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Peng C, Leng M, Gao Y, Feng Q, Miao X. DNA tetrahedral molecular sieve for size-selective fluorescence sensing of miRNA 21 in living cells. Talanta 2024; 276:126218. [PMID: 38759363 DOI: 10.1016/j.talanta.2024.126218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/09/2024] [Accepted: 05/05/2024] [Indexed: 05/19/2024]
Abstract
In situ monitoring of intracellular microRNAs (miRNAs) often encounters the challenges of surrounding complexity, coexistence of precursor miRNAs (pre-miRNAs) and the degradation of biological enzyme in living cells. Here, we designed a novel probe encapsulated DNA tetrahedral molecular sieve (DTMS) to realize the size-selective detection of intracellular miRNA 21 that can avoid the interference of pre-miRNAs. In such strategy, quencher (BHQ-1) labeled probe DNA (S6-BHQ 1) was introduced into the inner cavity of fluorophore (FAM) labeled DNA tetrahedral scaffolds (DTS) to prepare DTMS, making the FAM and BHQ-1 closely proximate, and resulting the sensor in a "signal-off" state. In the presence of miRNA 21, strand displacement reaction happened to form more stable DNA double-stranded structure, accompanied by the release of S6-BHQ 1 from the inner cavity of DTMS, making the sensor in a "signal-on" state. The DTMS based sensing platform can then realized the size-selective detection of miRNA 21 with a detection limit of 3.6 pM. Relying on the mechanical rigidity of DTS and the encapsulation of DNA probe using DTMS, such proposed method achieved preferable reproducibility and storage stability. Moreover, this sensing system exhibited good performance for monitoring the change of intracellular miRNA 21 level during the treatment with miRNA-related drugs, demonstrating great potential for biological studies and accurate disease diagnosis.
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Affiliation(s)
- Chenxu Peng
- School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Mingyu Leng
- School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Yongguang Gao
- Department of Radiology, Xuzhou Central Hospital, 199 Jiefang Road, Xuzhou, Jiangsu, China.
| | - Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Xiangmin Miao
- School of Life Science, Jiangsu Normal University, Xuzhou, 221116, China.
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2
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Wang L, Pu G, Liu T, Chen G, Li H, Amuda TO, Cao S, Yan H, Yin H, Fu B, Luo X. Parasite-derived microRNA let-7-5p detection for metacestodiasis based on rolling circular amplification-assisted CRISPR/Cas9. FASEB J 2024; 38:e23708. [PMID: 38805151 DOI: 10.1096/fj.202302449r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/23/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Metacestodiasis is an infectious disease caused by the larval stage of cestode parasites. This disease poses a serious health hazard to wildlife, livestock, and humans, and it incurs substantial economic losses by impacting the safety of the livestock industry, the quality of meat production, and public health security. Unfortunately, there is currently no available molecular diagnostic method capable of distinguishing cysticercus- and Echinococcus-derived microRNAs (miRNAs) from other helminthes and hosts in the plasma of metacestode-infected animals. This study aims to develop a specific, sensitive, and cost-efficient molecular diagnostic method for cysticercosis and echinococcosis, particularly for early detection. The study developed a rolling circular amplification (RCA)-assisted CRISPR/Cas9 detection method based on parasite-derived miRNA let-7-5p. Using a series of dilutions of the let-7 standard, the limit of detection (LOD) of the qPCR, RCA, and RCA-assisted CRISPR/Cas9 methods was compared. The specificity of qPCR and CRISPR/Cas9 was evaluated using four artificially synthesized let-7 standards from different species. A total of 151 plasma samples were used to evaluate the diagnostic performance. Additionally, the study also assessed the correlation between plasma levels of let-7-5p, the number of Taenia pisiformis cysticerci, and the weight of Echinococcus multilocularis cysts. The results demonstrated that the RCA-assisted CRISPR/Cas9 assay could significantly distinguish let-7 from cestodes and other species, achieving a LOD of 10 aM; the diagnostic sensitivity and specificity for rabbit cysticercosis and mouse E. multilocularis were 100% and 97.67%, and 100% and 100%, respectively. Notably, let-7-5p gradually increased in the plasma of T. pisiformis-infected rabbits from 15 days post infection (dpi), peaked at 60 dpi, and persisted until 120 dpi. In E. multilocularis-infected mice, let-7-5p gradually increased from 15 dpi and persisted until 90 dpi. Furthermore, the expression of let-7-5p positively correlated with the number of cysticerci and cyst weight. These results indicated that the let-7-5p-based RCA-assisted CRISPR/Cas9 assay is a sensitive and specific detection method that can be used as a universal diagnostic method for metacestodiasis, particularly for early diagnosis (15 dpi).
