1
|
Zhang Q, Zhang X, Xie P, Zhang W. Liquid biopsy: An arsenal for tumour screening and early diagnosis. Cancer Treat Rev 2024; 129:102774. [PMID: 38851148 DOI: 10.1016/j.ctrv.2024.102774] [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: 02/20/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Cancer has become the second leading cause of death in the world, and more than 50% of cancer patients are diagnosed at an advanced stage. Early diagnosis of tumours is the key to improving patient quality of life and survival time and reducing the socioeconomic burden. However, there is still a lack of reliable early diagnosis methods in clinical practice. In recent years, liquid biopsy technology has developed rapidly. It has the advantages of noninvasiveness, easy access to sample sources, and reproducibility. It has become the main focus of research on the early diagnosis methods of tumours. This review summarises the research progress of existing liquid biopsy markers, such as circulating tumour DNA, circulating viral DNA, DNA methylation, circulating tumour cells, circulating RNA, exosomes, and tumour education platelets in early diagnosis of tumours, and analyses the current advantages and limitations of various markers, providing a direction for the application and transformation of liquid biopsy research in early diagnosis of clinical tumours.
Collapse
Affiliation(s)
- Qi Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xiaoli Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Peipei Xie
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wen Zhang
- Department of Immunology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| |
Collapse
|
2
|
Wu D, Du H, Yan X, Jie G. Carbon quantum dot-based fluorescence quenching coupled with enzyme-assisted multiple cycle amplification for biosensing of miRNA. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
3
|
Du JF, Chen JS, Liu XP, Mao CJ, Jin BK. Coupled electrochemiluminescent and resonance energy transfer determination of microRNA-141 using functionalized Mxene composite. Mikrochim Acta 2022; 189:264. [PMID: 35776207 DOI: 10.1007/s00604-022-05359-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 10/17/2022]
Abstract
The electrochemiluminescence and resonance energy transfer (ECL-RET) method was adopted to detect miRNAs, in which the two-dimensional Ti3C2 Mxenes with high surface area modified with CdS:W nanocrystals (CdS:W NCs) were used as ECL signal emitter. Mxenes with a specific surface area of 5.2755 m2/g carried more emitters and promote ECL intensity. As an energy acceptor, BiOCl nanosheets (BiOCl NSs) have a wide UV-Vis absorption peak in the range 250 nm-700 nm, including the emission band of CdS:W NCs with 520 nm emission wavelength. Hence, BiOCl NSs are covalently bound to hairpin DNA 2 by amide bond to quench the ECL signal of CdS:W NCs. In the presence of miRNA-141, the hairpin DNA 1 modified on the GCE was unfold and then paired with hairpin DNA 2 to release miRNA-141 and quench the signal of the ECL biosensor. Then, the concentration signal of miRNA-141 was amplified by catalytic hairpin assembly. The novel specific biosensor demonstrated a satisfactory linear relationship with miRNA-141 in the range 0.6 pM to 4000 pM; the detection limit was as low as 0.26 pM (3 s/m) under the potential of 0 ~ -1.3 V and showed outstanding RSD of 1.19%. The findings of the present work with high accuracy and sensitivity will be of positive significance for the clinical diagnosis of miRNA in the future work. The construction process of the biosensor and electrochemiluminescence mechanism.
Collapse
Affiliation(s)
- Jin-Feng Du
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), School of Chemistry and Chemical Engineering, Anhui University, Hefei, 230601, Anhui, China
| | - Jing-Shuai Chen
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), School of Chemistry and Chemical Engineering, Anhui University, Hefei, 230601, Anhui, China
| | - Xing-Pei Liu
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), School of Chemistry and Chemical Engineering, Anhui University, Hefei, 230601, Anhui, China.
| | - Chang-Jie Mao
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), School of Chemistry and Chemical Engineering, Anhui University, Hefei, 230601, Anhui, China.
| | - Bao-Kang Jin
- Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Ministry of Education), School of Chemistry and Chemical Engineering, Anhui University, Hefei, 230601, Anhui, China
| |
Collapse
|
4
|
Gao Y, Zhang S, Wu C, Li Q, Shen Z, Lu Y, Wu ZS. Self-Protected DNAzyme Walker with a Circular Bulging DNA Shield for Amplified Imaging of miRNAs in Living Cells and Mice. ACS NANO 2021; 15:19211-19224. [PMID: 34854292 DOI: 10.1021/acsnano.1c04260] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Abnormal expression of miRNAs is often detected in various human cancers. DNAzyme machines combined with gold nanoparticles (AuNPs) hold promise for detecting specific miRNAs in living cells but show short circulation time due to the fragility of catalytic core. Using miRNA-21 as the model target, by introducing a circular bulging DNA shield into the middle of the catalytic core, we report herein a self-protected DNAzyme (E) walker capable of fully stepping on the substrate (S)-modified AuNP for imaging intracellular miRNAs. The DNAzyme walker exhibits 5-fold enhanced serum resistance and more than 8-fold enhanced catalytic activity, contributing to the capability to image miRNAs much higher than commercial transfection reagent and well-known FISH technique. Diseased cells can accurately be distinguished from healthy cells. Due to its universality, DNAzyme walker can be extended for imaging other miRNAs only by changing target binding domain, indicating a promising tool for cancer diagnosis and prognosis.
Collapse
Affiliation(s)
- Yansha Gao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Songbai Zhang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- College of Chemistry and Materials Engineering, Hunan University of Arts and Science, Changde 415000, China
| | - Chengwei Wu
- 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, 325035, China
| | - Qian Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, 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, 325035, China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| |
Collapse
|
5
|
Zhang M, Wang H, Wang H, Wang F, Li Z. CRISPR/Cas12a-Assisted Ligation-Initiated Loop-Mediated Isothermal Amplification (CAL-LAMP) for Highly Specific Detection of microRNAs. Anal Chem 2021; 93:7942-7948. [PMID: 34038095 DOI: 10.1021/acs.analchem.1c00686] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) has been increasingly applied in nucleic acid detection for clinical diagnosis and monitoring pathogenic microorganisms due to its isothermal nature and high sensitivity. However, the false-positive signal resulting from the non-specific amplification and the complexity of primer design are still technically challenging for wide applications. In this paper, we developed the CRISPR/Cas12a-assisted sequence-specific detection of LAMP products to eliminate the effect of non-specific amplification from primer dimers and spurious amplicons. Moreover, by designing a pair of target-specific stem-loop DNA probes, we greatly simplified the primer design for LAMP. The DNA probes could be ligated to form a double-stem-loop DNA template by the detected target, which initiated LAMP reaction and achieved one-nucleotide resolution due to the highly specific ligase reaction. Using microRNAs (miRNAs) as the model targets, the CRISPR/Cas12a-assisted ligation-initiated loop-mediated isothermal amplification (CAL-LAMP) can sensitively detect as low as 0.1 fM miRNAs with high specificity.
