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Huang T, Lu Z, Mo P, Liu P, Liu S, Peng J, Li R, Jia N, Li M, Dai Z, Chen J, Chen J. A DNA walker based on hairpin-shaped DNA aligner and fueled by nicking endonuclease for sensitive and rapid miRNA analysis. Anal Chim Acta 2024; 1316:342873. [PMID: 38969432 DOI: 10.1016/j.aca.2024.342873] [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: 04/12/2024] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND DNA walker-based strategies have gained significant attention in nucleic acid analysis. However, they face challenges related to balancing design complexity, sequence dependence, and amplification efficiency. Furthermore, most existing DNA walkers rely on walking and lock probes, requiring optimization of various parameters like DNA probe sequence, walking-to-lock probe ratio, lock probe length, etc. to achieve optimal performance. This optimization process is time-consuming and adds complexity to experiments. To enhance the performance and reliability of DNA walker nanomachines, there is a need for a simpler, highly sensitive, and selective alternative strategy. RESULTS A sensitive and rapid miRNA analysis strategy named hairpin-shaped DNA aligner and nicking endonuclease-fueled DNA walker (HDA-NE DNA walker) was developed. The HDA-NE DNA walker was constructed by modifying hairpin-shaped DNA aligner (HDA) probe and substrate report (SR) probe on the surface of AuNPs. Under normal conditions, HDA and SR remained stable. However, in the presence of miR-373, HDA underwent a conformational transition to an activated structure to continuously cleave the SR probe on the AuNPs with the assistance of Nt.AlwI nicking endonuclease, resulting in sensitive miRNA detection with a detection limit as low as 0.23 pM. Additionally, the proposed HDA-NE DNA walker exhibited high selectivity in distinguishing miRNAs with single base differences and can effectively analyze miR-373 levels in both normal and breast cancer patient serums. SIGNIFICANCE The proposed HDA-NE DNA walker system was activated by a conformational change of HDA probe only in the presence of the target miRNA, eliminating the need for a lock probe and without sequence dependence for SR probe. This strategy demonstrated a rapid reaction rate of only 30 min, minimal background noise, and a high signal-to-noise ratio (S/B) compared to capture/lock-based DNA walker. The method is expected to become a powerful tool and play an important role in disease diagnosis and precision therapy.
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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, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhenbang Lu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Peixian Mo
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Piao Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Simin Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jing Peng
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Rongtian Li
- Southern University of Science and Technology Hospital, Shenzhen, 518055, China
| | - Nuan Jia
- Southern University of Science and Technology Hospital, Shenzhen, 518055, China.
| | - Minmin Li
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, 510632, China.
| | - Zong Dai
- School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Jinxiang Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
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Liu L, Cai J, Yang K, Sun B, Liu W, Li Y, Hu H. Molecular beacon-peptide probe based double recycling amplification for multiplexed detection of serum exosomal microRNAs. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5202-5211. [PMID: 38994818 DOI: 10.1039/d4ay00629a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Exosomal microRNAs (exomiRs) have been shown to play crucial roles as biomarkers for early detection and prognosis of cancer. However, simultaneous quantification of multiplex exomiRs is hindered by methods that require additional steps, such as labeling with fluorophores or gel visualization, which are susceptible to various factors. Herein, we developed a mass spectrometry-detectable and target-triggered method for multiplexed exomiR detection using three enzyme-based double recycling amplification in combination with well-designed molecular beacon-peptide (MBP) probes, called molecular beacon-peptide probe-based double recycling amplification (MBPDRA). MBP probes mediated the double recycling amplification reaction and were released as mass-detectable reporter peptides. In particular, the hybridization of the target microRNAs (miRNAs) with the stem-loop of the probe triggers two consecutive processes. The first cycle involved polymerase strand displacement amplification, leading to the production of complementary DNA (cycle I), and the second cycle encompassed the recycling exonuclease cleavage of the MBP probe (cycle II). Subsequently, excess probes were removed by interaction with streptavidin beads via biotin-streptavidin binding. The reporter peptides were released using trypsin and subsequently detected by mass spectrometry. Our method enables quantitative detection of multiple exomiRs with a dynamic range from 0.1 fM to 10 pM and a limit of quantification of 0.1 fM. Moreover, the proposed assay was successfully employed for quantification of three exomiRs, exmiR-21, exmiR-191, and exmiR-451a, in the sera of patients with pancreatic cancer. Based on these findings, we believe that the MBPDRA assay holds significant promise as a reliable method for quantifying multiple miRNAs in biomedical research and clinical diagnostics.
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Affiliation(s)
- Liang Liu
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 169 Donghu Road, Wuchang District, Wuhan 430071, China.
| | - Junlong Cai
- Department of Clinical Trial Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Kun Yang
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 169 Donghu Road, Wuchang District, Wuhan 430071, China.
| | - Bo Sun
- Department of Pharmacy, The First People's Hospital of Lianyungang, Lianyungang, 222000, China
| | - Wei Liu
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Yang Li
- Department of Blood Transfusion, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuchang District, Wuhan, 430071, China.
| | - Hankun Hu
- Department of Pharmacy, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 169 Donghu Road, Wuchang District, Wuhan 430071, China.
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Shetti D, Mallela VR, Ye W, Sharif M, Ambrozkiewicz F, Trailin A, Liška V, Hemminki K. Emerging role of circulating cell-free RNA as a non-invasive biomarker for hepatocellular carcinoma. Crit Rev Oncol Hematol 2024; 200:104391. [PMID: 38795877 DOI: 10.1016/j.critrevonc.2024.104391] [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: 03/14/2024] [Revised: 04/30/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a severe neoplastic disease associated with high morbidity and mortality rates. HCC is often detected at advanced stages leading to ineffective curative treatments. Recently, liquid biopsy has emerged as a non-invasive method to identify highly specific HCC biomarkers in bodily fluids such as blood, serum, urine, and saliva. Circulating cell-free nucleic acids (cfNAs), particularly cell-free DNA (cfDNA) and cell-free RNA (cfRNA), have become promising candidates for biomarkers in liquid biopsy applications. While cfDNA presented significant challenges, researchers have turned their attention to cfRNA, which can be efficiently identified through various methods and is considered a potential biomarker for cancer diagnosis and prognosis. This review primarily focuses on studies related to detecting various cfRNA in body fluids as biomarkers. The aim is to provide a summary of available information to assist researchers in their investigations and the development of new diagnostic and prognostic tools.
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Affiliation(s)
- Dattatrya Shetti
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic.
| | - Venkata Ramana Mallela
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Wenjing Ye
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Mahyar Sharif
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University,Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Filip Ambrozkiewicz
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Andriy Trailin
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic
| | - Václav Liška
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic; Department of Surgery, University Hospital in Pilsen and Faculty of Medicine in Pilsen, Charles University, Alej Svobody 80, Pilsen 323 00, Czech Republic
| | - Kari Hemminki
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, Pilsen 323 00, Czech Republic; Department of Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
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Jia Y, Zhao S, Wang A, Huang J, Yang J, Yang L. Target-induced multiregion MNAzyme nanowires for ultrasensitive homogeneous detection of microRNAs. Int J Biol Macromol 2024; 277:134175. [PMID: 39067728 DOI: 10.1016/j.ijbiomac.2024.134175] [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: 05/31/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
A target-induced multiregion MNAzyme nanowire system is designed for the ultrasensitive and homogeneous detection of microRNAs (miRNAs). miRNA-21 and miRNA-375 are chosen as analytes, and a miRNA-induced primer exchange reaction (PER) is utilized to construct a long DNA strand with repetitive sequences. This innovative design enables the efficient anchoring of numerous MNAzymes. This unique architecture significantly boosts the effective local concentration of MNAzymes, thereby enhancing the sensitivity and efficiency of miRNA detection. Notably, the limit of detection (LOD) achieved with our target-induced multiregion MNAzyme nanowire approach is over an order of magnitude lower than most other MNAzyme-based methods, while the MNAzyme reaction time is reduced from several hours to 50 min. The method has demonstrated successful applications in quantitatively determining the expression levels of two miRNAs in cell lysates of MCF-7, HeLa and MCF-10 A cells, highlighting its potential for assaying miRNA biomarkers in clinical samples.