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Affiliation(s)
- Liqun Wang
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Guiting Pu
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Tingli Liu
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Guoliang Chen
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Hong Li
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Tharheer Oluwashola Amuda
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Shanling Cao
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Hongbin Yan
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Hong Yin
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Baoquan Fu
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xuenong Luo
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
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3
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Wang Y, Shao L, Zhao Z, Huang C, Jiao Y, Sun D, Liu R, Jiang D, Gao X. Simultaneous detection of dual microRNAs related to EV71 using ICP-MS based on metal nanoparticle labeling with hybridization chain reaction. Anal Chim Acta 2024; 1294:342272. [PMID: 38336408 DOI: 10.1016/j.aca.2024.342272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Hand, foot, and mouth (HMFD) disease caused by enterovirus 71 (EV 71), is closely associated with severe clinical manifestations and can be deadly. Early detection of EV 71 can be achieved by detecting the increment in miR296 and miR16 in the serum. Using HCR to amplify signals and convert biological signals into metal nanoparticle signals detectable by ICP-MS is a detection method that can collect more accurate and reliable information, compared with traditional methods, in the detection of biological samples. RESULTS We described a strategy for the simultaneous detection of miR296 and miR16 by ICP-MS based on metal nanoparticles (NPs) labeling with HCR. Briefly, single-stranded DNA (ssDNA) and magnetic beads (MBs), as well as NPs and signal probes for miRNA (Sp-miR) were firstly conjugated via the streptavidin-biotin recognition system, constituting ssDNA-MBs and NPs-Sp-miR complex, respectively. The latter complex then hybridized with the former through HCR, generating the nanosensors for targets. Then, the targets were added and hybridized with ssDNA, and the HCR complex with NPs was released into the solution. Finally, the corresponding signals of the NPs were measured by ICP-MS. Results demonstrated that the developed method had good sensitivity and satisfactory selectivity and precision. Furthermore, when applied to biological samples with a complex matrix, the developed method also showed good recovery (88 % - 92 %) and reproducibility (RSD<10 %). SIGNIFICANCE This method contributes to the early diagnosis of HFMD and opens up ideas for the further development of high-throughput biomarker detection. The strategy has practical potential for miR296 and miR16 detection in biological samples and provides a promising tool for multiple miRNA detection.
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Affiliation(s)
- Yuxin Wang
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, PR China; Shandong Academy of Preventive Medicine, Shandong Center for Food Safety Risk Assessment, Shandong Center for Disease Control and Prevention, Jinan, PR China; Department of Transfusion Medicine, West China Hospital, Sichuan University, Chengdu, PR China
| | - Lijun Shao
- Shandong Academy of Preventive Medicine, Shandong Center for Food Safety Risk Assessment, Shandong Center for Disease Control and Prevention, Jinan, PR China
| | - Zhigang Zhao
- Shandong Academy of Preventive Medicine, Shandong Center for Food Safety Risk Assessment, Shandong Center for Disease Control and Prevention, Jinan, PR China
| | - Chao Huang
- Department of Pharmacy, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, PR China
| | - Yanni Jiao
- Shandong Academy of Preventive Medicine, Shandong Center for Food Safety Risk Assessment, Shandong Center for Disease Control and Prevention, Jinan, PR China
| | - Dapeng Sun
- Shandong Academy of Preventive Medicine, Shandong Center for Food Safety Risk Assessment, Shandong Center for Disease Control and Prevention, Jinan, PR China
| | - Rui Liu
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, PR China; Shandong Academy of Preventive Medicine, Shandong Center for Food Safety Risk Assessment, Shandong Center for Disease Control and Prevention, Jinan, PR China
| | - Dafeng Jiang
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, PR China; Shandong Academy of Preventive Medicine, Shandong Center for Food Safety Risk Assessment, Shandong Center for Disease Control and Prevention, Jinan, PR China.
