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Zhang L, Luo S, Fan R, Li R, Li W, Chen S, Lan F, Zhu Y, Ji T, Zhang Y, Li L. Localized Cas12a-based cascade amplification for sensitive and robust detection of APE1. Talanta 2024; 280:126773. [PMID: 39197313 DOI: 10.1016/j.talanta.2024.126773] [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: 06/24/2024] [Revised: 07/30/2024] [Accepted: 08/24/2024] [Indexed: 09/01/2024]
Abstract
APE1, an essential enzyme for DNA repair, is overexpressed in various cancers and has been identified as a potential biomarker for cancer diagnosis. However, detecting APE1 at low expression levels in the early stage of cancer presents a significant obstacle. Here, we introduced a novel localized Cas12a-based cascade amplification (LCas12a-CA) method. This method confined both the terminal deoxynucleotidyl transferase and the crRNA/Cas12a complex onto the surfaces of gold nanoparticles (AuNPs). This confinement not only boosts the stability of the multiple enzymes but also induces a substrate channeling effect. As a result, it significantly accelerates the reaction rate and enhances the sensitivity of APE1 detection. Upon the addition of APE1, the AP sites within the APE1 primer can be recognized and cleaved by APE1, exposing the 3'-OH ends. In the presence of LCas12a-CA, polyA sequences are generated at 3'-OH ends with the help of TdT and dATP. The sequences directly enter the Cas12a system, activating the trans-cleavage activity of Cas12a, thereby cutting the reporters on the surface of AuNPs and releasing fluorescence. Our platform demonstrates a detection limit (LOD) as low as 2.51 × 10-6 U/mL, which is more than 60 times lower than that of free Cas12a-CA. Furthermore, the LCas12a-CA exhibits enhanced resistance ability in extreme environments and has been proven effective for the detection of APE1 in clinical samples. Overall, this work offers a promising platform for robust biosensing in cancer diagnosis and prognosis.
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Affiliation(s)
- Lifeng Zhang
- School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China; Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Shihua Luo
- Center for Clinical Laboratory Diagnosis and Research, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China; Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi of Guangxi Higher Education Institutions, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi, China
| | - Rui Fan
- School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China; Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Ruixi Li
- School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China
| | - Wenbin Li
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Siting Chen
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Fei Lan
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yitong Zhu
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Tingting Ji
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Ye Zhang
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Ling Li
- School of Medical Technology, Guangdong Medical University, Dongguan, 523808, China; School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
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Liao Y, Yin X, Liu W, Du Z, Du J. Chaperone Copolymer-Assisted Catalytic Hairpin Assembly for Highly Sensitive Detection of Adenosine. Polymers (Basel) 2024; 16:2179. [PMID: 39125205 PMCID: PMC11314456 DOI: 10.3390/polym16152179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Adenosine is an endogenous molecule that plays a vital role in biological processes. Research indicates that abnormal adenosine levels are associated with a range of diseases. The development of sensors capable of detecting adenosine is pivotal for early diagnosis of disease. For example, elevated adenosine levels are closely associated with the onset and progression of cancer. In this study, we designed a novel DNA biosensor utilizing chaperone copolymer-assisted catalytic hairpin assembly for highly sensitive detection of adenosine. The functional probe comprises streptavidin magnetic beads, an aptamer, and a catalytic chain. In the presence of adenosine, it selectively binds to the aptamer, displacing the catalytic chain into the solution. The cyclic portion of H1 hybridizes with the catalytic strand, while H2 hybridizes with the exposed H1 fragment to form an H1/H2 complex containing a G-quadruplex. Thioflavin T binds specifically to the G-quadruplex, generating a fluorescent signal. As a nucleic acid chaperone, PLL-g-Dex expedites the strand exchange reaction, enhancing the efficiency of catalytic hairpin assembly, thus amplifying the signal and reducing detection time. The optimal detection conditions were determined to be a temperature of 25 °C and a reaction time of 10 min. Demonstrating remarkable sensitivity and selectivity, the sensor achieved a lowest limit of detection of 9.82 nM. Furthermore, it exhibited resilience to interference in complex environments such as serum, presenting an effective approach for rapid and sensitive adenosine detection.
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Affiliation(s)
| | | | | | | | - Jie Du
- School of Materials Science and Engineering, Hainan University, Haikou 570228, China; (Y.L.); (X.Y.); (W.L.); (Z.D.)