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Affiliation(s)
- Yaxue Jia
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, China
| | - Siqi Zhao
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, China
| | - Anping Wang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, China
| | - Jing Huang
- Laboratory Department of The First Hospital of Jilin University, Changchun, P. R. China
| | - Jinlan Yang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, China
| | - Li Yang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, China.
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Fan Q, Sun XH, Wu N, Wang YH, Wang JH, Yang T. An extracellular vesicle microRNA-initiated 3D DNAzyme motor for colorectal cancer diagnosis. Analyst 2024; 149:3910-3919. [PMID: 38910520 DOI: 10.1039/d4an00635f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
MicroRNA is regarded as a significant biomarker for cancer diagnosis, disease process evaluation and therapeutic guidance, and dual-parameter measurement may contribute to a more accurate and realistic assessment. To meet the urgent need for simultaneous detection of multiple biomarkers, we combined three-dimensional DNAzyme motors with single molecule imaging technique to construct a convenient, intuitive, and sensitive approach for the simultaneous detection of dual miRNAs in the free state or in extracellular vesicles. Quantification of target miRNAs can be realized through the detection of amplified fluorescence signals generated by the target miRNA-initiated cleavage of fluorescent substrate strands by the DNAzyme motors. The practicability was systematically validated with microRNA-21-5p and microRNA-10b-5p as targets, acquiring a satisfactory sensitivity sufficient to detect low abundance targets at 0.5 or 1 pM to 100 pM. Besides, the extracellular vesicular miRNAs can be conveniently detected without extraction. The clinical applicability was verified with a series of extracellular vesicles from clinical samples, which exhibited good distinguishability between colorectal cancer patients and healthy donors. In addition to the advantages of good specificity and high sensitivity, the system has potential to be easily adapted by minor alteration of the DNA sequences and fluorophore sets for detection of multiple miRNAs and even other types of biomarkers such as proteins. Therefore, it shows promise to be widely applied in various fields such as early diagnosis of cancer and its prognostic assessment.
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Affiliation(s)
- Qian Fan
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xu-Hong Sun
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Na Wu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
- Institute of Precision Medicine, Fujian Medical University, Fujian 350004, China
| | - Yuan-He Wang
- Department of Gastrointestinal Cancer, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, Shenyang 110042, China.
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Ting Yang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
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Pan W, Niu H, Luo S, Chen L, Wu ZS. Intelligent Reconfiguration-Promoted Cellular Internalization of Core-Shell DNA Nanoprobe Equipped with Successive Dual Stimuli-Responsive Protective Satellites for Amplification Fluorescence Imaging of Tumor Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2311388. [PMID: 38282377 DOI: 10.1002/smll.202311388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Indexed: 01/30/2024]
Abstract
Although DNA probes have attracted increasing interest for precise tumor cell identification by imaging intracellular biomarkers, the requirement of commercial transfection reagents, limited targeting ligands, and/or non-biocompatible inorganic nanostructures has hampered the clinic translation. To circumvent these shortcomings, a reconfigurable ES-NC (Na+-dependent DNAzyme (E)-based substrate (S) cleavage core/shell DNA nanocluster (NC)) entirely from DNA strands is assembled for precise imaging of cancerous cells in a successive dual-stimuli-responsive manner. This nanoprobe is composed of a strung DNA tetrahedral satellites-based protective (DTP) shell, parallelly aligned target-responsive sensing (PTS) interlayer, and hydrophobic cholesterol-packed innermost layer (HCI core). Tetrahedral axial rotation-activated reconfiguration of DTP shell promotes the exposure of interior hydrophobic moieties, enabling cholesterol-mediated cellular internalization without auxiliary elements. Within cells, over-expressed glutathione triggers the disassembly of the DTP protective shell (first stimulus), facilitating target-stimulated signal transduction/amplification process (second stimuli). Target miRNA-21 is detected down to 10.6 fM without interference from coexisting miRNAs. Compared with transfection reagent-mediated counterpart, ES-NC displays a higher imaging ability, resists nuclease degradation, and has no detectable damage to healthy cells. The blind test demonstrates that the ES-NC is suitable for the identification of cancerous cells from healthy cells, indicating a promising tool for early diagnosis and prediction of cancer.
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Affiliation(s)
- Wenhao Pan
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Huimin Niu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
- Fujian Key Laboratory of Aptamers Technology, The 900th Hospital of Joint Logistics Support Force, Fuzhou, 350025, China
| | - Shasha Luo
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Linhuan Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zai-Sheng 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 Science, Wenzhou Medical University, Wenzhou, 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
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Chen Z, Tian Z, Wang Z, Wang Z, Liu W, Gu Q, Liu S, Wu Y. A Portable Device for in Situ Noninvasive Monitoring of Cell Secretions and Communications with Fluorescence and Nanochannel Electrochemistry. Anal Chem 2024; 96:9218-9227. [PMID: 38781682 DOI: 10.1021/acs.analchem.4c01380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
In situ monitoring of cell secretions and communications plays a fundamental role in screening of disease diagnostic biomarkers and drugs. Quantitative detection of cell secretions and monitoring of intercellular communication have been separately reported, which often rely on target labeling or complex pretreatment steps, inevitably causing damage to the target. Simultaneous in situ noninvasive detection of cell secretions and monitoring of intercellular communication are challenging and have never been reported. Herein, we smartly developed a portable device for in situ label-free monitoring of cell secretions and communications with fluorescence and ion-transport-based nanochannel electrochemistry. Based on the dual signal mode, a series of nonelectroactive secretions were sensitively and accurately quantified. The detection limits for VEGF, MUC1, and ATP were 3.84 pg/mL, 32.7 pg/mL, and 47.4 fM (3σ/S), which were 1/3.9, 1/1.1, and 1/41 of those of commercial ELISA kits, respectively. More interestingly, under the released secretions, the gradual opening of the nanochannel connected the two cells in the left and right chambers of the device; thus, the secretion mediated intercellular communication can be monitored. The proposed platform may provide a promising tool for understanding the mechanism of intercellular communication and discovering new therapeutic targets.
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Affiliation(s)
- Zixuan Chen
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Zhaoyan Tian
- State Key Laboratory for Macromolecule Drugs and Large-Scale Manufacturing, School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China
| | - Zhi Wang
- Wuxi Institute of Inspection, Testing and Certification, Wuxi 214125, China
| | - Zhaohan Wang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Weiwei Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Qinglin Gu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yafeng Wu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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Zhao M, Li Q, Zhao Y, Zhou H, Yan Y, Kong RM, Tan Q, Kong W, Qu F. Dual-Aptamer Recognition of DNA Logic Gate Sensor-Based Specific Exosomal Proteins for Ovarian Cancer Diagnosis. ACS Sens 2024; 9:2540-2549. [PMID: 38635557 DOI: 10.1021/acssensors.4c00270] [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: 04/20/2024]
Abstract
Clinical diagnosis of ovarian cancer lacks high accuracy due to the weak selection of specific biomarkers along with the circumstance biomarkers localization. Clustering analysis of proteins transported on exosomes enables a more precise screening of effective biomarkers. Herein, through bioinformatics analysis of ovarian cancer and exosome proteomes, two coexpressed proteins, EpCAM and CD24, specifically enriched, were identified, together with the development of an as-derived dual-aptamer targeted exosome-based strategy for ovarian cancer screening. In brief, a DNA ternary polymer with aptamers targeting EpCAM and CD24 was designed to present a logic gate reaction upon recognizing ovarian cancer exosomes, triggering a rolling circle amplification chemiluminescent signal. A dynamic detection range of 6 orders of magnitude was achieved by quantifying exosomes. Moreover, for clinical samples, this strategy could accurately differentiate exosomes from healthy persons, other cancer patients, and ovarian cancer patients, enabling promising in situ detection. By accurately selecting biomarkers and constructing a dual-targeted exosomal protein detection strategy, the limitation of insufficient specificity of traditional protein markers was circumvented. This work contributed to the development of exosome-based prognosis monitoring in ovarian cancer through the identification of disease-specific exosome protein markers.