| | - Xibao Gao
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, PR China.
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Chen Q, Chen H, Kong H, Chen R, Gao S, Wang Y, Zhou P, Huang W, Cheng H, Li L, Feng J. Enzyme-free sensitive SERS biosensor for the detection of thalassemia-associated microRNA-210 using a cascade dual-signal amplification strategy. Anal Chim Acta 2024; 1292:342255. [PMID: 38309848 DOI: 10.1016/j.aca.2024.342255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/28/2023] [Accepted: 01/15/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND β-thalassemia is a blood disorder caused by autosomal mutations. Gene modulation therapy to activate the γ-globin gene to induce fetal hemoglobin (HbF) synthesis has become a new option for the treatment of β-thalassemia. MicroRNA-210 (miR-210) contributes to studying the mechanism regulating γ-globin gene expression and is a potential biomarker for rapid β-thalassemia screening. Traditional miRNA detection methods perform well but necessitate complex and time-consuming miRNA sample processing. Therefore, the development of a sensitive, accurate, and simple miRNA level monitoring method is essential. RESULTS We have developed a non-enzymatic surface-enhanced Raman scattering (SERS) biosensor utilizing a signal cascade amplification of catalytic hairpin assembly reaction (CHA) and proximity hybridization-induced hybridization chain reaction (HCR). Au@Ag NPs were used as the SERS substrate, and methylene blue (MB)- modified DNA hairpins were used as the SERS tags. The SERS assay involved two stages: implementing the CHA-HCR cascade signal amplification strategy and conducting SERS measurements on the resulting product. The HCR was started by the products of target-triggered CHA, which formed lengthy nicked double-stranded DNA (dsDNA) on the Au@Ag NPs surface to which numerous SERS tags were attached, leading to a significant increase in the SERS signal intensity. High specificity and sensitivity for miR-210 detection was achieved by monitoring MB SERS intensity changes. The suggested SERS biosensor has a low detection limit of 5.13 fM and is capable of detecting miR-210 at concentration between 10 fM and 1.0 nM. SIGNIFICANCE The biosensor can detect miR-210 levels in the erythrocytes of β-thalassemia patients, enabling rapid screening for β-thalassemia and suggesting a novel approach for investigating the regulation mechanism of miR-210 on γ-globin gene expression. In the meantime, this innovative technique has the potential to detect additional miRNAs and to become an important tool for the early diagnosis of diseases and for biomedical research.
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Affiliation(s)
- Qiying Chen
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China
| | - Huagan Chen
- Department of Clinical Laboratory, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001, Guangxi, PR China
| | - Hongxing Kong
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China; Provine and Ministry Co-sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi, PR China
| | - Ruijue Chen
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China
| | - Si Gao
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China
| | - Ying Wang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China
| | - Pei Zhou
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China
| | - Wenyi Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China; Provine and Ministry Co-sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi, PR China
| | - Hao Cheng
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China; Provine and Ministry Co-sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi, PR China
| | - Lijun Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China; Provine and Ministry Co-sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi, PR China.
| | - Jun Feng
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Department of Medicine/ College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, 545006, Guangxi, PR China.