Collapse
Affiliation(s)
- Mai Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Fangfang Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| |
Collapse
|
6
|
Wang F, Wang H, Zhang P, Su F, Wang H, Li Z. Ultrasensitive multiplexed detection of miRNA targets of interest based on encoding probe extension in improved cDNA library. Anal Chim Acta 2021; 1152:338281. [PMID: 33648652 DOI: 10.1016/j.aca.2021.338281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/15/2023]
Abstract
MicroRNAs (miRNAs) are a class of regulatory small RNA molecules that play critical roles in a wide variety of biological processes. Abnormally expressed miRNAs have been increasingly utilized as biomarkers for cancer diagnosis. Generally, a specific cancer is associated with expression alterations of several species of miRNAs and different types of cancers are related to different miRNA species. Therefore, a universal method for multiplexed detection of miRNA targets of interest is now desirable for cancer diagnosis. In this paper, by adding an enzymatic digestion step to reduce the nonspecific adaptor dimers, we firstly improved the method to construct cDNA library of all miRNAs, which greatly increased the cDNA yield. By specifically designing DNA probes to hybridize with the cDNAs at key positions and doubly encoding DNA probes with different lengths and different fluorophores during single-base extension, each miRNA could produce a unique product, which could be separated and detected by capillary electrophoresis. Thus, miRNA targets of interest could be simultaneously detected with great specificity at single-base resolution. By using seventeen randomly selected miRNAs as the model, as low as 1.0 fM of each miRNA target could be simultaneously determined. Furthermore, we had achieved accurate analysis of multiple miRNAs in real biological RNA samples and found that several miRNAs expressed differently between cancer cells and normal cells, indicating that the proposed method had the ability to pick out aberrant expression miRNAs in real biological samples. Compared with high-throughput sequencing methods, the proposed method is simpler and specific, and very suitable for the detection of specific miRNAs associated with a disease, which shows great potential for cancer diagnosis.
Collapse
Affiliation(s)
- Fangfang Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Pengbo Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Fengxia Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China.
| |
Collapse
|
7
|
Zhang W, Hao W, Liu X, Sun X, Yan J, Wang Y. Visual detection of miRNAs using enzyme-free amplification reactions and ratiometric fluorescent probes. Talanta 2020; 219:121332. [DOI: 10.1016/j.talanta.2020.121332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 12/31/2022]
|
8
|
Bao J, Qiu X, Yang H, Lu W, Yang M, Gu W, Wu L, Huo D, Luo Y, Hou C. Disposable 3D GNAs/AuNPs DNA-Circuit Strip for miRNAs Dynamic Quantification. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001416. [PMID: 32865862 DOI: 10.1002/smll.202001416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Real-time quantitative monitoring of miRNAs plays an essential role in diagnosis and therapeutics. Herein, a DSN-coupled graphene nanoarray/gold nanoparticles (GNAs/AuNPs) carbon paper (CP) electrode for the dynamic, sensitive, and real-time analysis of miRNAs is reported. GNAs are vertically grown on the conductive CP by radio frequency plasma enhanced chemical vapor deposition, and AuNPs are electrodeposited on CP/GNAs to build a 3D ultrasensitive sensing interface with large specific surface area, good conductivity and biocompatibility. The dynamic quantitative monitoring of microRNA-21 (miR-21) is realized by cyclic voltammetry with a series of different concentrations within 16 min, and this 3D GNAs/AuNPs DNA-circuit strip shows good performance for the simultaneous detection of miR-21 and miR-155, and the detection limits are as low as 21.4 and 30.3 am, respectively. Moreover, comparable detection results are achieved for clinical samples between the proposed sensor and qRT-PCR, suggesting the reliability of the constructed sensor. This ultrasensitive sensing and disposable DNA-circuit strip with 3D structure can efficiently shorten the diffusion distance between reactive biomolecules and the sensing interface, enhance the hybridization of probes and improve the sensitivity of the biosensor, holding great promise for the rapid, quantitative and dynamic monitoring of multiple low concentrations of biomolecules in point-of-care clinical analysis.
Collapse
Affiliation(s)
- Jing Bao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, China
| | - Xiaopei Qiu
- Department of Clinical Laboratory, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Huisi Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, China
| | - Wenqiang Lu
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, China
| | - Wei Gu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, China
- Center of Smart Laboratory and Molecular Medicine, Medical School of Chongqing University, Chongqing, 400044, China
| | - Lixiang Wu
- Department of Clinical Laboratory Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, No. 181 Han Yu Road, Chongqing, 400030, China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, China
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, Medical School of Chongqing University, Chongqing, 400044, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Department of Nuclear Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, China
- Chongqing Key Laboratory of Bio-perception and Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, China
| |
Collapse
|
9
|
Sun HH, He F, Wang T, Yin BC, Ye BC. A Cas12a-mediated cascade amplification method for microRNA detection. Analyst 2020; 145:5547-5552. [PMID: 32609115 DOI: 10.1039/d0an00370k] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) play a vital role in various biological processes and act as important biomarkers for clinical cancer diagnosis, prognosis, and therapy. Here, we took advantage of Cas12a trans-cleavage activity to develop an enzyme-assisted cascade amplification method for isothermal miRNA detection. A target miRNA-initiated ligation reaction would allow for the production of transcription templates that triggered the transcriptional amplification of RNA strands. These RNA strands were cleaved by the 8-17E DNAzyme to generate crRNAs and recycled RNAs which have the same sequence as the target miRNA. The amplified abundant crRNAs bound to Cas12a and dsDNA activators to form the complex, which trans-cleaved the ssDNA reporters to generate a fluorescence signal for miRNA quantitative analysis. The proposed method exhibits a femtomolar limit of detection and a good specificity in distinguishing the homologous sequences of miRNAs. Its practical application ability was further tested in different cell lines.