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Affiliation(s)
- Mingzhu Zhao
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, Shandong, China
| | - Qin Li
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, Zhejiang, China
| | - Yan Zhao
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, Shandong, China
| | - Hanlin Zhou
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, Shandong, China
| | - Yuntian Yan
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, Shandong, China
| | - Rong-Mei Kong
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, Shandong, China
| | - Qingqing Tan
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, Zhejiang, China
| | - Weiheng Kong
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, Shandong, China
| | - Fengli Qu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, Zhejiang, China
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Xu S, Wang G, Feng Y, Zheng J, Huang L, Liu J, Jiang Y, Wang Y, Liu N. PNA-Functionalized, Silica Nanowires-Filled Glass Microtube for Ultrasensitive and Label-Free Detection of miRNA-21. Anal Chem 2024; 96:7470-7478. [PMID: 38696229 DOI: 10.1021/acs.analchem.3c05839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
MicroRNAs (miRNAs) are endogenous and noncoding single-stranded RNA molecules with a length of approximately 18-25 nucleotides, which play an undeniable role in early cancer screening. Therefore, it is very important to develop an ultrasensitive and highly specific method for detecting miRNAs. Here, we present a bottom-up assembly approach for modifying glass microtubes with silica nanowires (SiNWs) and develop a label-free sensing platform for miRNA-21 detection. The three-dimensional (3D) networks formed by SiNWs make them abundant and highly accessible sites for binding with peptide nucleic acid (PNA). As a receptor, PNA has no phosphate groups and exhibits an overall electrically neutral state, resulting in a relatively small repulsion between PNA and RNA, which can improve the hybridization efficiency. The SiNWs-filled glass microtube (SiNWs@GMT) sensor enables ultrasensitive, label-free detection of miRNA-21 with a detection limit as low as 1 aM at a detection range of 1 aM-100 nM. Noteworthy, the sensor can still detect miRNA-21 in the range of 102-108 fM in complex solutions containing 1000-fold homologous interference of miRNAs. The high anti-interference performance of the sensor enables it to specifically recognize target miRNA-21 in the presence of other miRNAs and distinguish 1-, 3-mismatch nucleotide sequences. Significantly, the sensor platform is able to detect miRNA-21 in the lysate of breast cancer cell lines (e.g., MCF-7 cells and MDA-MB-231 cells), indicating that it has good potential in the screening of early breast cancers.
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Affiliation(s)
- Shiwei Xu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Guofeng Wang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yueyue Feng
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Juanjuan Zheng
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Liying Huang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Jiahao Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yisha Jiang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yajun Wang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Nannan Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
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10
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Wang W, Li C, Luo S, Wu ZS. Spherical Nucleic Acid-Mediated Spatial Matching-Guided Nonenzymatic DNA Circuits for the Prediction and Prevention of Malignant Tumor Invasion. Anal Chem 2024; 96:7091-7100. [PMID: 38663871 DOI: 10.1021/acs.analchem.4c00476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Detection of intracellular miRNAs, especially sensitive imaging of in vivo miRNAs, is vital to the precise prediction and timely prevention of tumorgenesis but remains a technical challenge in terms of nuclease resistance and signal amplification. Here, we demonstrate a gold nanoparticle-based spherical nucleic acid-mediated spatial matching-guided nonenzymatic DNA circuit (SSDC) for efficient screening of intracellular miRNAs and, in turn, finding cancerous tissues in living organisms before the appearance of clinical symptoms. Due to the substantially enhanced nuclease resistance, the false positive signal is avoided even in a complex biological medium. Target miRNA can straighten out the hairpin DNA probe to be linear, allowing the probe to penetrate into the internal region of a core/shell DNA-functionalized signal nanoampfilier and initiate a strand displacement reaction, generating an amplified fluorescence signal. The detection limit is as low as 17 pM, and miRNA imaging is in good accordance with the gold standard polymerase chain reaction method. The ability to image intracellular miRNAs is substantially superior to that of conventional fluorescence in situ hybridization techniques, making in vivo SSDC-based imaging competent for the precise prediction of tumorigenesis. By intratumoral chemotherapy guided by SSDC-based imaging, tumorigenesis and progression are efficiently controlled before the onset of clinical symptoms.
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Affiliation(s)
- Weijun Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
- College of Chemistry and Food Science, Nanchang Normal University, Nanchang 330032, China
| | - Congcong Li
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Shasha Luo
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zai-Sheng Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
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11
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Ye J, Huang W, Jia X, Song H, Zhou Y, Yuan R, Xu W. Short-stranded DNA segment-modulated LAMP/H + as signal transducer to guide CHA-cooperated amplifiable electrochemical biosensing. Anal Chim Acta 2024; 1295:342329. [PMID: 38355233 DOI: 10.1016/j.aca.2024.342329] [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: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Modulating loop-mediated isothermal amplification (mLAMP) by short-stranded DNA segment trigger (T) to generate byproducts H+ ions (mLAMP/H+) as signal transducer is intriguing for developing catalytic hairpin assembly (CHA)-cooperated amplifiable electrochemical biosensors. This would be a big challenge for traditional LAMP that is basically suitable for amplifying long-stranded oligonucleotides up to 200-300 nt. To address this inherent limitation of traditional LAMP, many researchers have put in efforts to explore improvements in this that would allow LAMP to be used for a wider range of target species amplification. RESULTS Here in this work, we are inspired to explore two-step loop-mediated amplification, firstly forming T-activated double-loop dumbbell structure (DLDS) intermediate by a recognition hairpin and a hairpin precursor, and next DLDS-guided mLAMP process with the aid of two primers to yield mLAMP/H+ during successive DNA incorporation via nucleophilic attacking interaction. To manipulate the mLAMP/H+-directed transduction of input T, a pH-responsive triplex strand is designed with the ability of self-folding in Hoogsteen structure at slightly acidic conditions, resulting in the dehybridization of a fuel strand (FS) to participate in CHA between two hairpins on the modified electrode surface, in which FS is repetitively displaced and recycled to fuel the progressive CHA events. In the as-assembled dsDNA complexes, numerous electroactive ferrocene labels are immobilized in the electrode sensing interface, thereby generating significantly amplified electrochemical current signal that can sense the presented and varied T. SIGNIFICANCE It is clear that we have creatively constructed a unique electrochemical biosensor for disease detection. Benefited from the rational combination of mLAMP and CHA, our electrochemical strategy is highly sensitive, specific and simplified, and would provide a new paradigm to construct various mLAMP/H+-based biosensors for other short-stranded DNA or microRNAs markers.
