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Drula R, Braicu C, Neagoe IB. Current advances in circular RNA detection and investigation methods: Are we running in circles? WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1850. [PMID: 38702943 DOI: 10.1002/wrna.1850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 05/06/2024]
Abstract
Circular RNAs (circRNAs), characterized by their closed-loop structure, have emerged as significant transcriptomic regulators, with roles spanning from microRNA sponging to modulation of gene expression and potential peptide coding. The discovery and functional analysis of circRNAs have been propelled by advancements in both experimental and bioinformatics tools, yet the field grapples with challenges related to their detection, isoform diversity, and accurate quantification. This review navigates through the evolution of circRNA research methodologies, from early detection techniques to current state-of-the-art approaches that offer comprehensive insights into circRNA biology. We examine the limitations of existing methods, particularly the difficulty in differentiating circRNA isoforms and distinguishing circRNAs from their linear counterparts. A critical evaluation of various bioinformatics tools and novel experimental strategies is presented, emphasizing the need for integrated approaches to enhance our understanding and interpretation of circRNA functions. Our insights underscore the dynamic and rapidly advancing nature of circRNA research, highlighting the ongoing development of analytical frameworks designed to address the complexity of circRNAs and facilitate the assessment of their clinical utility. As such, this comprehensive overview aims to catalyze further advancements in circRNA study, fostering a deeper understanding of their roles in cellular processes and potential implications in disease. This article is categorized under: RNA Methods > RNA Nanotechnology RNA Methods > RNA Analyses in Cells RNA Methods > RNA Analyses In Vitro and In Silico.
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Affiliation(s)
- Rareș Drula
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana-Berindan Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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2
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Li H, Zhang Z, Gan L, Fan D, Sun X, Qian Z, Liu X, Huang Y. Signal Amplification-Based Biosensors and Application in RNA Tumor Markers. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23094237. [PMID: 37177441 PMCID: PMC10180857 DOI: 10.3390/s23094237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
Tumor markers are important substances for assessing cancer development. In recent years, RNA tumor markers have attracted significant attention, and studies have shown that their abnormal expression of post-transcriptional regulatory genes is associated with tumor progression. Therefore, RNA tumor markers are considered as potential targets in clinical diagnosis and prognosis. Many studies show that biosensors have good application prospects in the field of medical diagnosis. The application of biosensors in RNA tumor markers is developing rapidly. These sensors have the advantages of high sensitivity, excellent selectivity, and convenience. However, the detection abundance of RNA tumor markers is low. In order to improve the detection sensitivity, researchers have developed a variety of signal amplification strategies to enhance the detection signal. In this review, after a brief introduction of the sensing principles and designs of different biosensing platforms, we will summarize the latest research progress of electrochemical, photoelectrochemical, and fluorescent biosensors based on signal amplification strategies for detecting RNA tumor markers. This review provides a high sensitivity and good selectivity sensing platform for early-stage cancer research. It provides a new idea for the development of accurate, sensitive, and convenient biological analysis in the future, which can be used for the early diagnosis and monitoring of cancer and contribute to the reduction in the mortality rate.
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Affiliation(s)
- Haiping Li
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
- School of Pharmacy, Guangxi Medical University, Nanning 530021, China
| | - Zhikun Zhang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Lu Gan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Dianfa Fan
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Xinjun Sun
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Zhangbo Qian
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Xiyu Liu
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
| | - Yong Huang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning 530021, China
- School of Pharmacy, Guangxi Medical University, Nanning 530021, China
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3
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Dong J, Zeng Z, Huang Y, Chen C, Cheng Z, Zhu Q. Challenges and opportunities for circRNA identification and delivery. Crit Rev Biochem Mol Biol 2023; 58:19-35. [PMID: 36916323 DOI: 10.1080/10409238.2023.2185764] [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: 03/16/2023]
Abstract
Circular RNAs (circRNAs) are evolutionarily conserved noncoding RNAs with tissue-specific expression patterns, and exert unique cellular functions that have the potential to become biomarkers in therapeutic applications. Therefore, accurate and sensitive detection of circRNA with facile platforms is essential for better understanding of circRNA biological processes and circRNA-related disease diagnosis and prognosis; and precise regulation of circRNA through efficient delivery of circRNA or siRNA is critical for therapeutic purposes. Here, we reviewed the current development of circRNA identification methodologies, including overviewing the purification steps, summarizing the sequencing methods of circRNA, as well as comparing the advantages and disadvantages of traditional and new detection methods. Then, we discussed the delivery and manipulation strategies for circRNAs in both research and clinic treatment. Finally, the challenges and opportunities of analyzing circRNAs were addressed.