Collapse
Affiliation(s)
- Huan-Huan Sun
- Laboratory of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | | | | | | | | |
Collapse
|
10
|
Wang H, Wang H, Sun Y, Liu X, Liu Y, Wang C, Zhang P, Li Z. A general strategy for highly sensitive analysis of genetic biomarkers at single-base resolution with ligase-based isothermally exponential amplification. Talanta 2020; 212:120754. [DOI: 10.1016/j.talanta.2020.120754] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 01/17/2023]
|
11
|
Mujica ML, Zhang Y, Bédioui F, Gutiérrez F, Rivas G. Label-free graphene oxide–based SPR genosensor for the quantification of microRNA21. Anal Bioanal Chem 2020; 412:3539-3546. [DOI: 10.1007/s00216-020-02593-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/13/2022]
|
12
|
Zhang M, Li X, Xiao D, Lu T, Qin B, Zheng Z, Zhang Y, Liu Y, Yan T, Han X. Identification of differentially expressed microRNAs and their target genes in the hippocampal tissues of Fmr1 knockout mice. Am J Transl Res 2020; 12:813-824. [PMID: 32269714 PMCID: PMC7137065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/02/2019] [Indexed: 06/11/2023]
Abstract
Fragile X syndrome (FXS) is one of the most common forms of inherited mental retardation; it is usually associated with the transcriptional silencing of the Fmr1 gene and loss of its encoded protein, the fragile X mental retardation protein (FMRP). FMRP is an RNA-binding protein and participates in regulating the development of dendritic spines and synaptic plasticity. To uncover the possible role of microRNAs (miRNAs) in FXS and their relationship with FMRP, we used microarray analysis to investigate the miRNA expression profiles in the hippocampal tissues of Fmr1 knockout (Fmr1-KO) mice and wild type (WT) mice. A total of 75 differentially expressed miRNAs were identified, of which 58 were significantly upregulated and no miRNAs were significantly downregulated in Fmr1-KO mice. Quantitative real-time PCR (qRT-PCR) analysis was applied to validate the expression of 7 upregulated miRNAs; results indicated that the levels of only miR-449a and miR-720 were significantly upregulated. We further used bioinformatics software and databases to predict the target genes of these two miRNAs. The genes were related to dendritic spine development and synaptic plasticity; the qRT-PCR and western blotting results showed that cyclin-dependent kinase 5 (CDK5) and synaptotagmin 1 (SYT1) were differentially expressed in the Fmr1-KO mice and WT mice. In conclusion, this study evidenced diverse changes in the expression of miRNAs, and validated the miRNAs and their targeted genes in Fmr1-KO mice. Although further studies are required to better understand the function of miRNAs in FXS, the present research highlights a potential role of miRNAs in the pathogenesis of FXS.
Collapse
Affiliation(s)
- Malan Zhang
- Department of Rehabilitation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Hexian Memorial Affiliated Hospital of Southern Medical UniversityGuangzhou, China
| | - Xin Li
- The First Affiliated Hospital of Jinan UniversityGuangzhou, China
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical UniversityGuangzhou, China
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of University of Science and Technology of ChinaHefei, China
| | - Du Xiao
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical UniversityGuangzhou, China
| | - Tao Lu
- Department of Neurology, The Fourth Affiliated Hospital of Guangxi Medical UniversityLiuzhou, China
| | - Bing Qin
- The First Affiliated Hospital of Jinan UniversityGuangzhou, China
| | - Zhigang Zheng
- Department of Intensive Care Unit, Pingxiang Hospital, Southern Medical UniversityPingxiang, China
| | - Yonggen Zhang
- Department of Intensive Care Unit, Pingxiang Hospital, Southern Medical UniversityPingxiang, China
| | - Yi Liu
- Department of Intensive Care Unit, Pingxiang Hospital, Southern Medical UniversityPingxiang, China
| | - Tiebin Yan
- Department of Rehabilitation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Engineering Technology Research Center for Rehabilitation and Elderly CareGuangzhou, China
| | - Xinjia Han
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical UniversityGuangzhou, China
| |
Collapse
|
13
|
Pan L, Zhang H, Zhao J, Ogungbe IV, Zhao S, Liu Y. A New One‐Pot Fluorescence Derivatization Strategy for Highly Sensitive MicroRNA Analysis. Chemistry 2020; 26:5639-5647. [DOI: 10.1002/chem.201905639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Li Pan
- Department of Chemistry and BiochemistryJackson State University 1400 Lynch Street Jackson Mississippi 39217 USA
| | - Huaisheng Zhang
- Department of Chemistry and BiochemistryJackson State University 1400 Lynch Street Jackson Mississippi 39217 USA
| | - Jingjin Zhao
- Department of Chemistry and BiochemistryJackson State University 1400 Lynch Street Jackson Mississippi 39217 USA
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal ResourcesGuangxi Normal University Guilin 541004 China
| | - Ifedayo Victor Ogungbe
- Department of Chemistry and BiochemistryJackson State University 1400 Lynch Street Jackson Mississippi 39217 USA
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal ResourcesGuangxi Normal University Guilin 541004 China
| | - Yi‐Ming Liu
- Department of Chemistry and BiochemistryJackson State University 1400 Lynch Street Jackson Mississippi 39217 USA
| |
Collapse
|
14
|
de Almeida BC, dos Anjos LG, Uno M, da Cunha IW, Soares FA, Baiocchi G, Baracat EC, Carvalho KC. Let-7 miRNA's Expression Profile and Its Potential Prognostic Role in Uterine Leiomyosarcoma. Cells 2019; 8:cells8111452. [PMID: 31744257 PMCID: PMC6912804 DOI: 10.3390/cells8111452] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/06/2019] [Accepted: 11/14/2019] [Indexed: 02/06/2023] Open
Abstract
The lethal-7 (let-7) family is an important microRNA (miRNA) group that usually exerts functions as a tumor suppressor. We aimed to evaluate the expression profile of let-7a, let-7b, let-7c, let-7d, let-7e, let-7f, let-7g, and let-7i and to assess their value as prognostic markers in uterine leiomyosarcoma (LMS) patients. The miRNAs expression profile was assessed in 34 LMS and 13 normal myometrium (MM) paraffin-embedded samples. All let-7 family members showed downregulation in LMS. Our findings showed that patients with let-7e downregulation had worse overall survival (OS) and is an independent prognostic factor (hazard ratio [HR] = 2.24). In addition, almost half the patients had distant metastasis. LMS patients with downregulated let-7b and let-7d had worse disease-free survival (DFS); they are not independent prognostic factors (HR = 2.65). Patients’ ages were associated with let-7d, let-7e and let-7f (p = 0.0160) downregulation. In conclusion, all the let-7 family members were downregulated in LMS patients, and the greater the loss of expression of these molecules, the greater their relationship with worse prognosis of patients. Let-7e expression might influence the OS, while let-7b and le-7d might influence the DFS. The lowest expression levels of let-7d, let-7e, and let-7f were associated with the oldest patients. Our findings indicate strong evidence of let-7’s role as a potential prognostic biomarker in LMS.