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Affiliation(s)
- Jingjing Ye
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Weixiang Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Xinyue Jia
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Honglin Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yifu Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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12
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Ye Z, Ma M, Chen Y, Liu R, Zhang Y, Ma P, Song D. Dual-microRNA-Controlled Electrochemiluminescence Biosensor for Breast Cancer Diagnosis and Supplemental Identification of Breast Cancer Metastasis. Anal Chem 2024; 96:3636-3644. [PMID: 38357821 DOI: 10.1021/acs.analchem.3c05766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Breast cancer remains the most frequently diagnosed cancer globally, and the metastasis of this malignancy is the primary cause of mortality in breast cancer patients. Hence, prompt diagnosis and timely detection of metastatic breast cancer are critical for effective therapeutic intervention. Both progression and metastasis of this malignancy are closely associated with aberrant expression of specific microRNAs (miRNAs) and enzymes. To facilitate breast cancer diagnosis and concomitant identification of metastatic breast cancer, we have engineered an innovative electrochemiluminescence (ECL)-based sensing platform integrated with enzyme-free DNA amplification circuits for dual functionality. Specifically, microRNA-21 (miR-21) is employed as a biomarker for breast cancer, and miR-21 induces the quenching of the ECL signal from luminophores via a strategically designed catalytic three-hairpin assembly (CTHA) circuit. Subsequently, miR-105 levels are measured via toehold-mediated strand displacement reactions (TSDR). Here, miR-105 restores the initially quenched ECL signal, enabling the assessment of the metastatic propensity. Our experimental data demonstrate that the devised ECL biosensor offers broad linear detection ranges and low detection limits for both miR-21 and miR-105. Importantly, our novel platform was also successfully validated by using cellular and serum samples. This biosensor not only discriminates breast cancer cell lines MCF-7 and MDA-MB-231 from nonbreast cancer cells like HepG2, TPC-1, and HeLa, but it also distinguishes between malignant MCF-7 and metastatic MDA-MB-231 cells. Consequently, our novel approach holds significant promise for clinical applications and precise cancer screening.
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Affiliation(s)
- Zhuoxin Ye
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Mo Ma
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
- School of Pharmacy, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Yuxuan Chen
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Ruiyan Liu
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Yan Zhang
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Pinyi Ma
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Daqian Song
- College of Chemistry, Jilin Province Research Center for Engineering and Technology of Spectral Analytical Instruments, Jilin University, Qianjin Street 2699, Changchun 130012, China
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13
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Wang HY, Wang B, Sun C, Zhang TY, Xu YT, Zhao WW, Chen HY, Xu JJ. θ-Nanopore Ratiometry. ACS NANO 2024; 18:4551-4558. [PMID: 38264998 DOI: 10.1021/acsnano.3c12238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Developing nanoscale ratiometric techniques capable of biochemical response should prove of significance for precise applications with stringent spatial and biological restrictions. Here we present and devise the concept of θ-nanopore ratiometry, which uses ratiometric signals that could well address the serious concerns about device deviation in fabrication and nonspecific adsorption in the detection. As exemplified by a 200 nm θ-nanopore toward miRNA detection, the ±20 nm aperture drift could be mitigated and the issue of nonspecific adsorption could be minimized in the complex cytosolic environment. Practical application of this θ-nanopore ratiometry realizes the measurements of cytosolic miRNA-10b. This work has not only established a nanoscopic ratiometric technique but also enriched the extant armory of nanotools for single-cell studies and beyond.
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Affiliation(s)
- Hai-Yan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Bing Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Chao Sun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tian-Yang Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yi-Tong Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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14
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Jiang S, Liu T, Liu Q, Zhang Q, Han Y, Tian X, Zhang CY. Rapid, Sensitive, and Label-Free Detection of Long Noncoding RNAs in Breast Cancer Tissues by RecJ f Exonuclease-Assisted Recombinase Polymerase Amplification. Anal Chem 2023; 95:15133-15139. [PMID: 37751602 DOI: 10.1021/acs.analchem.3c03920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
An abnormal expression level of long noncoding RNAs (lncRNAs) is implicated in multiple cancers, and their sensitive and rapid measurement is pivotal for early cancer diagnosis and cancer treatment. The conventional lncRNA assays often suffer from labor-intensive/time-consuming procedures and limited sensitivity. Herein, we report a simple and sensitive fluorescent biosensor for rapid and label-free measurement of lncRNAs based on recombinase polymerase amplification (RPA) without the involvement of thermal cycling and reverse transcription. Target lncRNAs can bind with the 5'-end of the DNA template to create a DNA-lncRNA hybrid, protecting the DNA template from RecJf exonuclease-mediated degradation. Subsequently, the primers hybridize with the intact DNA templates and are extended to generate the dsDNA products with the assistance of polymerase. The resultant dsDNA products may be amplified by exponential recombinase polymerase amplification to produce abundant dsDNAs, generating a distinct fluorescence signal within 10 min. This biosensor achieves a wide dynamic range from 10-17 to 10-9 M and high sensitivity with a detection limit of 1.23 aM. Moreover, it can distinguish the expressions of lncRNA HOTAIR in the tissues of healthy individuals and breast cancer patients, with broad application prospects in lncRNA-related research and early diagnosis of cancers.
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Affiliation(s)
- Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Ting Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Qian Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yun Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Xiaorui Tian
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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15
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Su J, Wang M, Lin P, Huang Z, Li G, Chen X, Yan H, Zhou L. Trigger-activated autonomous DNA machine for amplified liver cancer biomarker microRNA21 imaging. ANAL SCI 2023; 39:1661-1667. [PMID: 37552462 DOI: 10.1007/s44211-023-00397-3] [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: 07/06/2022] [Accepted: 09/03/2022] [Indexed: 08/09/2023]
Abstract
MicroRNA-21 (miRNA-21) is a kind of RNA that exists in biological fluids such as blood, urine and saliva. It has over expression in liver cancer and has different expression in different stages of cancer. However, due to the characteristics of small base number, short length, low abundance and easy degradation of miRNA-21, the detection of miRNA-21 is a challenging subject. Visualization, sensitive, specific and stable detection of tumor suppressor or oncogene microRNAs (miRNAs) remains challenging and is highly significant for clinical diagnostics. To solve this problem, we have developed a target-triggered hybridization assembly DNA machine for intracellular miRNA imaging based on strand displacement amplification (SDA) and branched hybridization chain reaction (B-HCR). In this approach, the target miRNA could hybridize with the template probe to trigger the SDA, resulting in the formation of nicked fragments (NFs) that hybridized with hairpin probe1 (HP1). The opened HP1 could hybridize with hairpin probe2 (HP2), leading to the self-assembly of hyperbranched DNA nanostructures through B-HCR. As expected, the newly developed method exhibits a detection limit down to 11.3 pM miRNA-21 and achieves high selectivity toward miRNA-21 against other interfering miRNAs. Due to its superior sensitivity and selectivity, our method can be further used to detect miRNA-21 in human serum samples. By taking advantage of intelligent design, the proposed method was also used for image miRNA-21 expression levels in different cell lines. This method shows a broad application in clinical diagnosis.
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Affiliation(s)
- Jiqin Su
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Maolin Wang
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Peiyi Lin
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Zhishu Huang
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Guibin Li
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Xiangru Chen
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Huidi Yan
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China.
| | - Lixin Zhou
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China.