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Ahmad W, Baby J, Gull B, Mustafa F. Liquid and Solid Hybridization Methods to Detect RNAs. Methods Mol Biol 2024; 2822:125-141. [PMID: 38907916 DOI: 10.1007/978-1-0716-3918-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Northern blotting (NB) has been a long-standing method for RNA detection. However, its labor-intensive nature, reliance on high-quality RNA, and use of radioactivity have diminished its appeal over time. Nevertheless, the emergence of microRNAs (miRNAs) has reignited the demand for sensitive and quantitative NB techniques. We have recently developed cost-effective and rapid protocols for RNA detection using solid and liquid hybridization (LH) techniques which exhibit high sensitivity without the need for radioactive or specialized reagents like locked nucleic acid (LNA) probes. Our assays incorporate biotinylated probes and improved techniques for probe hybridization, transfer, cross-linking, and signal enhancement. We demonstrate that while NB is sensitive in detecting mRNAs and small RNAs, our LH protocol efficiently detects these as well as miRNAs at lower amounts of RNA, achieving higher sensitivity comparable to radiolabeled probes. Compared to NB, LH offers benefits of speed, sensitivity, and specificity in detecting mRNAs, small RNAs, and miRNAs.
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Affiliation(s)
- Waqar Ahmad
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates (UAE) University, Al Ain, United Arab Emirates
| | - Jasmin Baby
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates (UAE) University, Al Ain, United Arab Emirates
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
| | - Bushra Gull
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates (UAE) University, Al Ain, United Arab Emirates
| | - Farah Mustafa
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates (UAE) University, Al Ain, United Arab Emirates.
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Bai J, Shu E, Zhang T, Fan H. Identification, cleavage, and amplification (ICA): A versatile strategy for highly sensitive detection of miRNA. Anal Chim Acta 2023; 1276:341592. [PMID: 37573128 DOI: 10.1016/j.aca.2023.341592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 08/14/2023]
Abstract
MicroRNAs (miRNAs) are small RNA molecules that can play important roles as diagnostic/prognostic biomarkers and therapeutic targets for cancers and other diseases. Herein, an identification-cleavage-amplification (ICA) strategy for highly sensitive and versatile detection of miRNA has been proposed, and successfully applied to miR-155 and miR-21 assays. It combines an aligner-target mediated cleavage with strand displacement amplification (ATMC-SDA) to achieve the ICA process. During the identification process, a DNA-aligner (DA) and a DNA-amplicon (DM) can bind together with the help of target miRNA, forming a T-junction structure. Then, a nicking endonuclease (NEase), binding on the recognition sequence at the stem part of DA, can make a cleavage on DM, and the cleaved DM (CDM) can serve as an initiator to trigger the SDA reaction for signal amplification. Sharing the same set of enzymes and primers, the proposed ATMC-SDA can serve as a versatile ICA strategy for highly sensitive detection of various miRNAs, without the requirement of reverse transcription. Results show that the limits of detection (LOD) for miR-155 and miR-21 are 5.4 aM and 6.8 aM, respectively, with a dynamic range from 10.0 aM to 10.0 pM. The compatibility of ATMC-SDA with biological samples has also been tested by using human serum, indicating a promising potential for a wide variety of applications.
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Affiliation(s)
- Jie Bai
- School of Public Health, Hangzhou Medical College, Hangzhou, 310013, China
| | - Eryi Shu
- School of Public Health, Hangzhou Medical College, Hangzhou, 310013, China
| | - Tao Zhang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310023, China
| | - Hongliang Fan
- School of Public Health, Hangzhou Medical College, Hangzhou, 310013, China.