Collapse
Affiliation(s)
- Bruna Cristine de Almeida
- Laboratório de Ginecologia Estrutural e Molecular (LIM 58), Disciplina de Ginecologia, Departamento de Obstetricia e Ginecologia, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, HCFMUSP, SP, BR Av. Dr Arnaldo 455, sala 4121, Cerqueira Cesar, São Paulo 05403-010, Brazil; (B.C.d.A.); (L.G.d.A.); (E.C.B.)
| | - Laura Gonzalez dos Anjos
- Laboratório de Ginecologia Estrutural e Molecular (LIM 58), Disciplina de Ginecologia, Departamento de Obstetricia e Ginecologia, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, HCFMUSP, SP, BR Av. Dr Arnaldo 455, sala 4121, Cerqueira Cesar, São Paulo 05403-010, Brazil; (B.C.d.A.); (L.G.d.A.); (E.C.B.)
| | - Miyuki Uno
- Centro de Investigação Translacional em Oncologia (LIM 24), Instituto do Câncer do Estado de São Paulo (CTO/ICESP) Av Dr Arnaldo 251 sala 23 8 andar, São Paulo 01246000, Brazil;
| | - Isabela Werneck da Cunha
- Department of Pathology, Rede D’OR-São Luiz, Rua das Perobas, 344-Jabaquara, São Paulo 04321-120, Brazil; (I.W.d.C.); (F.A.S.)
- Hospital A C Camargo Cancer Center, SP, BR R. Tamandaré, 753 Liberdade, São Paulo 05403-010, Brazil
- National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, SP, BR R. Tamandaré, 753 Liberdade, São Paulo 05403-010, Brazil
| | - Fernando Augusto Soares
- Department of Pathology, Rede D’OR-São Luiz, Rua das Perobas, 344-Jabaquara, São Paulo 04321-120, Brazil; (I.W.d.C.); (F.A.S.)
- Hospital A C Camargo Cancer Center, SP, BR R. Tamandaré, 753 Liberdade, São Paulo 05403-010, Brazil
- National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, SP, BR R. Tamandaré, 753 Liberdade, São Paulo 05403-010, Brazil
| | - Glauco Baiocchi
- Department of Gynecology Oncology, A.C.Camargo Cancer Center, Rua Prof Antonio Prudente 211, São Paulo 01509-001, Brazil;
| | - Edmund Chada Baracat
- Laboratório de Ginecologia Estrutural e Molecular (LIM 58), Disciplina de Ginecologia, Departamento de Obstetricia e Ginecologia, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, HCFMUSP, SP, BR Av. Dr Arnaldo 455, sala 4121, Cerqueira Cesar, São Paulo 05403-010, Brazil; (B.C.d.A.); (L.G.d.A.); (E.C.B.)
| | - Katia Candido Carvalho
- Laboratório de Ginecologia Estrutural e Molecular (LIM 58), Disciplina de Ginecologia, Departamento de Obstetricia e Ginecologia, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, HCFMUSP, SP, BR Av. Dr Arnaldo 455, sala 4121, Cerqueira Cesar, São Paulo 05403-010, Brazil; (B.C.d.A.); (L.G.d.A.); (E.C.B.)
- Correspondence: ; Tel.: +55-011-3061-7486
| |
Collapse
|
15
|
Jeong B, Kim YJ, Jeong JY, Kim YJ. Label-free electrochemical quantification of microRNA-375 in prostate cancer cells. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
16
|
Analysis of the microRNA expression profiles in feline kidney cell line infected with feline panleukopenia virus. INFECTION GENETICS AND EVOLUTION 2019; 75:103945. [PMID: 31265913 DOI: 10.1016/j.meegid.2019.103945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/23/2019] [Accepted: 06/28/2019] [Indexed: 01/26/2023]
Abstract
MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of gene expression in many biological processes. Feline panleukopenia virus (FPV) is a highly infectious pathogen that can cause severe disease in pets, economically important animals and wildlife. In this study, miRNAs associated with FPV infection were identified using high-throughput sequencing. Our results showed that 673 known miRNAs and 278 novel miRNAs were identified and 57 significantly differential expression miRNAs were found post-FPV infection in feline kidney cell line. Stem-loop qRT-PCR was applied to validate the expression of the randomly selected miRNAs; the results were consistent with the sequencing data. Furthermore, the target genes of differential expression miRNAs were analyzed and predicated by GO and KEGG pathway. Altogether, our analysis provides a potential link between miRNA expression and the pathogenesis of FPV infection.
Collapse
|
17
|
Ouyang T, Liu Z, Han Z, Ge Q. MicroRNA Detection Specificity: Recent Advances and Future Perspective. Anal Chem 2019; 91:3179-3186. [DOI: 10.1021/acs.analchem.8b05909] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tinglan Ouyang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhiyi Han
- Department of Liver Diseases, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen 518033, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| |
Collapse
|
18
|
Li Q, Zeng F, Lyu N, Liang J. Highly sensitive and specific electrochemical biosensor for microRNA-21 detection by coupling catalytic hairpin assembly with rolling circle amplification. Analyst 2019; 143:2304-2309. [PMID: 29675521 DOI: 10.1039/c8an00437d] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND MicroRNA plays a significant role in gene regulation and is usually regarded as an important biological marker. Electrochemical biosensors are excellent tools for microRNA detection. METHODS In this experiment, we take miRNA-21 as a target, combining catalytic hairpin assembly (CHA) and rolling circle amplification (RCA) as a dual signal amplification strategy for the detection of microRNA in an electrochemical biosensor. RESULTS This strategy has a good linear range of 0.5-12 500 pmol of microRNA. The limit of detection (LOD) for miRNA is as low as 290 fmol, showing excellent performance. Finally, this method has been successfully applied to the detection of miRNA-21 from HeLa cells. CONCLUSION This method can be applied not only for microRNA detection with high sensitivity and speed, but can also detect small molecules and proteins combined with aptamers.
Collapse
Affiliation(s)
- Qing Li
- Xuzhou Central Hospital, Xuzhou, Jiangsu 221004, China.
| | | | | | | |
Collapse
|
19
|
Zhou D, Lin X, Gao W, Piao J, Li S, He N, Qian Z, Zhao M, Gong X. A novel template repairing-PCR (TR-PCR) reaction platform for microRNA detection using translesional synthesis on DNA templates containing abasic sites. Chem Commun (Camb) 2019; 55:2932-2935. [DOI: 10.1039/c8cc10226k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report template repairing-PCR, a novel reverse transcription-free RNA PCR based on miRNA-primed bypass synthesis at the abasic sites on the PCR template.