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16
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Wu W, Biyani M, Hirose D, Takamura Y. Rapid and Highly Sensitive Detection of Leishmania by Combining Recombinase Polymerase Amplification and Solution-Processed Oxide Thin-Film Transistor Technology. BIOSENSORS 2023; 13:765. [PMID: 37622851 PMCID: PMC10452724 DOI: 10.3390/bios13080765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023]
Abstract
Nucleic acid detection is widely used to identify infectious diseases and ensure food safety. However, conventional PCR-based techniques are time consuming. Thus, this study aims to combine recombinase polymerase amplification (RPA), which enables the rapid amplification of even trace amounts of nucleic acid fragments within 10-40 min at 37-42 °C, and solution-processed oxide thin-film transistor (TFT) technology, which exhibits high detection sensitivity, to detect Leishmania. A single-stranded anti-probe was incorporated into the RPA primer to facilitate effective hybridization between the RPA product and the immobilized probe on the solution-processed oxide TFT. The RPA-amplified product carrying an anti-probe enabled specific binding to the chip surface. Changes in current were monitored before and after sample incubation to identify the target nucleic acids in the samples accurately. The proposed method achieved a remarkable limit of detection of 101 copies/μL of the Leishmania HSP70 fragment within 30 min. The design of the probes on the solution-processed oxide TFT surface and the anti-probe simplified the detection of other target nucleic acids, eliminating the need to denature DNA double-strands for specific binding during nucleic acid detection. Thus, the novel method offers the advantage of requiring minimal reagent resources and eliminates the need for complex procedures.
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Affiliation(s)
- Weidong Wu
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi 923-1292, Ishikawa, Japan; (W.W.); (M.B.); (D.H.)
| | - Manish Biyani
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi 923-1292, Ishikawa, Japan; (W.W.); (M.B.); (D.H.)
- BioSeeds Corporation, JAIST Venture, Ishikawa Create Laboratory 202, Asahidai 2-13, Nomi 923-1292, Ishikawa, Japan
| | - Daisuke Hirose
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi 923-1292, Ishikawa, Japan; (W.W.); (M.B.); (D.H.)
| | - Yuzuru Takamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi 923-1292, Ishikawa, Japan; (W.W.); (M.B.); (D.H.)
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17
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Xia Y, Lei X, Ma X, Wang S, Yang Z, Wu Y, Ren X. Combination of RCA and DNAzyme for Dual-Signal Isothermal Amplification of Exosome RNA. Molecules 2023; 28:5528. [PMID: 37513400 PMCID: PMC10384651 DOI: 10.3390/molecules28145528] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/29/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023] Open
Abstract
The RNA contained in exosomes plays a crucial role in information transfer between cells in various life activities. The accurate detection of low-abundance exosome RNA (exRNA) is of great significance for cell function studies and the early diagnosis of diseases. However, their intrinsic properties, such as their short length and high sequence homology, represent great challenges for exRNA detection. In this paper, we developed a dual-signal isothermal amplification method based on rolling circle amplification (RCA) coupled with DNAzyme (RCA-DNAzyme). The sensitive detection of low-abundance exRNA, the specific recognition of their targets and the amplification of the detection signal were studied and explored. By designing padlock probes to specifically bind to the target exRNA, while relying on the ligation reaction to enhance recognition, the precise targeting of exosome RNA was realized. The combination of RCA and DNAzyme could achieve a twice-as-large isothermal amplification of the signal compared to RCA alone. This RCA-DNAzyme assay could sensitively detect a target exRNA at a concentration as low as 527 fM and could effectively distinguish the target from other miRNA sequences. In addition, this technology was successfully proven to be effective for the quantitative detection of miR-21 by spike recovery, providing a new research approach for the accurate detection of low-abundance exRNA and the exploration of unknown exRNA functions.
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Affiliation(s)
- Yuqing Xia
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xin Lei
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaochen Ma
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Shizheng Wang
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Zifu Yang
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Yifan Wu
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaojun Ren
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
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18
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Xi X, Wu Z, Zhang X, Li Y, Zhao Y, Wen W, Wang S. Endogenous Protease-Activatable Nanosensor Based on PNA-Peptide-DNA Engineering for AND-Gated and Dual-Model Detection of MicroRNA in Single Living Tumor Cells. ACS APPLIED MATERIALS & INTERFACES 2023; 15:21917-21928. [PMID: 37105764 DOI: 10.1021/acsami.3c02012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The in situ detection of low-content cancer biomarkers by an endogenous activator instead of an exogenous initiator in vitro remains a great challenge, leaving a gap in the development of a tumor-specific nanosensor with an endogenous protease-activatable manner. Herein, we proposed an endogenous protease-activatable nanosensor (PA-NS) guided by peptide nucleic acid-peptide-DNA copolymers to realize AND-gated and dual-model sensing of miRNA-21 (miR-21) by combining electrochemical detection with optical imaging in living tumor cells, without an additional introduction of an exogenous activator or nanomaterials. Moreover, the PA-NS can only be activated by "dual keys" (overexpressed miR-21 and cathepsin B protease in tumor cells) simultaneously, which enables effective improvement of the tumor-to-healthy cells ratio. The fluorescence intensity measured in single tumor cells was ∼3.5-fold higher than that in single healthy cells, and the electrochemical response decreased ∼30% in the presence of target miRNA. Furthermore, studies on regulation of the protease activity and miR-21 fluctuation under external stimulation have contributed to our understanding of the biological processes and drug screenings underlying disease development. This specific endogenous protease-mediated manner for dual-model detection of miRNA guarantees excellent tumor-selective capability, which offers new opportunities to study cell heterogeneity and provides more reliable fundamentals for the diagnosis and treatment of cancer down to the single-cell level.
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Affiliation(s)
- Xiaoxue Xi
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Zhen Wu
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Xiuhua Zhang
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Yuebin Li
- Faculty of Physics and Electronic Sciences, Wuhan 430062, Hubei, P. R. China
| | - Yuandi Zhao
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioformatics and Molecular Imaging Key Laboratory, Department of Biomedicine Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, P. R. China
| | - Wei Wen
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
| | - Shengfu Wang
- Collaborative Innovation Center for Advanced Organic Chemical Materials, Coconstruted by the Province and Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering. Hubei University, Wuhan 430062, P. R. China
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Liu X, Zhan W, Gao G, Jiang Q, Zhang X, Zhang H, Sun X, Han W, Wu FG, Liang G. Apoptosis-Amplified Assembly of Porphyrin Nanofiber Enhances Photodynamic Therapy of Oral Tumor. J Am Chem Soc 2023; 145:7918-7930. [PMID: 36987560 DOI: 10.1021/jacs.2c13189] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is the most common oral cancer, having high recurrence and metastasis features. In addition to surgery, photodynamic therapy (PDT) is considered as another effective approach for OSCC treatment. The water solubility of currently available PDT photosensitizers (PSs) is poor, lowering their singlet oxygen (1O2) yield and consequent PDT efficiency. Strategies of PS assembly have been reported to increase 1O2 yield, but it is still possible to further enhance PDT efficiency. In this work, we utilized apoptosis to amplify the assembly of porphyrin nanofibers for enhanced PDT of OSCC. A water-soluble porphyrin derivative, Ac-Asp-Glu-Val-Asp-Asp-TPP (Ac-DEVDD-TPP), was designed for this purpose. Upon caspase-3 (Casp3, an activated enzyme during apoptosis) cleavage and laser irradiation, Ac-DEVDD-TPP was converted to D-TPP, which spontaneously self-assembled into porphyrin nanofibers, accompanied by 1.4-fold and 2.1-fold 1O2 generations in vitro and in cells, respectively. The as-formed porphyrin nanofiber induced efficient cell apoptosis and pyroptosis. In vivo experiments demonstrated that, compared with the scrambled control compound Ac-DEDVD-TPP, Ac-DEVDD-TPP led to 6.2-fold and 1.3-fold expressions of Casp3 in subcutaneous and orthotopic oral tumor models, respectively, and significantly suppressed the tumors. We envision that our strategy of apoptosis-amplified porphyrin assembly might be applied for OSCC treatment in the clinic in the near future.
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20
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Liu B, Wang F, Chao J. Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing. SENSORS (BASEL, SWITZERLAND) 2023; 23:3313. [PMID: 36992023 PMCID: PMC10051322 DOI: 10.3390/s23063313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.