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Affiliation(s)
- Jiani Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Zhuoer Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China.,Division of Biomedical Engineering, The James Watt School of Engineering, University of Glasgow, Glasgow, UK
| | - Ying Huang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Zeneng Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, China
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4
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Song P, Zhang P, Qin K, Su F, Gao K, Liu X, Li Z. CRISPR/Cas13a induced exponential amplification for highly sensitive and specific detection of circular RNA. Talanta 2022; 246:123521. [DOI: 10.1016/j.talanta.2022.123521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/24/2022] [Accepted: 04/30/2022] [Indexed: 10/18/2022]
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5
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Wei SH, Liu M, Hu J, Zhang CY. Target-Initiated Cascade Signal Amplification Lights up a G-Quadruplex for a Label-Free Detection of Circular Ribonucleic Acids. Anal Chem 2022; 94:9193-9200. [PMID: 35703015 DOI: 10.1021/acs.analchem.2c01901] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Circular ribonucleic acids (circRNAs) are a type of RNA that originates through back-splicing events from linear primary transcripts. CircRNAs display high structural resistance and tissue specificity. Accurate quantification of the circRNA expression level is of vital importance to disease diagnosis. Herein, we construct a label-free fluorescent biosensor for ultrasensitive analysis of circRNAs based on the integration of target-initiated cascade signal amplification strategy with a light-up G-quadruplex. This assay involves only one assistant probe that targets the circRNA-specific back-splice junction. When circRNA is present, it hybridizes with the assistant probe to initiate the duplex-specific nuclease (DSN)-catalyzed cyclic cleavage reaction, producing abundant triggers with 3'OH termini. Then, terminal deoxynucleotidyl transferase (TdT) catalyzes the addition of dGTP and dATP at the 3'-OH termini of the resultant triggers to obtain abundant long G-rich DNA sequences that can form efficient G-quadruplex products. The addition of Thioflavin T (ThT) can light up G-quadruplex, generating an enhanced fluorescence. This assay may be performed isothermally without the involvement of any nucleic acid templates, exogenous primers, and specific labeled probes. Importantly, this biosensor can discriminate target circRNA from one-base mismatched circRNA and exhibits good performance in human serum. Moreover, it can accurately detect circRNA in cancer cells at a single-cell level and even differentiate the circRNA levels in the tissues of healthy persons and nonsmall cell lung cancer (NSCLC) patients, with promising applications in circRNA-related cancer diagnosis and therapeutics.
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Affiliation(s)
- Shu-Hua Wei
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Juan Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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Zhang Y, Zhang X, Xu Y, Fang S, Ji Y, Lu L, Xu W, Qian H, Liang ZF. Circular RNA and Its Roles in the Occurrence, Development, Diagnosis of Cancer. Front Oncol 2022; 12:845703. [PMID: 35463362 PMCID: PMC9021756 DOI: 10.3389/fonc.2022.845703] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/14/2022] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) are non-coding single-stranded covalently closed circular RNA, mainly produced by reverse splicing of exons of precursor mRNAs (pre-mRNAs). The characteristics of high abundance, strong specificity, and good stability of circRNAs have been discovered. A large number of studies have reported its various functions and mechanisms in biological events, such as the occurrence and development of cancer. In this review, we focus on the classification, characterization, biogenesis, functions of circRNAs, and the latest advances in cancer research. The development of circRNAs as biomarkers in cancer diagnosis and treatment also provides new ideas for studying circRNAs research.
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Affiliation(s)
- Yue Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xinyi Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yumeng Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shikun Fang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ying Ji
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ling Lu
- Child Healthcare Department, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wenrong Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Hui Qian
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zhao Feng Liang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
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Liu Y, Li R, Liang F, Deng C, Seidi F, Xiao H. Fluorescent paper-based analytical devices for ultra-sensitive dual-type RNA detections and accurate gastric cancer screening. Biosens Bioelectron 2022; 197:113781. [PMID: 34781178 DOI: 10.1016/j.bios.2021.113781] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/29/2021] [Accepted: 11/08/2021] [Indexed: 12/18/2022]
Abstract
Demand on the quick screening of gastric cancer (GC) has significantly stimulated the development of biomarker sensing techniques. Herein, we report the novel fluorescent paper-based analytical devices (PADs) for detections of GC-related microRNA-21 (miRNA-21) and circular RNA from Hippocampus Abundant Transcript 1 gene (circRNA-HIAT1) with prominent reliability and sensitivity. The PADs, constructed by in-situ synthesis of blue-emissive carbon dots (CDs) and conjugations of probe DNAs, exhibit the superior uniformity and stability. In the presence of targets, rolling circle amplifications (RCA) are triggered to generate long DNA strands for the assemblies of green-/red-emissive labels. Consequently, remarkable blue-to-green and blue-to-red emission color transitions of the PADs are achieved, implementing the color-analysis of miRNA-21 and circRNA-HIAT1, respectively. Benefited from the efficient RCA, coupled with the drastic ratiometric fluorescent changes, the limit of detections (LODs) of PADs are found to be several fM with the upper limit of the linear detection range at 1 nM. More importantly, the fluorescent PADs possess excellent specificity, as well as anti-interference capability in biological settings, enabling their applications in accurate GC screening with plasma samples. Overall, the proposed fluorescent PADs are featured with robust sensing platform, facile signal readout, and exceptional dual-type RNA sensing performance, holding high potential in point-of-care testing (POCT).