Collapse
Affiliation(s)
- Dianming Zhou
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Xiaohui Lin
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Weichen Gao
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology
- Tianjin 300072
- China
| | - Jiafang Piao
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology
- Tianjin 300072
- China
| | - Shufei Li
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Ning He
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Zhiyong Qian
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Miao Zhao
- Department of Toxicology
- Tianjin Centers for Disease Control and Prevention
- Tianjin 300011
- China
| | - Xiaoqun Gong
- School of Life Sciences
- Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology
- Tianjin 300072
- China
| |
Collapse
|
20
|
Identification and comparative analysis of the miRNA expression profiles from four tissues of Micropterus salmoides using deep sequencing. Genomics 2018; 110:414-422. [DOI: 10.1016/j.ygeno.2018.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 09/21/2018] [Accepted: 09/27/2018] [Indexed: 01/05/2023]
|
21
|
Yang Z, Zhang S, Zhao H, Niu H, Wu ZS, Chang HT. Branched DNA Junction-Enhanced Isothermal Circular Strand Displacement Polymerization for Intracellular Imaging of MicroRNAs. Anal Chem 2018; 90:13891-13899. [DOI: 10.1021/acs.analchem.8b03063] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Zhe Yang
- Cancer Metastasis
Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer
Metastasis Chemoprevention and Chemotherapy, National and Local Joint
Biomedical Engineering Research Center on Photodynamic Technologies,
Fujian Engineering Research Center for Drug and Diagnoses-Treat of
Photodynamic Therapy, Pharmaceutical Photocatalysis of the State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Songbai Zhang
- Cancer Metastasis
Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer
Metastasis Chemoprevention and Chemotherapy, National and Local Joint
Biomedical Engineering Research Center on Photodynamic Technologies,
Fujian Engineering Research Center for Drug and Diagnoses-Treat of
Photodynamic Therapy, Pharmaceutical Photocatalysis of the State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
- College of Chemistry and Materials Engineering, Hunan University of Arts and Science, Changde 415000, China
| | - Hui Zhao
- Cancer Metastasis
Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer
Metastasis Chemoprevention and Chemotherapy, National and Local Joint
Biomedical Engineering Research Center on Photodynamic Technologies,
Fujian Engineering Research Center for Drug and Diagnoses-Treat of
Photodynamic Therapy, Pharmaceutical Photocatalysis of the State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Huimin Niu
- Cancer Metastasis
Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer
Metastasis Chemoprevention and Chemotherapy, National and Local Joint
Biomedical Engineering Research Center on Photodynamic Technologies,
Fujian Engineering Research Center for Drug and Diagnoses-Treat of
Photodynamic Therapy, Pharmaceutical Photocatalysis of the State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Zai-Sheng Wu
- Cancer Metastasis
Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer
Metastasis Chemoprevention and Chemotherapy, National and Local Joint
Biomedical Engineering Research Center on Photodynamic Technologies,
Fujian Engineering Research Center for Drug and Diagnoses-Treat of
Photodynamic Therapy, Pharmaceutical Photocatalysis of the State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, Roosevelt Road, Taipei 10617, Taiwan
| |
Collapse
|
22
|
Liu S, Fang H, Sun C, Wang N, Li J. Highly sensitive and multiplexed miRNA analysis based on digitally encoded silica microparticles coupled with RCA-based cascade amplification. Analyst 2018; 143:5137-5144. [DOI: 10.1039/c8an01393d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multiple miRNA sensitive analysis by coupling digitally encoded silica microparticles with RCA-based cascade amplification.
Collapse
Affiliation(s)
- Shengquan Liu
- Key Laboratory for Nano-Bio Interface Research
- Nano-Bio-Chem Centre
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
| | - Han Fang
- Key Laboratory for Nano-Bio Interface Research
- Nano-Bio-Chem Centre
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
| | - Chengjiao Sun
- Key Laboratory for Nano-Bio Interface Research
- Nano-Bio-Chem Centre
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
| | - Nana Wang
- Key Laboratory for Nano-Bio Interface Research
- Nano-Bio-Chem Centre
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
| | - Jiong Li
- Key Laboratory for Nano-Bio Interface Research
- Nano-Bio-Chem Centre
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
| |
Collapse
|
23
|
Yuan YH, Chi BZ, Wen SH, Liang RP, Li ZM, Qiu JD. Ratiometric electrochemical assay for sensitive detecting microRNA based on dual-amplification mechanism of duplex-specific nuclease and hybridization chain reaction. Biosens Bioelectron 2017; 102:211-216. [PMID: 29145074 DOI: 10.1016/j.bios.2017.11.030] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/26/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023]
Abstract
We propose a ratiometric electrochemical assay for detecting microRNA (miRNA) on the basis of dual-amplification mechanism by using distinguishable electrochemical signals from thionine (Thi) and ferrocene (Fc). The thiol-modified and ferrocene-labeled hairpin capture probes (CP) are first immobilized on an Au electrode via Au-S reaction. The target miRNA hybridizes with CP and unfolding the hairpin structure of CP to form miRNA-DNA duplexes. Then, kamchatka crab duplex specific nuclease (DSN) specifically cleaves the DNA in miRNA-DNA duplexes, leading to the release of miRNA and another cleaves cycle, meanwhile, numerous Fc leaves away from the electrode surface and leads to the signal-off of Fc. The residual fragment on electrode surface acts as a HCR primer to form dsDNA polymers through in situ HCR with the presence of the primer and two probes (HDNA and HDNA'), resulting in the capture of numerous DNA/Au NPs/Thi and the signal-on of Thi. The dual-amplification mechanism significantly amplifies the decrease of Fc signal and the increase of Thi signal for ratiometric readout (IThi/IFc), thus providing a sensitive method for the selective detection of miR-141 with a detection limit down to 11aM. The dual-signal ratiometric outputs have an intrinsic self-calibration to the effects from system, which is promising to be applied in biosensing and clinical diagnosis.
Collapse
Affiliation(s)
- Yan-Hong Yuan
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang 330031, China
| | - Bao-Zhu Chi
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang 330031, China
| | - Shao-Hua Wen
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang 330031, China
| | - Ru-Ping Liang
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang 330031, China.
| | - Zhi-Mei Li
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang 330031, China
| | - Jian-Ding Qiu
- College of Chemistry and Institute for Advanced Study, Nanchang University, Nanchang 330031, China; College of Materials and Chemical Engineering, Pingxiang University, Pingxiang 337055, China.
| |
Collapse
|
24
|
Wang H, Wang H, Duan X, Liu C, Li Z. Digital quantitative analysis of microRNA in single cell based on ligation-depended polymerase colony (Polony). Biosens Bioelectron 2017; 95:146-151. [DOI: 10.1016/j.bios.2017.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 12/16/2022]
|
25
|
Liang L, Lan F, Yin X, Ge S, Yu J, Yan M. Metal-enhanced fluorescence/visual bimodal platform for multiplexed ultrasensitive detection of microRNA with reusable paper analytical devices. Biosens Bioelectron 2017; 95:181-188. [DOI: 10.1016/j.bios.2017.04.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/02/2017] [Accepted: 04/20/2017] [Indexed: 01/20/2023]
|
26
|
Zhang Y, Zheng X, Xia L, You J, Ren R. A nucleic acid logic gate system that distinguishes different sets of inputs from one miRNA collection with shared members. RSC Adv 2017. [DOI: 10.1039/c7ra05807a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A proof-of-principle logic system was established to process multi-input and multi-output logic relationships with the aim of identifying the tissue origins of cancer in light of their established relationships with miRNA distributions.