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Affiliation(s)
- Bing Liu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Fan Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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21
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Wang Q, He Y, He S, Yu S, Jiang Y, Wang F. An entropy-driven DNA nanomachine for microRNA detection using a personal glucose meter. Chem Commun (Camb) 2023; 59:1345-1348. [PMID: 36647734 DOI: 10.1039/d2cc06479k] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Herein, we developed a reliable and portable biosensor (TDR-PGM nanomachine) for the sensitive detection of microRNA by integrating an efficient toehold-mediated strand displacement reaction module (TDR) and a personal glucose meter (PGM). The system provides a versatile methodology for microRNA detection in real samples and holds broad prospects in point-of-care diagnosis.
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Affiliation(s)
- Qing Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Shizhen He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Yuqian Jiang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China. .,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, Hubei, 430072, P. R. China
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22
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Chen Y, Ye L, Chen H, Fan T, Qiu C, Chen Y, Jiang Y. Simple Isothermal and Label-Free Strategy for Colorectal Cancer Potential Biomarker miR-625-5p Detection. BIOSENSORS 2023; 13:78. [PMID: 36671913 PMCID: PMC9855811 DOI: 10.3390/bios13010078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
miRNA is considered a novel biomarker for cancer diagnosis and due to its low level in vivo, the development of new detection methods for it has become a research hotspot in recent years. Here, we firstly found that miR-625-5p was significantly upregulated in colorectal cancer tissues by means of differential expression analysis of the dbDEMC database and clinical validation. Subsequently, it was found that miR-625-5p promoted cell proliferation and migration but inhibited apoptosis through phenotypic experiments; thus, we initially identified miR-625-5p as a potential biomarker for colorectal cancer. Moreover, in order to monitor slight changes in the miR-625-5p level, we developed a novel detection method for it based on strand displacement amplification (SDA). In this system, a hairpin was designed to recognize and pair with miR-625-5p, which was used as a primer to initiate SDA, and a large number of complementary DNAs were generated via cyclic amplification, followed by the addition of SYBR Gold to achieve quantitative analysis of miR-625-5p. Moreover, this method showed a good response to miR-625-5p with a detection limit of 8.6 pM and a dynamic range of 0.01 to 200 nM, and the specificity of it was verified using a set of other miRNAs as an interference. Finally, we set up different concentrations of biologic samples for detection to verify the practicability of the method. The results of this study indicate that this detection method has great potential in clinical diagnosis.
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Affiliation(s)
- Yifei Chen
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Lizhen Ye
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Hui Chen
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Tingting Fan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Cheng Qiu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yan Chen
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yuyang Jiang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
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23
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Dong Z, Xu X, Ni J, Li Y, An K, Meng L, Wu H. Cruciate DNA probes for amplified multiplexed imaging of microRNAs in living cells. J Mater Chem B 2022; 11:204-210. [PMID: 36504047 DOI: 10.1039/d2tb02027k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The real-time imaging of low-abundance tumor-related microRNAs (miRNAs) in living cells holds great potential for early clinical diagnosis of cancers. However, the relatively low detection sensitivity and possible false-positive signals of a probe in complex cellular matrices remain critical challenges for accurate RNA detection. Herein, we developed a novel aptamer-functionalized cruciate DNA probe that enabled amplified multiple miRNA imaging in living cells via catalytic hairpin assembly (CHA). The cross-shaped design of the cruciate DNA probe improved the stability against nucleases and acted as a modular scaffold for CHA circuits for efficient delivery into tumor cells. The cruciate DNA probe allowed self-assembly through thermal annealing and displayed excellent performance for sensitive miRNA detection in vitro. The cruciate DNA probe could be internalized into nucleolin-overexpressed cells specifically via cell-targeting of the AS1411 aptamer, achieving amplified fluorescence imaging and quantitative evaluation of the expression of miRNAs in living cells. Through the simultaneous detection of intracellular multiple miRNAs, the developed cruciate DNA probe could provide more accurate information and reduce the chances of false positive signals for cancer diagnosis. This approach offers a new opportunity for promoting the development of miRNA-related biomedical research and tumor diagnostic applications.
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Affiliation(s)
- Zhe Dong
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.,State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Xizhu Xu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Jing Ni
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Yuancheng Li
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Kang An
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Ling Meng
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Han Wu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
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24
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Su J, Du J, Ge R, Sun C, Qiao Y, Wei W, Pang X, Zhang Y, Lu H, Dong H. Metal–Organic Framework-Loaded Engineering DNAzyme for the Self-Powered Amplified Detection of MicroRNA. Anal Chem 2022; 94:13108-13116. [DOI: 10.1021/acs.analchem.2c02547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiaxin Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Jinya Du
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Rujiao Ge
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Chenyang Sun
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Yuchun Qiao
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Wei Wei
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Xuejiao Pang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Yufan Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Huiting Lu
- Department of Chemistry, School of Chemistry and Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
- Marshall Laboratory of Biomedical Engineering, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Guangdong 518060, P. R. China
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25
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Concentration-Dependent Study of Nucleic Acid Blockers Used for Sequence-Specificity Enhancement in Nucleic Acids Detection. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2022. [DOI: 10.1007/s13369-022-06972-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Di Z, Lu X, Zhao J, Jaklenec A, Zhao Y, Langer R, Li L. Mild Acidosis-Directed Signal Amplification in Tumor Microenvironment via Spatioselective Recruitment of DNA Amplifiers. Angew Chem Int Ed Engl 2022; 61:e202205436. [PMID: 35652128 DOI: 10.1002/anie.202205436] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Indexed: 12/29/2022]
Abstract
DNA biotechnology offers intriguing opportunities for amplification-based sensitive detection. However, spatiotemporally-controlled manipulation of signal amplification for in situ imaging of the tumor microenvironment remains an outstanding challenge. Here, we demonstrate a DNA-based strategy that can spatial-selectively amplify the acidic signal in the extracellular milieu of the tumor to achieve specific imaging with improved sensitivity. The strategy, termed mild acidosis-targeted amplification (MAT-amp), leverages the specific acidic microenvironment to engineer tumor cells with artificial DNA receptors through a pH (low) insertion peptide, which permits controlled recruitment of fluorescent amplifiers via a hybridization chain reaction. The acidosis-responsive amplification cascade enables significant fluorescence enhancement in tumors with a reduced background signal in normal tissues, leading to improved signal-to-background ratio. These results highlight the utility of MAT-amp for in situ imaging of the microenvironment characterized by pH disequilibrium.
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Affiliation(s)
- Zhenghan Di
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueguang Lu
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ana Jaklenec
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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27
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Zhang Y, Du XK, Liu WJ, Liu M, Zhang CY. Programmable Ligation-Transcription Circuit-Driven Cascade Amplification Machinery for Multiple Long Noncoding RNAs Detection in Lung Tissues. Anal Chem 2022; 94:10573-10578. [PMID: 35867839 DOI: 10.1021/acs.analchem.2c02685] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The measurement of long noncoding RNAs (lncRNAs) is essential to diagnosis and treatment of various diseases such as cancers. Herein, we develop a simple method to simultaneously detect multiple lncRNAs using programmable ligation-transcription circuit-driven cascade amplification and single-molecule counting. The presence of targets lncRNA HOTAIR and lncRNA MALAT1 activates the ligation-transcription circuits to produce two corresponding functional RNAs. The functional RNAs then cyclically initiate the digestion of signal probes by duplex-specific nuclease to liberate Cy5 and Cy3 molecules. After magnetic separation, the liberated Cy5 and Cy3 molecules are measured by single-molecule counting. In this assay, a single lncRNA can activate ligation-transcription circuit to generate abundant functional RNAs, endowing this assay with high sensitivity. Integration of single-molecule counting ensures the high sensitivity. This method shows extremely high sensitivity with a limit of detection (LOD) of 0.043 aM for HOX gene antisense intergenic RNA (lncRNA HOTAIR) and 0.126 aM for mammalian metastasis-related lung adenocarcinoma transcript 1 (lncRNA MALAT1). Importantly, this method enables simultaneous measurement of multiple endogenous lncRNAs at the single-cell level, and it may discriminate the expressions of various lncRNA in lung tumor tissues of nonsmall cell lung cancer (NSCLC) patients and their corresponding healthy adjacent tissues, offering a promising platform for clinical diagnosis and biomedical research.
