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Xie X, Wei Q, Han J, Fang X, Yang W, Zhou X, Wang Y, Weng X. Steric hindrance of N6-methyl in m 6A and its application for specific loci detection. Chem Commun (Camb) 2024; 60:4479-4482. [PMID: 38564258 DOI: 10.1039/d4cc01041h] [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: 04/04/2024]
Abstract
We found that the N6 methyl group of N6-methyladenine is able to hinder the methylation of N6-methyladenine at the N1 position by DMS. Based on this, we have devised a novel method for detecting N6-methyladenine, which was successfully applied to identify specific m6A loci in 28S rRNA.
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Affiliation(s)
- Xiaoyi Xie
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei, China.
| | - Qi Wei
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei, China.
| | - Jingyu Han
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei, China.
| | - Xin Fang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei, China.
| | - Wei Yang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei, China.
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei, China.
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan 430071, Hubei, China.
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei, China.
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Luo L, Dong F, Li D, Li X, Li X, Fan Y, Qi C, Luo J, Li L, Shen B. Enhancing 3D DNA Walker-Induced CRISPR/Cas12a Technology for Highly Sensitive Detection of ExomicroRNA Associated with Osteoporosis. ACS Sens 2024; 9:1438-1446. [PMID: 38451610 DOI: 10.1021/acssensors.3c02533] [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: 03/08/2024]
Abstract
Exosomal microRNAs (exomiRNAs) have emerged as promising biomarkers for the early clinical diagnosis of osteoporosis. However, their limited abundance and short length in peripheral blood present significant challenges for the accurate detection of exomiRNAs. Herein, we have designed and implemented an efficacious fluorescence-based biosensor for the highly sensitive detection of exomiRNA associated with osteoporosis, leveraging the enhancing 3D DNA walker-induced CRISPR/Cas12a technology. The engineered DNA walker is capable of efficiently transforming target exomiRNA into amplifying DNA strands, thereby enhancing the sensitivity of the developed biosensor. Concurrently, the liberated DNA strands serve as activators to trigger Cas12a trans-cleavage activity, culminating in a significantly amplified fluorescent signal for the highly sensitive detection of exomiRNA-214. Under optimal conditions, the devised technology demonstrated the capacity to detect target exomiRNA-214 at concentrations as low as 20.42 fM, encompassing a wide linear range extending from 50.0 fM to 10.0 nM. Moreover, the fluorescence-based biosensor could accurately differentiate between healthy individuals and osteoporosis patients via the detection of exomiRNA-214, which was in agreement with RT-qPCR results. As such, this biosensing technology offers promise as a valuable tool for the early diagnosis of osteoporosis.
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Affiliation(s)
- Lijuan Luo
- Department of Laboratory Medicine, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, PR China
| | - Fang Dong
- Department of Gerontology, The First Branch of The First Affiliated Hospital of Chongqing Medical University, Chongqing 400000, PR China
| | - Dandan Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400072, PR China
| | - Xinmin Li
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, PR China
| | - Xinyu Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Yunpeng Fan
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, PR China
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Caihong Qi
- Department of Laboratory Medicine, Chongqing General Hospital, Chongqing 401147, PR China
| | - Jinyong Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Li Li
- Department of Laboratory Medicine, Chongqing General Hospital, Chongqing 401147, PR China
| | - Bo Shen
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, PR China
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Zhong K, Wu Y, Zhou J, Yang X, Yi C, Ge L, Li Z, He W, Cao J, Jiang G, Wang H, Li J. Isothermal Amplification-Based Detection of Single-Base RNA N6-Methyladenosine. Anal Chem 2023; 95:18821-18827. [PMID: 38049147 DOI: 10.1021/acs.analchem.3c03961] [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: 12/06/2023]
Abstract
N6-methyladenosine (m6A) has recently gained much attention due to its diverse biological functions. Currently, the commonly used detection methods for locus-specific m6A marks are complicated to operate, it is difficult to quantify the methylation level, and they have high false-positive levels. Here, we report a new method for locus-specific m6A detection based on the methylate-sensitive endonuclease activity of MazF and the simultaneous amplification and testing (SAT) method, termed "m6A-MazF-SAT". Mechanically, MazF fails to cleave the A (m6A) CA motif; therefore, the undigested template can be SAT-amplified using specific probes targeting the upstream and downstream of sites of interest. Fluorescent signals of SAT amplification can be detected by real-time PCR, and therefore, they achieve the detection of m6A existence. After the condition optimization, m6A-MazF-SAT can significantly, accurately, and rapidly detect the m6A-modified sites in mRNA, rRNA, and lncRNA at the fmol level, as well as 10% m6A at the fmol level. In addition, m6A-MazF-SAT can quantify the abundance of target m6A in biological samples and can be used for the inhibitor selection of m6A-related enzymes. Together, we offer a new approach to detect locus-specific m6A both qualitatively and quantitatively; it is easy to operate, results can be obtained rapidly, and it has low false-positive levels and high repeatability.
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Affiliation(s)
- Ke Zhong
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - You Wu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiangli Zhou
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xianyuan Yang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Yi
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Lichen Ge
- Department of Laboratory Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Zigang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518067, China
| | - Weiling He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Jie Cao
- Department of General Surgery, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou 510180, China
| | - Guanmin Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 2528000, Guangdong, China
| | - Hongsheng Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiexin Li
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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