Collapse
Affiliation(s)
- You Zhang
- Key Laboratory of Life-Organic Analysis of Shandong Province
- Qufu Normal University
- Qufu 273165
- P. R. China
| | - Xiangjiang Zheng
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers
- School of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276000
- P. R. China
| | - Lian Xia
- Key Laboratory of Life-Organic Analysis of Shandong Province
- Qufu Normal University
- Qufu 273165
- P. R. China
| | - Jinmao You
- Key Laboratory of Life-Organic Analysis of Shandong Province
- Qufu Normal University
- Qufu 273165
- P. R. China
| | - Rui Ren
- Key Laboratory of Life-Organic Analysis of Shandong Province
- Qufu Normal University
- Qufu 273165
- P. R. China
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers
| |
Collapse
|
27
|
Sun Y, Tian H, Liu C, Sun Y, Li Z. One-step detection of microRNA with high sensitivity and specificity via target-triggered loop-mediated isothermal amplification (TT-LAMP). Chem Commun (Camb) 2017; 53:11040-11043. [DOI: 10.1039/c7cc06140d] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A target-triggered loop-mediated isothermal amplification (TT-LAMP) mechanism is developed for simple one-step but highly sensitive detection of microRNAs.
Collapse
Affiliation(s)
- Yuanyuan Sun
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
| | - Hui Tian
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
| | - Yueying Sun
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
| |
Collapse
|
28
|
A gold nanoparticle-based colorimetric strategy coupled to duplex-specific nuclease signal amplification for the determination of microRNA. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-2030-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
29
|
Tian H, Sun Y, Liu C, Duan X, Tang W, Li Z. Precise Quantitation of MicroRNA in a Single Cell with Droplet Digital PCR Based on Ligation Reaction. Anal Chem 2016; 88:11384-11389. [DOI: 10.1021/acs.analchem.6b01225] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hui Tian
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Yuanyuan Sun
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Chenghui Liu
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Xinrui Duan
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Wei Tang
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Zhengping Li
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| |
Collapse
|
30
|
Li D, Cheng W, Li Y, Xu Y, Li X, Yin Y, Ju H, Ding S. Catalytic Hairpin Assembly Actuated DNA Nanotweezer for Logic Gate Building and Sensitive Enzyme-Free Biosensing of MicroRNAs. Anal Chem 2016; 88:7500-6. [PMID: 27367785 DOI: 10.1021/acs.analchem.5b04844] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A target-switched DNA nanotweezer is designed for AND logic gate operation and enzyme-free detection of microRNAs (miRNAs) by catalytic hairpin assembly (CHA) and proximity-dependent DNAzyme formation. The double crossover motif-based nanotweezer consists of an arched structure as the set strand for target inputs and two split G-rich DNAs at the termini of two arms for signal output. Upon a CHA, a small amount of binary target inputs can switch numerous open nanotweezers to a closed state, which leads to the formation of proximity-dependent DNAzyme in the presence of hemin to produce a highly sensitive biosensing system. The binary target inputs can be used for successful building of AND logic gate, which is validated by polyacrylamide gel electrophoresis, surface plasmon resonance and the biosensing signal. The developed biosensing system shows a linear response of the output chemiluminescence signal to input binary miRNAs with a detection limit of 30 fM. It can be used for miRNAs analysis in complex sample matrix. This system provides a simple and reusable platform for logic gate operation and enzyme-free, highly sensitive, and specific multianalysis of miRNAs.
Collapse
Affiliation(s)
- Dandan Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Wei Cheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China.,The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Yujian Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - YongJie Xu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Xinmin Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Yibing Yin
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| | - Huangxian Ju
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China.,State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University , Nanjing 210023, People's Republic of China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University , Chongqing 400016, People's Republic of China
| |
Collapse
|
31
|
Xu Y, Li D, Cheng W, Hu R, Sang Y, Yin Y, Ding S, Ju H. Chemiluminescence imaging for microRNA detection based on cascade exponential isothermal amplification machinery. Anal Chim Acta 2016; 936:229-35. [PMID: 27566360 DOI: 10.1016/j.aca.2016.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/29/2016] [Accepted: 07/05/2016] [Indexed: 11/29/2022]
Abstract
A novel G-quadruplex DNAzyme-driven chemiluminescence (CL) imaging method was developed for ultrasensitive and specific detection of miRNA based on the cascade exponential isothermal amplification reaction (EXPAR) machinery. A structurally tailored hairpin probe switch was designed to selectively recognise miRNA and form hybridisation products to trigger polymerase and nicking enzyme machinery, resulting in the generation of product I, which was complementary to a region of the functional linear template. Then, the response of the functional linear template to the generated product I further activated the exponential isothermal amplification machinery, leading to synthesis of numerous horseradish peroxidase mimicking DNAzyme units for CL signal transduction. The amplification paradigm generated a linear response from 10 fM to 100 pM, with a low detection limit of 2.91 fM, and enabled discrimination of target miRNA from a single-base mismatched target. The developed biosensing platform demonstrated the advantages of isothermal, homogeneous, visual detection for miRNA assays, offering a promising tool for clinical diagnosis.
Collapse
Affiliation(s)
- Yongjie Xu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Dandan Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Rong Hu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Ye Sang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yibing Yin
- 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.
| | - Huangxian Ju
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210023, China.
| |
Collapse
|
32
|
A novel surface plasmon resonance biosensor for enzyme-free and highly sensitive detection of microRNA based on multi component nucleic acid enzyme (MNAzyme)-mediated catalyzed hairpin assembly. Biosens Bioelectron 2016; 80:98-104. [DOI: 10.1016/j.bios.2016.01.048] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
|
33
|
Egatz-Gomez A, Wang C, Klacsmann F, Pan Z, Marczak S, Wang Y, Sun G, Senapati S, Chang HC. Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine. BIOMICROFLUIDICS 2016; 10:032902. [PMID: 27190565 PMCID: PMC4859827 DOI: 10.1063/1.4948525] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/20/2016] [Indexed: 05/05/2023]
Abstract
Nucleic acid biomarkers have enormous potential in non-invasive diagnostics and disease management. In medical research and in the near future in the clinics, there is a great demand for accurate miRNA, mRNA, and ctDNA identification and profiling. They may lead to screening of early stage cancer that is not detectable by tissue biopsy or imaging. Moreover, because their cost is low and they are non-invasive, they can become a regular screening test during annual checkups or allow a dynamic treatment program that adjusts its drug and dosage frequently. We briefly review a few existing viral and endogenous RNA assays that have been approved by the Federal Drug Administration. These tests are based on the main nucleic acid detection technologies, namely, quantitative reverse transcription polymerase chain reaction (PCR), microarrays, and next-generation sequencing. Several of the challenges that these three technologies still face regarding the quantitative measurement of a panel of nucleic acids are outlined. Finally, we review a cluster of microfluidic technologies from our group with potential for point-of-care nucleic acid quantification without nucleic acid amplification, designed to overcome specific limitations of current technologies. We suggest that integration of these technologies in a modular design can offer a low-cost, robust, and yet sensitive/selective platform for a variety of precision medicine applications.