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Ahmad W, Panicker NG, Akhlaq S, Gull B, Baby J, Khader TA, Rizvi TA, Mustafa F. Global Down-regulation of Gene Expression Induced by Mouse Mammary Tumor Virus (MMTV) in Normal Mammary Epithelial Cells. Viruses 2023; 15:v15051110. [PMID: 37243196 DOI: 10.3390/v15051110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Mouse mammary tumor virus (MMTV) is a betaretrovirus that causes breast cancer in mice. The mouse mammary epithelial cells are the most permissive cells for MMTV, expressing the highest levels of virus upon infection and being the ones later transformed by the virus due to repeated rounds of infection/superinfection and integration, leading eventually to mammary tumors. The aim of this study was to identify genes and molecular pathways dysregulated by MMTV expression in mammary epithelial cells. Towards this end, mRNAseq was performed on normal mouse mammary epithelial cells stably expressing MMTV, and expression of host genes was analyzed compared with cells in its absence. The identified differentially expressed genes (DEGs) were grouped on the basis of gene ontology and relevant molecular pathways. Bioinformatics analysis identified 12 hub genes, of which 4 were up-regulated (Angp2, Ccl2, Icam, and Myc) and 8 were down-regulated (Acta2, Cd34, Col1a1, Col1a2, Cxcl12, Eln, Igf1, and Itgam) upon MMTV expression. Further screening of these DEGs showed their involvement in many diseases, especially in breast cancer progression when compared with available data. Gene Set Enrichment Analysis (GSEA) identified 31 molecular pathways dysregulated upon MMTV expression, amongst which the PI3-AKT-mTOR was observed to be the central pathway down-regulated by MMTV. Many of the DEGs and 6 of the 12 hub genes identified in this study showed expression profile similar to that observed in the PyMT mouse model of breast cancer, especially during tumor progression. Interestingly, a global down-regulation of gene expression was observed, where nearly 74% of the DEGs in HC11 cells were repressed by MMTV expression, an observation similar to what was observed in the PyMT mouse model during tumor progression, from hyperplasia to adenoma to early and late carcinomas. Comparison of our results with the Wnt1 mouse model revealed further insights into how MMTV expression could lead to activation of the Wnt1 pathway independent of insertional mutagenesis. Thus, the key pathways, DEGs, and hub genes identified in this study can provide important clues to elucidate the molecular mechanisms involved in MMTV replication, escape from cellular anti-viral response, and potential to cause cell transformation. These data also validate the use of the MMTV-infected HC11 cells as an important model to study early transcriptional changes that could lead to mammary cell transformation.
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Affiliation(s)
- Waqar Ahmad
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain 15551, United Arab Emirates
| | - Neena G Panicker
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain 15551, United Arab Emirates
| | - Shaima Akhlaq
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain 15551, United Arab Emirates
| | - Bushra Gull
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain 15551, United Arab Emirates
| | - Jasmin Baby
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain 15551, United Arab Emirates
| | - Thanumol A Khader
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain 15551, United Arab Emirates
| | - Tahir A Rizvi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), UAE University, Al Ain 15551, United Arab Emirates
- Zayed Center for Health Sciences (ZCHS), UAE University, Al Ain 15551, United Arab Emirates
- ASPIRE Research Institute in Precision Medicine, Abu Dhabi, UAE University, Al Ain 15551, United Arab Emirates
| | - Farah Mustafa
- Department of Biochemistry & Molecular Biology, College of Medicine and Health Sciences (CMHS), United Arab Emirates (UAE) University, Al Ain 15551, United Arab Emirates
- Zayed Center for Health Sciences (ZCHS), UAE University, Al Ain 15551, United Arab Emirates
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8
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Self-assembly of DNA-hyperbranched aggregates catalyzed by a dual-targets recognition probe for miRNAs SERS detection in single cells. Biosens Bioelectron 2023; 222:114997. [PMID: 36516629 DOI: 10.1016/j.bios.2022.114997] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are very important for the early diagnosis and prognosis of tumors. In this work, we achieved the simultaneous detection of microRNA-155 (miR-155) and microRNA-21 (miR-21) with a dual target recognition probe (DRP) based on the nonlinear hybridization chain reaction (HCR). The multi-branched DNA products, three-dimensional multi-hotspot DNA dendrimers (3DmhD) were used in the amplification of the target miRNAs signal. The DRP is constructed with a core of gold nanocages (AuNCs), modified by nucleic acid probes and labeled with Raman signaling molecules ROX and Cy3. Experiments demonstrated that DRP could activate the multi-branched DNA reaction and generate 3DmhD in the presence of miR-155 and miR-21, which can achieve effective amplification of miR-21 and miR-155. When Surface Enhanced Raman Scattering (SERS) analysis was performed on 3DmhD, the multi-hot spot effect of 3DmhD significantly enhanced the signals of ROX and Cy3, allowing ultra-sensitive detection of miR-21 and miR-155 in vitro. To our delight, DRP also exhibited sensitive specificity and significant signal amplification for intracellular miRNAs. These results revealed that DRP has the potential to screen tumor cells by analyzing the expression levels of intracellular miRNAs.