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Affiliation(s)
- Yuqian Liu
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China.
| | - Ruyi Li
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Fangyuan Liang
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Chao Deng
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Farzad Seidi
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, New Brunswick, E3B5A3, Canada.
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Mi Z, Zhongqiang C, Caiyun J, Yanan L, Jianhua W, Liang L. Circular RNA detection methods: A minireview. Talanta 2022; 238:123066. [PMID: 34808570 DOI: 10.1016/j.talanta.2021.123066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/21/2022]
Abstract
Circular RNA (circRNA), a novel type of covalently closed RNA, is implicated in several developmental and metabolic disease processes. CircRNAs exhibit tissue-specific expression, and are stable, abundant, and highly conserved, making them ideal biomarkers for diagnosis and prognosis. Accurate profiling of circRNA, however, is a prerequisite for their clinical application. Traditional methods such as northern blotting, RT-qPCR, and microarray analysis provide useful but limited information. To address these issues, a number of novel assays have recently emerged, such as droplet digital PCR (ddPCR), isothermal exponential amplification, and rolling cycle amplification, which increase the sensitivity and specificity of circRNA detection. Herein, we summarize the advantages and limitations of the new detection methods and discuss the challenges as well as future directions.
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Affiliation(s)
- Zhang Mi
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Chen Zhongqiang
- School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Jiang Caiyun
- Department of Pharmacy, The Third Affiliate Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Liu Yanan
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Wu Jianhua
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Liu Liang
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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9
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Liu X, Zhang P, Gao K, Wang X, Li Z. Multiple stem-loop primers induced cascaded loop-mediated isothermal amplification for direct recognition and specific detection of circular RNAs. Analyst 2022; 147:2124-2129. [DOI: 10.1039/d2an00261b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Through specific recognition of circRNA's unique junction sequence, a multiple stem-loop primers induced cascaded loop-mediated isothermal amplification method is designed for sensitive and specific quantification of sequence-specific circRNAs.
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Affiliation(s)
- Xin Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Pengbo Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Kejian Gao
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Xiaoyu Wang
- School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Zhengping Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
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Tao M, Zheng M, Xu Y, Ma S, Zhang W, Ju S. CircRNAs and their regulatory roles in cancers. Mol Med 2021; 27:94. [PMID: 34445958 PMCID: PMC8393742 DOI: 10.1186/s10020-021-00359-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/18/2021] [Indexed: 01/17/2023] Open
Abstract
Circular RNAs (circRNAs), a novel type of non-coding RNAs (ncRNAs), have a covalently closed circular structure resulting from pre-mRNA back splicing via spliceosome and ribozymes. They can be classified differently in accordance with different criteria. As circRNAs are abundant, conserved, and stable, they can be used as diagnostic markers in various diseases and targets to develop new therapies. There are various functions of circRNAs, including sponge for miR/proteins, role of scaffolds, templates for translation, and regulators of mRNA translation and stability. Without m7G cap and poly-A tail, circRNAs can still be degraded in several ways, including RNase L, Ago-dependent, and Ago-independent degradation. Increasing evidence indicates that circRNAs can be modified by N-6 methylation (m6A) in many aspects such as biogenesis, nuclear export, translation, and degradation. In addition, they have been proved to play a regulatory role in the progression of various cancers. Recently, methods of detecting circRNAs with high sensitivity and specificity have also been reported. This review presents a detailed overview of circRNAs regarding biogenesis, biomarker, functions, degradation, and dynamic modification as well as their regulatory roles in various cancers. It’s particularly summarized in detail in the biogenesis of circRNAs, regulation of circRNAs by m6A modification and mechanisms by which circRNAs affect tumor progression respectively. Moreover, existing circRNA detection methods and their characteristics are also mentioned.