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Affiliation(s)
- Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250200, China
| | - Xue-Ke Du
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Wen-Jing Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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28
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Programmable, Universal DNAzyme Amplifier Supporting Pancreatic Cancer-Related miRNAs Detection. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10070276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The abnormal expression of miRNA is closely related to the occurrence of pancreatic cancer. Herein, a programmable DNAzyme amplifier for the universal detection of pancreatic cancer-related miRNAs was proposed based on its programmability through the rational design of sequences. The fluorescence signal recovery of the DNAzyme amplifier showed a good linear relationship with the concentration of miR-10b in the range of 10–60 nM, with a detection limit of 893 pM. At the same time, this method displayed a high selectivity for miR-10b, with a remarkable discrimination of a single nucleotide difference. Furthermore, this method was also successfully used to detect miR-21 in the range of 10–60 nM based on the programmability of the DNA amplifier, exhibiting the universal application feasibility of this design. Overall, the proposed programmable DNAzyme cycle amplifier strategy shows promising potential for the simple, rapid, and universal detection of pancreatic cancer-related miRNAs, which is significant for improving the accuracy of pancreatic cancer diagnosis.
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29
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Zheng C, Hu X, Sun S, Zhu L, Wang N, Zhang J, Huang G, Wang Y, Huang X, Wang L, Shen Z. Hairpin allosteric molecular beacons-based cascaded amplification for effective detection of lung cancer-associated microRNA. Talanta 2022; 244:123412. [DOI: 10.1016/j.talanta.2022.123412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 02/07/2022] [Accepted: 03/25/2022] [Indexed: 12/25/2022]
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30
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Huang G, Zhou H, Xiang Q, Zhang J, Hu X, Cheng R, Lan L, Wang Y, Shen Z. Exponential and efficient target-catalyst rolling circle amplification for label-free and ultrasensitive fluorescent detection of miR-21 and p53 gene. Anal Chim Acta 2022; 1221:340132. [DOI: 10.1016/j.aca.2022.340132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/10/2022] [Accepted: 06/25/2022] [Indexed: 11/01/2022]
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31
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Wang L, Hast K, Aggarwal T, Baci M, Hong J, Izgu EC. MicroRNA detection in biologically relevant media using a split aptamer platform. Bioorg Med Chem 2022; 69:116909. [PMID: 35779513 DOI: 10.1016/j.bmc.2022.116909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/19/2022] [Accepted: 06/23/2022] [Indexed: 11/02/2022]
Abstract
MicroRNA (miRNA)-based intercellular communication has been implicated in many functional and dysfunctional biological processes. This has raised interest in the potential use of miRNAs as biomarkers for diagnosis and prognosis. Though the list of clinically significant miRNA biomarkers is expanding, it remains challenging to adapt current chemical tools to investigate miRNAs in complex environments native to cells and tissues. We describe here a methodology for rapidly developing aptamer-based fluorescent biosensors that can specifically detect miRNAs in biologically relevant media (10-30% v/v), including medium collected from cultured HeLa cells, human serum, and human plasma. This methodology involves the semi-rational design of the hybridization between DNA oligonucleotides and the miRNA target to build a pool of potential aptamers, and the screening of this pool for high signal-to-background ratio and target specificity. The DNA oligonucleotides are readily available and require no chemical modification, rendering these chemical tools highly adaptable to any novel and niche miRNA target. Following this approach, we developed sensors that detect distinct oncogenic miRNA targets (miR-19b, miR-21, and miR-92a) at concentrations as low as 5 nM without amplification and are selective against single-nucleotide mutants. This work provides a systematic approach toward the development of miRNA biosensors that are easily accessible and can perform in biological environments with minimal sample handling.
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Affiliation(s)
- Liming Wang
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Kern Hast
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Tushar Aggarwal
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Melih Baci
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Jonathan Hong
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA
| | - Enver Cagri Izgu
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ 08901, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ 08901, USA
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32
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Di Z, Lu X, Zhao J, Jaklenec A, Zhao Y, Langer R, Li L. Mild Acidosis‐Directed Signal Amplification in Tumor Microenvironment via Spatioselective Recruitment of DNA Amplifiers. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Zhenghan Di
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Beijing 100049 China
| | - Xueguang Lu
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- David H. Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Beijing 100049 China
| | - Ana Jaklenec
- David H. Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Beijing 100049 China
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33
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Mana T, Bhattacharya B, Lahiri H, Mukhopadhyay R. XNAs: A Troubleshooter for Nucleic Acid Sensing. ACS OMEGA 2022; 7:15296-15307. [PMID: 35571783 PMCID: PMC9096816 DOI: 10.1021/acsomega.2c00581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
The strategies for nucleic acid sensing based on nucleic acid hybridization between the target sequence and the capture probe sequence are considered to be largely successful as far as detection of a specific target of known sequence is concerned. However, when compared with other complementary methods, like direct sequencing, a number of results are still found to be either "false positives" or "false negatives". This suggests that modifications in these strategies are necessary to make them more accurate. In this minireview, we propose that one way toward improvement could be replacement of the DNA capture probes with the xeno nucleic acid or XNA capture probes. This is because the XNAs, especially the locked nucleic acid, the peptide nucleic acid, and the morpholino, have shown better single nucleobase mismatch discrimination capacity than the DNA capture probes, indicating their capacity for more precise detection of nucleic acid sequences, which is beneficial for detection of gene stretches having point mutations. Keeping the current trend in mind, this minireview will include the recent developments in nanoscale, fluorescent label-free applications, and present the cases where the XNA probes show clear advantages over the DNA probes.
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Affiliation(s)
- Tanushree Mana
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Budhaditya Bhattacharya
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Hiya Lahiri
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Rupa Mukhopadhyay
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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34
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Wang H, He Y, Wei J, Wang H, Ma K, Zhou Y, Liu X, Zhou X, Wang F. Construction of an Autocatalytic Hybridization Assembly Circuit for Amplified In Vivo MicroRNA Imaging. Angew Chem Int Ed Engl 2022; 61:e202115489. [PMID: 35076991 DOI: 10.1002/anie.202115489] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Indexed: 12/15/2022]
Abstract
Lowly expressed analyte in complex cytoplasmic milieu necessitates the development of non-enzymatic autocatalytic DNA circuits with high amplification and anti-interference performance. Herein, we engineered a versatile and robust stimuli-responsive autocatalytic hybridization assembly (AHA) circuit for high-performance in vivo bioanalysis. Under a moderately confined condition, the initiator motivated the autonomous and cooperative cross-activation of cascade hybridization reaction and catalytic DNA assembly for generating an exponentially amplified readout without the parasite steric hindrance and random diffusion side effects. The AHA circuit was systematically investigated by a series of experimental studies and theoretical simulations. The successively guaranteed target recognition and synergistically accelerated signal-amplification enabled the sensitive and selective detection of analyte, and realized the robust miRNA imaging in living cells and mice. This autocatalytic DNA circuit could substantially expand the toolbox for accurate diagnosis and programmable therapeutics.