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Zhang X, Zhang Q, Cheng L, Liu D, Wang H, Zhou Y, Ma L, Wang J, Li F. A New Biotin Labeling and High-Molecular-Weight RNA Northern Method and Its Application in Viral RNA Detection. Viruses 2022; 14:v14122664. [PMID: 36560668 PMCID: PMC9785142 DOI: 10.3390/v14122664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/26/2022] [Accepted: 11/26/2022] [Indexed: 11/30/2022] Open
Abstract
Viruses cause severe crop losses. Studying the interaction between viruses and plants is very important for development of control measures. Northern blot is a well-accepted but very challenging technique to monitor the infection of viruses. Here, we modified the high-molecular-weight (hmw)RNA Northern blot experiment process, utilizing vertical electrophoresis to separate the RNA with denatured agarose gel. This protocol is compatible with regular equipment for Western blots and small RNA Northern blots and requires less input of total RNA. A new method to label the probe with biotin was also developed, which requires commonly used T4 DNA polymerase and detects viral RNA with high sensitivity. These new protocols made hmwRNA Northern blot cost-effective and easy-to-operate, very suitable for studying virus-host interactions.
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Liu X, Zhao X, Yuan Y, Cao Z, Zhu M, Li T, Wu Z. Accurate detection of lung cancer-related microRNA through CRISPR/Cas9-assisted garland rolling circle amplification. J Thorac Dis 2022; 14:4427-4434. [PMID: 36524084 PMCID: PMC9745504 DOI: 10.21037/jtd-22-1405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/03/2022] [Indexed: 02/19/2024]
Abstract
BACKGROUND MicroRNA (miRNA) is reported to be closely related to a variety of pathophysiological processes for carcinoma and considered a potential biomarker for the diagnosis of lung cancer with brain metastasis. However, developing an accurate and sensitive miRNA detection method has proven to be a challenge. The aim of the present study was to integrate the advantages of rolling circle amplification (RCA), clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nucleases 9 (Cas9), and catalytic hairpin assembly (CHA) technologies to develop an miRNA detection method. METHODS In the present study, we developed a novel approach for the sensitive and accurate detection of miRNA through integrating garland RCA and CRISPR/Cas9-assisted signal generation. In this method, target miRNA cyclized dumbbell padlock and triggered the RCA process to form long single-stranded DNA products with a repeated hairpin structure. Double-stranded DNA sequences (dsDNA) were formed with the addition of complementary sequences. With the assistance of the Cas9 enzyme for specific recognition and cleavage of formed dsDNA, RCA products were disassembled into hairpin probes. The generated hairpin probe could be unfolded by target miRNA to initiate the CHA process for signal generation. RESULTS Through integration of the RCA and CHA processes, the method demonstrated favorable detection performance. The correlation equation between the signal and concentration of target miRNA was determined to be Y=312.3 × lgC + 2108, with a high correlation coefficient of 0.9786. The approach also exhibited high selectivity to the mismatched miRNAs. CONCLUSIONS Our method could be used in the screening, diagnosis, and prognosis of multiple diseases without complicated thermal cycling instrumentation.