Collapse
Affiliation(s)
- Ana Egatz-Gomez
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Ceming Wang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Flora Klacsmann
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Zehao Pan
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Steve Marczak
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Yunshan Wang
- Electrical and Computer Engineering, University of Utah , Salt Lake City, Utah 84112, USA
| | - Gongchen Sun
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Satyajyoti Senapati
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| | - Hsueh-Chia Chang
- Center for Microfluidics and Medical Diagnostics, Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, USA
| |
Collapse
|
34
|
Yin F, Liu H, Li Q, Gao X, Yin Y, Liu D. Trace MicroRNA Quantification by Means of Plasmon-Enhanced Hybridization Chain Reaction. Anal Chem 2016; 88:4600-4. [DOI: 10.1021/acs.analchem.6b00772] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Fangfei Yin
- College
of Chemistry, Research Center for Analytical Sciences, State Key Laboratory
of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular
Recognition and Biosensing, Nankai University, Tianjin 300071, China
| | - Huiqiao Liu
- College
of Chemistry, Research Center for Analytical Sciences, State Key Laboratory
of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular
Recognition and Biosensing, Nankai University, Tianjin 300071, China
| | - Qiang Li
- College
of Chemistry, Research Center for Analytical Sciences, State Key Laboratory
of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular
Recognition and Biosensing, Nankai University, Tianjin 300071, China
| | - Xia Gao
- College
of Chemistry, Research Center for Analytical Sciences, State Key Laboratory
of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular
Recognition and Biosensing, Nankai University, Tianjin 300071, China
| | - Yongmei Yin
- College
of Chemistry, Research Center for Analytical Sciences, State Key Laboratory
of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular
Recognition and Biosensing, Nankai University, Tianjin 300071, China
| | - Dingbin Liu
- College
of Chemistry, Research Center for Analytical Sciences, State Key Laboratory
of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular
Recognition and Biosensing, Nankai University, Tianjin 300071, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300071, China
| |
Collapse
|
35
|
Gao X, Xu LP, Wu T, Wen Y, Ma X, Zhang X. An enzyme-amplified lateral flow strip biosensor for visual detection of MicroRNA-224. Talanta 2016; 146:648-54. [DOI: 10.1016/j.talanta.2015.06.060] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/15/2015] [Accepted: 06/20/2015] [Indexed: 12/21/2022]
|
36
|
Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges. Anal Bioanal Chem 2015; 408:2793-811. [DOI: 10.1007/s00216-015-9240-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/13/2015] [Accepted: 12/01/2015] [Indexed: 11/27/2022]
|
37
|
Wang H, Wang H, Liu C, Duan X, Li Z. Enzyme-free and multiplexed microRNA detection using microRNA-initiated DNA molecular motor. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5537-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
38
|
Liu H, Bei X, Xia Q, Fu Y, Zhang S, Liu M, Fan K, Zhang M, Yang Y. Enzyme-free electrochemical detection of microRNA-21 using immobilized hairpin probes and a target-triggered hybridization chain reaction amplification strategy. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1636-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
39
|
Cheng FF, Zhang JJ, He TT, Shi JJ, Abdel-Halim ES, Zhu JJ. Bimetallic Pd-Pt supported graphene promoted enzymatic redox cycling for ultrasensitive electrochemical quantification of microRNA from cell lysates. Analyst 2015; 139:3860-5. [PMID: 24976373 DOI: 10.1039/c4an00777h] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The expression of microRNAs (miRNAs) is related to some cancer diseases. Recently, miRNAs have emerged as new candidate diagnostic and prognostic biomarkers for detecting a wide variety of cancers. Due to low levels, short sequences and high sequence homology among family members, the quantitative miRNA analysis is still a challenge. A novel electrochemical biosensor with triple signal amplification for the ultrasensitive detection of miRNA was developed based on phosphatase, redox-cycling amplification, a bimetallic Pd-Pt supported graphene functionalized screen-printed gold electrode, and two stem-loop structured DNAs as target capturers. The proposed biosensor is highly sensitive due to the enhanced electrochemical signal of Pd-Pt supported graphene and sufficiently selective to discriminate the target miRNA from homologous miRNAs in the presence of loop-stem structure probes with T4 DNA ligase. Therefore, this strategy provided a new and ultrasensitive platform for amplified detection and subsequent analysis of miRNA in biomedical research and clinical diagnosis.
Collapse
Affiliation(s)
- Fang-Fang Cheng
- State Key Lab of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, P.R.China.
| | | | | | | | | | | |
Collapse
|
40
|
Shi K, Dou B, Yang C, Chai Y, Yuan R, Xiang Y. DNA-Fueled Molecular Machine Enables Enzyme-Free Target Recycling Amplification for Electronic Detection of MicroRNA from Cancer Cells with Highly Minimized Background Noise. Anal Chem 2015; 87:8578-83. [DOI: 10.1021/acs.analchem.5b02418] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Kai Shi
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Baoting Dou
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Cuiyun Yang
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry, Ministry of Education, School
of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| |
Collapse
|
41
|
Zhang Y, Yan Y, Chen W, Cheng W, Li S, Ding X, Li D, Wang H, Ju H, Ding S. A simple electrochemical biosensor for highly sensitive and specific detection of microRNA based on mismatched catalytic hairpin assembly. Biosens Bioelectron 2015; 68:343-349. [DOI: 10.1016/j.bios.2015.01.026] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/09/2015] [Accepted: 01/12/2015] [Indexed: 12/21/2022]
|
42
|
Guo X, Yang X, Liu P, Wang K, Wang Q, Guo Q, Huang J, Li W, Xu F, Song C. Multiple amplification detection of microRNA based on the host–guest interaction between β-cyclodextrin polymer and pyrene. Analyst 2015; 140:4291-7. [DOI: 10.1039/c5an00626k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The proposed multiple amplification strategy based on the host–guest interaction between β-CDP and pyrene is homogeneous, sensitive and rapid.
Collapse
|
43
|
Yu Y, Chen Z, Shi L, Yang F, Pan J, Zhang B, Sun D. Ultrasensitive Electrochemical Detection of MicroRNA Based on an Arched Probe Mediated Isothermal Exponential Amplification. Anal Chem 2014; 86:8200-5. [DOI: 10.1021/ac501505a] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yanyan Yu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Zuanguang Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Lijuan Shi
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Fan Yang
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, Hubei 430065, China
| | - Jianbin Pan
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Beibei Zhang
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Duanping Sun
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| |
Collapse
|
44
|
Zhang P, Liu Y, Zhang Y, Liu C, Wang Z, Li Z. Multiplex ligation-dependent probe amplification (MLPA) for ultrasensitive multiplexed microRNA detection using ribonucleotide-modified DNA probes. Chem Commun (Camb) 2014; 49:10013-5. [PMID: 24042239 DOI: 10.1039/c3cc45760e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Using the ribonucleotide-modified DNA probes, multiple microRNAs can be simultaneously detected in one ligation-based PCR reaction. As low as 0.2 fM microRNA can be accurately detected with high specificity.
