: 37656446 DOI: 10.1021/acs.jafc.3c03619] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Non-nucleic acid targets have posed a serious challenge to food safety. The detection of non-nucleic acid targets can enable us to monitor food contamination in a timely manner. In recent years, the CRISPR/Cas system has been extensively explored in biosensing. However, there is a lack of a summary of CRISPR/Cas-powered detection tailored to non-nucleic acid targets involved in food safety. This review comprehensively summarizes the recent advances on the construction of CRISPR/Cas-powered detection and the promising applications in the field of food safety related non-nucleic acid targets. The current challenges and futuristic perspectives are also proposed accordingly. The rapidly evolving CRISPR/Cas system has provided a powerful propellant for non-nucleic acid target detection via integration with aptamer and/or DNAzyme. Compared with traditional analytical methods, CRISPR/Cas-powered detection is conceptually novel, essentially eliminates the dependence on large instruments, and also demonstrates the capability for rapid, accurate, sensitive, and on-site testing.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yajie Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Nan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
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23
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Wang Y, Liu Y, Wang LL, Zhang QL, Xu L. Integrating Ligands into Nucleic Acid Systems. Chembiochem 2023; 24:e202300292. [PMID: 37401635 DOI: 10.1002/cbic.202300292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/12/2023] [Accepted: 07/04/2023] [Indexed: 07/05/2023]
Abstract
Signal transduction from non-nucleic acid ligands (small molecules and proteins) to structural changes of nucleic acids plays a crucial role in both biomedical analysis and cellular regulations. However, how to bridge between these two types of molecules without compromising the expandable complexity and programmability of the nucleic acid nanomachines is a critical challenge. Compared with the previously most widely applied transduction strategies, we review the latest advances of a kinetically controlled approach for ligand-oligonucleotide transduction in this Concept article. This new design works through an intrinsic conformational alteration of the nucleic acid aptamer upon the ligand binding as a governing factor for nucleic acid strand displacement reactions. The functionalities and applications of this transduction system as a ligand converter on biosensing and DNA computation are described and discussed. Furthermore, we propose some potential scenarios for utilization of this ligand transduction design to regulate gene expression through synthetic RNA switches in the cellular contexts. Finally, future perspectives regarding this ligand-oligonucleotide transduction platform are also discussed.
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Affiliation(s)
- Yang Wang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging National-Regional Key Technology Engineering Laboratory for Medical Ultrasound School of Biomedical Engineering, School of Medicine, Shenzhen, 518060, China
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiu-Long Zhang
- School of Pharmacy and Medical Technology, Putian University, Putian, 351100, Fujian, China
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
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