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Affiliation(s)
- Xiaoya Liu
- Department of Oncology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xianxian Zhao
- Department of Clinical Laboratory, Southwest Hospital, Army Medical University, Chongqing, China
| | - Ye Yuan
- Department of Clinical Laboratory, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zhenrui Cao
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mingxue Zhu
- Department of Pharmacy, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tingting Li
- Breast Disease Center, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zhongjun Wu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Li X, Ma F, Deng L, Yang M, Chen X. A wheel-like DNA nanosensor with background correction for analysis of miRNA-21 in living cells. Chem Commun (Camb) 2022; 58:8270-8273. [PMID: 35788226 DOI: 10.1039/d2cc02736d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A silica ring-based ratiometric fluorescence nanosensing and imaging platform was established for the quantification of miRNA-21 with carbon dots and nucleic-functionalized gold nanoparticles inside and outside the ring, respectively. In the presence of miRNA-21, on one hand, the fluorescence emission signal of the originally quenched 6-carboxyfluorescein (FAM), which was labeled on the nucleic acid molecules that modified on the gold nanoparticles, was re-emitted. On the other hand, the fluorescence intensity of the carbon dots inside the ring remained essentially unchanged, which served to eliminate background interference. The ring rather than the shell well maintained the fluorescence of the carbon dots. The ratio of the recovered fluorescence intensity of FAM to the fluorescence intensity of the carbon dots was linearly correlated with the logarithm of miRNA-21 concentration. The linear range of the probe for miRNA detection was more than 3 orders of magnitude, and the detection limit was as low as 2.5 aM. The feasibility of the method for clinical application was verified by the quantitative analysis of intracellular miRNA.
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Affiliation(s)
- Xiaoqing Li
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, P. R. China.
| | - Fanghui Ma
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, P. R. China.
| | - Lei Deng
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, P. R. China.
| | - Minghui Yang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan Province, 410083, P. R. China. .,The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China.
| | - Xiang Chen
- The Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China. .,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan Province, 410083, P. R. China
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12
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Yang T, Zhang M, Zhang N. Modified Northern blot protocol for easy detection of mRNAs in total RNA using radiolabeled probes. BMC Genomics 2022; 23:66. [PMID: 35057752 PMCID: PMC8772191 DOI: 10.1186/s12864-021-08275-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 12/22/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Northern blotting is still used as a gold standard for validation of the data obtained from high-throughput whole transcriptome-based methods. However, its disadvantages of lower sensitivity, labor-intensive operation, and higher quality of RNA required limit its utilization in a routine molecular biology laboratory to monitor gene expression at RNA level. Therefore, it is necessary to optimize the traditional Northern protocol to make the technique more applicable for standard use. RESULTS In this paper, we report modifications and tips used to improve the traditional Northern protocol for the detection of mRNAs in total RNA. To maximize the retention of specifically bound radiolabeled probes on the blot, posthybridization washes were performed under only with moderate-stringency until the level of radioactivity retained on the filter decreased to 20~50 counts per second, rather than normally under high and low stringency sequentially for scheduled time or under only high stringent condition. Successful detection of the low-expression gene using heterologous DNA probes in 20 µg of total RNA after a two-day exposure suggested an improvement in detection sensitivity. Quantitatively controlled posthybridization washes combined with an ethidium bromide-prestaining RNA procedure to directly visualize prestained RNA bands at any time during electrophoresis or immediately after electrophoresis, which made the progress of the Northern procedure to be monitored and evaluated step by step, thereby making the experiment reliable and controllable. We also report tips used in the modified Northern protocol, including the moderate concentration of formaldehyde in the gel, the accessory capillary setup, and the staining jar placed into an enamel square tray with a lid used for hybridization. Using our modified Northern protocol, eight rounds of rehybridization could be performed on a single blot. The modification made and tips used ensured the efficient proceeding of the experiment and the resulting good performance, but without using special reagents or equipment. CONCLUSIONS The modified Northern protocol improved detection sensitivity and made the experiment easy, less expensive, reliable, and controllable, and can be employed in a routine molecular biology laboratory to detect low-expressed mRNAs with heterologous DNA probes in total RNA.