Collapse
Affiliation(s)
- Pengbo Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province, P. R. China.
| | | | | | | | | | | |
Collapse
|
45
|
Duan R, Zuo X, Wang S, Quan X, Chen D, Chen Z, Jiang L, Fan C, Xia F. Quadratic isothermal amplification for the detection of microRNA. Nat Protoc 2014; 9:597-607. [DOI: 10.1038/nprot.2014.036] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
46
|
Shi C, Liu Q, Ma C, Zhong W. Exponential strand-displacement amplification for detection of microRNAs. Anal Chem 2013; 86:336-9. [PMID: 24345199 DOI: 10.1021/ac4038043] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRNAs) are promising targets for disease diagnosis. However, miRNA detection requires rapid, sensitive, and selective detection to be effective as a diagnostic tool. Herein, a miRNA-initiated exponential strand-displacement amplification (SDA) assay was reported. With the Klenow fragment, nicking enzyme Nt.AlwI, and two primers, the miRNA target can trigger two cycles of nicking, polymerization, and displacement reactions. These reaction cycles amplified the target miRNA exponentially and generated dsDNAs detectable with SYBR Green I in real-time PCR. As low as 16 zmol of the target miRNA was detected by this one-pot assay within 90 min, and the dynamic range spanned over 9 orders of magnitude. Negligible impact from the complex biological matrix was observed on the amplification reaction, indicating the assay's capability to directly detect miRNAs in biofluids.
Collapse
Affiliation(s)
- Chao Shi
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , Qingdao, Shandong 266042, P. R. China
| | | | | | | |
Collapse
|
47
|
Wen Y, Liu G, Pei H, Li L, Xu Q, Liang W, Li Y, Xu L, Ren S, Fan C. DNA nanostructure-based ultrasensitive electrochemical microRNA biosensor. Methods 2013; 64:276-82. [DOI: 10.1016/j.ymeth.2013.07.035] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/27/2013] [Indexed: 11/25/2022] Open
|
48
|
Fraley SI, Hardick J, Masek BJ, Jo Masek B, Athamanolap P, Rothman RE, Gaydos CA, Carroll KC, Wakefield T, Wang TH, Yang S. Universal digital high-resolution melt: a novel approach to broad-based profiling of heterogeneous biological samples. Nucleic Acids Res 2013; 41:e175. [PMID: 23935121 PMCID: PMC3794612 DOI: 10.1093/nar/gkt684] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Comprehensive profiling of nucleic acids in genetically heterogeneous samples is important for clinical and basic research applications. Universal digital high-resolution melt (U-dHRM) is a new approach to broad-based PCR diagnostics and profiling technologies that can overcome issues of poor sensitivity due to contaminating nucleic acids and poor specificity due to primer or probe hybridization inaccuracies for single nucleotide variations. The U-dHRM approach uses broad-based primers or ligated adapter sequences to universally amplify all nucleic acid molecules in a heterogeneous sample, which have been partitioned, as in digital PCR. Extensive assay optimization enables direct sequence identification by algorithm-based matching of melt curve shape and Tm to a database of known sequence-specific melt curves. We show that single-molecule detection and single nucleotide sensitivity is possible. The feasibility and utility of U-dHRM is demonstrated through detection of bacteria associated with polymicrobial blood infection and microRNAs (miRNAs) associated with host response to infection. U-dHRM using broad-based 16S rRNA gene primers demonstrates universal single cell detection of bacterial pathogens, even in the presence of larger amounts of contaminating bacteria; U-dHRM using universally adapted Lethal-7 miRNAs in a heterogeneous mixture showcases the single copy sensitivity and single nucleotide specificity of this approach.
Collapse
Affiliation(s)
- Stephanie I Fraley
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA, Department of Emergency Medicine, The Johns Hopkins University, Baltimore, MD 21218, USA, Division of Infectious Disease, Department of Medicine, The Johns Hopkins University, Baltimore, MD 21218, USA, Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University, Baltimore, MD 21218, USA, The Johns Hopkins Hospital, Baltimore, MD 21287, USA and Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Duan R, Zuo X, Wang S, Quan X, Chen D, Chen Z, Jiang L, Fan C, Xia F. Lab in a Tube: Ultrasensitive Detection of MicroRNAs at the Single-Cell Level and in Breast Cancer Patients Using Quadratic Isothermal Amplification. J Am Chem Soc 2013; 135:4604-7. [DOI: 10.1021/ja311313b] [Citation(s) in RCA: 298] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ruixue Duan
- School of
Chemistry and Chemical
Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaolei Zuo
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shutao Wang
- Beijing National Laboratory for
Molecular Sciences (BNLMS), Key Laboratory of Organic Solids, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiyun Quan
- The Pathology Department of Zhuzhou No. 1 Hospital, Hunan 412000, China
| | - Dongliang Chen
- The Pathology Department of Zhuzhou No. 1 Hospital, Hunan 412000, China
| | - Zhifei Chen
- School of
Chemistry and Chemical
Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lei Jiang
- Beijing National Laboratory for
Molecular Sciences (BNLMS), Key Laboratory of Organic Solids, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Chunhai Fan
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Fan Xia
- School of
Chemistry and Chemical
Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
50
|
Yan J, Zhang N, Qi C, Liu X, Shangguan D. One-step real time RT-PCR for detection of microRNAs. Talanta 2013; 110:190-5. [PMID: 23618193 DOI: 10.1016/j.talanta.2013.02.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/11/2013] [Accepted: 02/14/2013] [Indexed: 01/26/2023]
Abstract
Rapid and simple methods for microRNA (miRNA) detection are essential for biological research of miRNAs and clinical diagnosis. Here we describe a sensitive and specific real time RT-PCR (also RT-qPCR) method for miRNA quantification. The whole detection process including reverse transcription and PCR is performed in one PCR tube by a one-step operation on a real-time PCR system. The results display a wide linear range from 0.1 amol to 10 fmol with a detection limit of 12.6 zmol for miRNA let-7a detection. Let-7a in small RNA samples extracted from tumor cells has been successfully detected by this method. This method is cost-effective, simple and rapid, and has the advantages in the high-throughput routing assay of given miRNAs, as well as in non-model research that has less specific kits and reagents.
Collapse
Affiliation(s)
- Jingli Yan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | | | | | | | | |
Collapse
|