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Lai F, Xia K, Lin W, Jian F, Yang H. CRISPR/Cas12a-Based APE1 Enzyme Cleavage Assay for Drug Resistance Analysis of Staphylococcus aureus-Related Pneumonia. ACS OMEGA 2024; 9:31166-31172. [PMID: 39035885 PMCID: PMC11256342 DOI: 10.1021/acsomega.4c04790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024]
Abstract
Drug resistance analysis of Staphylococcus aureus is responsible for generating significant mortality and morbidity in numerous diseases. However, sensitive and accurate analysis of drug resistance of S. aureus remains a huge challenge. In this study, we present the development of a fluorescence biosensor based on the CRISPR/Cas12a system that enables label-free and ultrasensitive detection of the mecA gene in methicillin-resistant S. aureus (MRSA). The biosensor identified the mecA gene in MRSA using Cas12a/crRNA. This recognition triggered the trans-cleavage activity of Cas12a and the release of RNA1, which subsequently induced Apurinic/apyrimidinic endonuclease 1 (APE1) enzyme-assisted target recycling and G-quadruplexes/Thioflavin T-based signal reaction. Based on this, the biosensor effectively detects the mecA gene with a low limit of detection of 212 aM and a high degree of selectivity, even toward single base mutations. Compared with the traditional CRISPR-Cas12a system-based methods, in which the signal amplification process is prone to generate nucleic acid sequence mismatch, which causes errors, the biosensor used APE1 to improve nucleic acid sequence recognition specificity to ensure that the RNA1 sequence released after Cas12a/crRNA cleavage can specifically guide the signal cycle. In addition to enhancing the CRISPR toolkit, the developed biosensor offers a novel method for the precise and sensitive identification of drug-resistant microbes that cause infections.
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Affiliation(s)
| | | | - Wei Lin
- Pediatric department, Longyan
First Affiliated Hospital of Fujian Medical University, Longyan City, Fujian Province 364000, China
| | - Fanghua Jian
- Pediatric department, Longyan
First Affiliated Hospital of Fujian Medical University, Longyan City, Fujian Province 364000, China
| | - Hua Yang
- Pediatric department, Longyan
First Affiliated Hospital of Fujian Medical University, Longyan City, Fujian Province 364000, China
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Li C, Hu Y, Shi T, Dong K, Wu T. Label-free colorimetric detection platform based on catalytic hairpin self-assembly and G-quadruplex/hemin DNAzyme for comprehensive biomarker profiling. Talanta 2024; 272:125835. [PMID: 38422905 DOI: 10.1016/j.talanta.2024.125835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 02/24/2024] [Indexed: 03/02/2024]
Abstract
The expression level of human apurinic/apyrimidinic endonuclease 1 (APE1) is closely associated with the onset of various diseases, establishing it as a crucial clinical biomarker and a target in anti-cancer efforts. This study accomplished colorimetric and visual detection of APE1 by harnessing its endonuclease activity through catalytic hairpin self-assembly (CHA) and G-quadruplex/hemin DNAzyme. Optimization of the freedom degrees of the G-rich sequence significantly improved the detection performance of the strategy by influencing DNAzyme formation. Additionally, we replaced the signal reporting system with a molecular beacon to develop a fluorescence detection strategy, which served as an extension of the signal amplification system for validation and signal readout. The fluorescent probe method achieved a detection limit of 3.37 × 10-4 U/mL, while the colorimetric method yielded a detection limit of 6.5 × 10-3 U/mL, with a linear range spanning from 0.01 to 0.25 U/mL. Subsequently, the colorimetric approach effectively assessed APE1 activity in biological samples and facilitated the screening of APE1 activity inhibitors. Furthermore, this CHA/G-quadruplex/hemin DNAzyme strategy was adapted for the colorimetric detection of adenosine, showcasing its broad applicability across various biomarkers. The developed colorimetric analytical strategy represents a pivotal biosensing platform for diagnosing and treating diseases.
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Affiliation(s)
- Changjiang Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuqiang Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Tianzi Shi
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Huang R, Li M, Qu Z, Liu Y, Lu X, Li R, Zou L. Label-free fluorescence detection of mercury ions based on thymine-mercury-thymine structure and CRISPR-Cas12a. Food Res Int 2024; 180:114058. [PMID: 38395579 DOI: 10.1016/j.foodres.2024.114058] [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: 10/27/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
In this work, we developed a novel label-free fluorescent sensor for the highly sensitive detection of mercury ions (Hg2+) based on the coordination chemistry of thymine-Hg2+-thymine (T-Hg2+-T) structures and the properties of CRISPR-Cas12a systems. Most notably, two T-rich sequences (a blocker and an activator) were designed to form stable double-stranded structures in the presence of Hg2+ via the T-Hg2+-T base pairing. The formation of T-T mismatched double-stranded DNA between the blocker and the activator prevented the cleavage of G-rich sequences by Cas12a, allowing them to fold into G-quadruplex-thioflavin T complexes, resulting in significantly enhanced fluorescence. Under the optimized conditions, the developed sensor showed an excellent response for Hg2+ detection in the linear range of 0.05 to 200 nM with a detection limit of 23 pM. Moreover, this fluorescent sensor exhibited excellent selectivity and was successfully used for the detection of Hg2+ in real samples of Zhujiang river water and tangerine peel, demonstrating its potential in environmental monitoring and food safety applications.