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Affiliation(s)
- Tao Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, 610065, Chengdu, People's Republic of China
| | - Mingdi Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, 610065, Chengdu, People's Republic of China
| | - Nianhui Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan, 610065, Chengdu, People's Republic of China.
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13
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Ivanov YD, Goldaeva KV, Malsagova KA, Pleshakova TO, Galiullin RA, Popov VP, Kushlinskii NE, Alferov AA, Enikeev DV, Potoldykova NV, Archakov AI. Nanoribbon Biosensor in the Detection of miRNAs Associated with Colorectal Cancer. MICROMACHINES 2021; 12:1581. [PMID: 34945431 PMCID: PMC8705149 DOI: 10.3390/mi12121581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023]
Abstract
A nanoribbon biosensor (NRBS) was developed to register synthetic DNAs that simulate and are analogous to miRNA-17-3p associated with colorectal cancer. Using this nanoribbon biosensor, the ability to detect miRNA-17-3p in the blood plasma of a patient diagnosed with colorectal cancer has been demonstrated. The sensing element of the NRBS was a nanochip based on a silicon-on-insulator (SOI) nanostructure. The nanochip included an array of 10 nanoribbons and was designed with the implementation of top-down technology. For biospecific recognition of miRNA-17-3p, the nanochip was modified with DNA probes specific for miRNA-17-3p. The performance of the nanochip was preliminarily tested on model DNA oligonucleotides, which are synthetic analogues of miRNA-17-3p, and a detection limit of ~10-17 M was achieved. The results of this work can be used in the development of serological diagnostic systems for early detection of colorectal cancer.
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Affiliation(s)
- Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| | - Kristina V. Goldaeva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| | - Kristina A. Malsagova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| | - Tatyana O. Pleshakova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| | - Rafael A. Galiullin
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Nikolay E. Kushlinskii
- N.N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (N.E.K.); (A.A.A.)
| | - Alexander A. Alferov
- N.N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (N.E.K.); (A.A.A.)
| | - Dmitry V. Enikeev
- Institute of Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.V.E.); (N.V.P.)
| | - Natalia V. Potoldykova
- Institute of Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.V.E.); (N.V.P.)
| | - Alexander I. Archakov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
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14
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Huang T, Chen G, Liu B, Yang Z, Huang Y, Xie B, Li MM, Chen JX, Chen J, Dai Z. An intramolecular DNAzyme-based amplification for miRNA analysis with improving reaction kinetics and high sensitivity. Talanta 2021; 239:123137. [PMID: 34920260 DOI: 10.1016/j.talanta.2021.123137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 12/15/2022]
Abstract
Sensitive, specific and rapid methods for detecting microRNAs (miRNAs) play critical roles in disease diagnosis and therapy. Enzyme-free amplification techniques based on DNAzyme assembly have recently been developed for the highly specific miRNA analysis. However, traditional DNAzyme-based assembly (free DNAzyme) amplifiers is mainly dependent on the target-induced split DNAzyme fragments to assemble into activated DNAzyme structures, which have made a compromise between the sensitivity and specificity due to the random diffusion of dissociative probes in a bulk solution with poor kinetics. Herein, based on a rationally designed DNA probe, we developed an intramolecular DNAzyme assembly (intra-DNAzyme) method to overcome these challenges. The miR-373 is used as model analyte for our current proof-of-concept experiments. Compared with the free-DNAzyme method, our method showed significantly improved analytical performance in terms of dynamic range, assay sensitivity and speed. This method can detect miR-373 specifically with a detection limit as low as 4.3 fM, which is about 83.7 times lower than the previous free-DNAzyme method. This intra-DNAzyme strategy would be of great value in both basic research and clinical diagnosis.
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Affiliation(s)
- Ting Huang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Guixun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Birong Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zizhong Yang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yuanwei Huang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Baoping Xie
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Min-Min Li
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, 510632, PR China
| | - Jin-Xiang Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Jun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Zong Dai
- Key Laboratory of Sensing Techno Logy and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, PR China
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