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Affiliation(s)
- Mei Tao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.,Medical School of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Ming Zheng
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.,Medical School of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Yanhua Xu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.,Medical School of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Shuo Ma
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.,Medical School of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Weiwei Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China. .,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No.20, Nantong, 226001, Jiangsu, China.
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Dong J, Zeng Z, Sun R, Zhang X, Cheng Z, Chen C, Zhu Q. Specific and sensitive detection of CircRNA based on netlike hybridization chain reaction. Biosens Bioelectron 2021; 192:113508. [PMID: 34284304 DOI: 10.1016/j.bios.2021.113508] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/30/2021] [Accepted: 07/13/2021] [Indexed: 01/08/2023]
Abstract
Circular RNA (circRNA), as a new class of biomarker, plays an important role in the occurrence and development of cancer. However, the limitations of detection methods in recent years have severely restricted the related research of circRNA. Here, we have developed an effective circRNA detection method based on the thermostatic netlike hybridization chain reaction (HCR). It combines reverse transcription-rolling circle amplification (RT-RCA) with well-designed netlike HCR to achieve dual selection and dual signal amplification, which can eliminate the interference of linear isomers. This two-dimensional netlike HCR is composed of an ingeniously designed trigger chain and two hairpin fuel probes, which can generate a stable network structure with RT-RCA products containing multiple sets of repeats at a constant temperature, thereby producing enhanced fluorescent signals. Systematic studies reveal that the optimized netlike HCR system has higher detection efficiency for DNA strands containing multiple sets of repetitive sequences, can detect circRNA as low as 0.1 pM, and has excellent selectivity. By using human tumor cell lines and tissues, it has been verified that the netlike HCR-based method can accurately detect specific circRNA in real biological samples without RNase R enrichment, which provides a simple and useful platform for detecting low-abundance circRNA. Furthermore, the proposed strategy is also a potential method for detecting some genes containing repetitive sequences, such as telomere DNA, centromere DNA and ribosomal DNA (rDNA).
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Affiliation(s)
- Jiani Dong
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Zhuoer Zeng
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Ruowei Sun
- Hunan Zaochen Nanorobot Co., Ltd, Liuyang, 410300, Hunan, China.
| | - Xun Zhang
- Hunan Zaochen Nanorobot Co., Ltd, Liuyang, 410300, Hunan, China.
| | - Zeneng Cheng
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
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12
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Sun Y, Han B, Sun F. Ultra-specific genotyping of single nucleotide variants by ligase-based loop-mediated isothermal amplification coupled with a modified ligation probe. RSC Adv 2021; 11:17058-17063. [PMID: 35479710 PMCID: PMC9032167 DOI: 10.1039/d1ra00851j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/25/2021] [Indexed: 12/18/2022] Open
Abstract
Specific and accurate detection of single nucleotide variants (SNVs) plays significant roles in pathogenic gene research and clinical applications. However, the sensitive but ultra-specific detection of rare variants in biological samples still remains challenging. Herein, we report a novel, robust and practical SNV assay by integrating the outstanding features of high selectivity of an artificial mismatched probe, and the powerful loop-mediated isothermal amplification. In this strategy, we rationally introduce artificial mismatched bases into the 3′-terminal regions of the probe located in the ligation region to reduce the risk of nonspecific ligation, which can dramatically improve the specificity for the SNV assay. The proposed method can discern as little as 0.01% mutant DNA in the high background of wild-type DNA with high sensitivity (10 aM). In virtue of its outstanding performance, the artificial mismatched probe may also be employed and expanded in various DNA and RNA genetic analyses with ligase-assisted approaches, showing great potential in biomedical research, clinical diagnostics, and bioanalysis. An artificial mismatched base introduced in a ligation probe can effectively reduce nonspecific ligation and improve the specificity for SNV assay.![]()
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Affiliation(s)
- Yuanyuan Sun
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University Zhengzhou 450052 Henan Province P. R. China .,School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710062 Shaanxi Province P. R. China
| | - Bingjie Han
- Department of Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University Zhengzhou 450052 Henan Province P. R. China
| | - Fangfang Sun
- Department of Gynecology, The First Affiliated Hospital of Zhengzhou University Zhengzhou 450052 Henan Province P. R. China
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13
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Amplified electrochemical detection of circular RNA in breast cancer patients using ferrocene-capped gold nanoparticle/streptavidin conjugates. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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