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Affiliation(s)
- Ruoying Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Mengyan Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Zenglin Qu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Yang Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Xiaoxing Lu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Ruimin Li
- School of Chemical Engineering and Technology, Guangdong Industry Polytechnic, Guangzhou 510300, PR China
| | - Li Zou
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510699, PR China.
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Zhou S, Li X, Shu X, Cai X, Wu H, Ding S, Yan Y. An all-in-one enzymatic DNA network based on catalytic hairpin assembly for label-free and highly sensitive detection of APE1. Anal Chim Acta 2023; 1278:341678. [PMID: 37709426 DOI: 10.1016/j.aca.2023.341678] [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: 05/25/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 09/16/2023]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1), identified as a prospective cancer biomarker, plays a vital role in the occurrence and progression of cancer cell lines and impacts on genome stability. However, conventional approaches typically rely on the interactions between the antigen and antibody, limiting their utility for qualitative assessments of APE1 expression. Herein, an all-in-one enzymatic DNA network (EDN) assay with catalytic hairpin assembly for label-free and ultrasensitive detection of APE1 has been developed. In this work, the blocking strand can inhibit the initiator by obstructing the complementary region, preventing the hairpin from hybridizing in the absence of APE1 targets. While the presence of targets can activate the unlocking of the initiator, which can trigger the catalytic hairpin reaction, and increase the fluorescent signal. Under optimal conditions, the developed sensing method can detect the target APE1 down to 4.78 × 10-6 U mL-1 with a wide linear range from 5 × 10-6 U mL-1 to 30 U mL-1. This strategy has also been successfully applied to the analysis of complicated biological samples compared to ELISA, demonstrating its potential applications in biochemical and molecular biology research as well as clinical diagnostics. Overall, benefiting from the high amplification efficiency, this strategy has successfully and simply detected low-abundance APE1 without additional enzyme isolation steps, presenting great potential for clinical detection applications.
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Affiliation(s)
- Shaoying Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China; Department of Clinical Laboratory, The People's Hospital of Yubei District of Chongqing City, Chongqing, 400120, China.
| | - Xingrong Li
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xiaojia Shu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaoying Cai
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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Li C, Wang Y, Li PF, Fu Q. Construction of rolling circle amplification products-based pure nucleic acid nanostructures for biomedical applications. Acta Biomater 2023; 160:1-13. [PMID: 36764595 DOI: 10.1016/j.actbio.2023.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
Nucleic acid nanomaterials with good biocompatibility, biodegradability, and programmability have important applications in biomedical field. Nucleic acid nanomaterials are usually combined with some inorganic nanomaterials to improve their biological stability. However, undefined toxic side effects of composite nanocarriers hamper their application in vivo. As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. RCA products with different functional parts can be customized by changing the sequence of the circular template, thereby generating complex multifunctional DNA nanostructures, such as DNA nanowire, nanoflower, origami, nanotube, nanoribbon, etc. More importantly, RCA products as nonnicked building blocks can enhance the biostability of DNA nanostructures, especially in vivo. These RCA products-based nucleic acid nanostructures can be used as scaffolds or nanocarriers to interact or load with metal nanoparticles, proteins, lipids, cationic polymers, therapeutic nucleic acids or drugs, etc. This paper reviews the assembly strategies of RCA based DNA nanostructures with different shape and their applications in biosensing, bioimaging and biomedicine. Finally, the development prospects of the nucleic acid nanomaterials in clinical diagnosis and treatment of diseases are described. STATEMENT OF SIGNIFICANCE: As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. This paper reviews the construction of various shapes of pure nucleic acid nanomaterials based on RCA products and their applications in biosensing, bioimaging and biomedicine. This will promote the development of biocompatible DNA nanovehicles and their further application in living systems, including bioimaging, molecular detection, disease diagnosis and drug delivery, finally producing a significant impact in the field of nanotechnology and nanomedicine.
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Affiliation(s)
- Congcong Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Qinrui Fu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
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Liu B, Wang F, Chao J. Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing. SENSORS (BASEL, SWITZERLAND) 2023; 23:3313. [PMID: 36992023 PMCID: PMC10051322 DOI: 10.3390/s23063313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.
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Affiliation(s)
- Bing Liu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Fan Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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Hu Z, Ye W, Zhang Z, Xie T, Yuan W, Wu T. Sensitive detection of abasic sites in double-stranded DNA based on the selective reaction of enzymes. Anal Chim Acta 2022; 1223:340220. [DOI: 10.1016/j.aca.2022.340220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/28/2022]
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