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Affiliation(s)
- Huimin Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China.,College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Jie Wei
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Hong Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Kang Ma
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Yangjie Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
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35
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Miao P, Chai H, Tang Y. DNA Hairpins and Dumbbell-Wheel Transitions Amplified Walking Nanomachine for Ultrasensitive Nucleic Acid Detection. ACS NANO 2022; 16:4726-4733. [PMID: 35188755 DOI: 10.1021/acsnano.1c11582] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nucleic acids, including circulating tumor DNA (ctDNA), microRNA, and virus DNA/RNA, have been widely applied as potential disease biomarkers for early clinical diagnosis. In this study, we present a concept of DNA nanostructures transitions for the construction of DNA bipedal walking nanomachine, which integrates dual signal amplification for direct nucleic acid assay. DNA hairpins transition is developed to facilitate the generation of multiple target sequences; meanwhile, the subsequent DNA dumbbell-wheel transition is controlled to achieve the bipedal walker, which cleaves multiple tracks around electrode surface. Through combination of strand displacement reaction and digestion cycles, DNA monolayer at the electrode interface could be engineered and target-induced signal variation is realized. In addition, pH-assisted detachable intermolecular DNA triplex design is utilized for the regeneration of electrochemical biosensor. The high consistency between this work and standard quantitative polymerase chain reaction is validated. Moreover, the feasibilities of this biosensor to detect ctDNA and SARS-CoV-2 RNA in clinical samples are demonstrated with satisfactory accuracy and reliability. Therefore, the proposed approach has great potential applications for nucleic acid based clinical diagnostics.
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Affiliation(s)
- Peng Miao
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
| | - Hua Chai
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
| | - Yuguo Tang
- University of Science and Technology of China, Hefei 230026, China
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36
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Xue C, Niu H, Hu S, Yang Z, Wang L, Wu ZS. Visually predicting microRNA-regulated tumor metastasis by intracellularly 3D counting of fluorescent spots based on in situ growth of DNA flares. J Adv Res 2022; 43:73-85. [PMID: 36585116 PMCID: PMC9811323 DOI: 10.1016/j.jare.2022.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/02/2022] [Accepted: 03/01/2022] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION MicroRNAs (miRNAs) have been revealed to be critical genetic regulators in various physiological processes and thus quantitative information on the expression level of critical miRNAs has important implications for the initiation and development of human diseases, including cancers. OBJECTIVES We herein develop three-dimensionally (3D) counting of intracellular fluorescent spots for accurately evaluating microRNA-21 (miRNA-21) expression in individual HeLa cells based on stimuli-activated in situ growth of optical DNA flares, grid-patterned DNA-protein hybrids (GDPHs). METHODS Target miRNA is sequence-specifically detected down to 10 pM owing to efficient signal amplification. Within living cells, GDPH flares are nuclease resistant and discrete objects with retarded mobility, enabling the screening of intracellular location and distribution of miRNAs and realizing in situ counting of target species with a high accuracy. RESULTS The quantitative results of intracellular miRNAs by 3D fluorescence counts are consistent with qPCR gold standard assay, exhibiting the superiority over 2D counts. By screening the expression of intracellular miR-21 that can down-regulate the programmed cell death 4 (PDCD4) protein, the proliferation and migration of HeLa cells, including artificially-regulated ones, were well estimated, thus enabling the prediction of cancer metastasis in murine tumor models. CONCLUSION The experiments in vitro, ex vivo and in vivo demonstrate that GDPH-based 3D fluorescence counts at the single cell level provide a valuable molecular tool for understanding biological function of miRNAs and especially for recognizing aggressive CTCs, offering a design blueprint for further expansion of DNA structural nanotechnology in predicting distant metastasis and prevention of tumor recurrence after primary resection.
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Affiliation(s)
- Chang Xue
- 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 350108, China
| | - Huimin Niu
- 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 350108, China,Fujian Key Laboratory of Aptamers Technology, The 900 Hospital of Joint Logistics Support Force, Fuzhou 350025, China
| | - Shuyao Hu
- 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 350108, China
| | - Zhe Yang
- 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 350108, China
| | - Lei Wang
- 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 350108, China,Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - 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 350108, China,Corresponding author.
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37
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Pallu J, Rabin C, Hui P, Moreira TS, Creste G, Calvet C, Limoges B, Mavré F, Branca M. Exponential amplification by redox cross-catalysis and unmasking of doubly protected molecular probes. Chem Sci 2022; 13:2764-2777. [PMID: 35356676 PMCID: PMC8890127 DOI: 10.1039/d1sc06086d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/10/2022] [Indexed: 11/21/2022] Open
Abstract
The strength of autocatalytic reactions lies in their ability to provide a powerful means of molecular amplification, which can be very useful for improving the analytical performances of a multitude of analytical and bioanalytical methods. However, one of the major difficulties in designing an efficient autocatalytic amplification system is the requirement for reactants that are both highly reactive and chemically stable in order to avoid limitations imposed by undesirable background amplifications. In the present work, we devised a reaction network based on a redox cross-catalysis principle, in which two catalytic loops activate each other. The first loop, catalyzed by H2O2, involves the oxidative deprotection of a naphthylboronate ester probe into a redox-active naphthohydroquinone, which in turn catalyzes the production of H2O2 by redox cycling in the presence of a reducing enzyme/substrate couple. We present here a set of new molecular probes with improved reactivity and stability, resulting in particularly steep sigmoidal kinetic traces and enhanced discrimination between specific and nonspecific responses. This translates into the sensitive detection of H2O2 down to a few nM in less than 10 minutes or a redox cycling compound such as the 2-amino-3-chloro-1,4-naphthoquinone down to 50 pM in less than 30 minutes. The critical reason leading to these remarkably good performances is the extended stability stemming from the double masking of the naphthohydroquinone core by two boronate groups, a counterintuitive strategy if we consider the need for two equivalents of H2O2 for full deprotection. An in-depth study of the mechanism and dynamics of this complex reaction network is conducted in order to better understand, predict and optimize its functioning. From this investigation, the time response as well as detection limit are found to be highly dependent on pH, nature of the buffer, and concentration of the reducing enzyme. Reduction of the non-specific background in autocatalytic molecular amplifications by a double masking strategy.![]()
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Affiliation(s)
- Justine Pallu
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Charlie Rabin
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Pan Hui
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Thamires S Moreira
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Geordie Creste
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Corentin Calvet
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Benoît Limoges
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - François Mavré
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Mathieu Branca
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
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38
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Wang H, He Y, Wei J, Wang H, Ma K, Zhou Y, Liu X, Zhou X, Wang F. Construction of an Autocatalytic Hybridization Assembly Circuit for Amplified
In Vivo
MicroRNA Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Huimin Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
- College of Biological and Pharmaceutical Sciences China Three Gorges University 443002 Yichang P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jie Wei
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Hong Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Kang Ma
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Yangjie Zhou
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
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39
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Non-enzymatic detection of miR-21 in cancer cells using a homogeneous mix-and-read smart probe assay. Anal Biochem 2022; 645:114601. [PMID: 35182494 DOI: 10.1016/j.ab.2022.114601] [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: 10/12/2021] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022]
Abstract
We report a new assay system for the detection of miR-21 in cancer cells. The new assay works at room temperature and it does not involve enzymatic amplification. It consists a hairpin smart probe, designed to specifically recognize miR-21 target sequence. We tested the performance and sequence recognition capability of the smart probe to confirm desired specifications. We used the smart probe for the sequence-specific recognition of synthetic miR-21 oligonucleotides as well as mismatch sequences and we found that the probe recognizes the target sequence-specifically, while discriminating against mismatched sequences. We determined the limit of detection and limit of quantitation for the miR-21 oligonucleotides to be 1.72 nM and 5.78 nM, respectively, while the sensitivity is 6.90 × 1011 c.p.sM-1. More importantly, we showed that the smart probe-based method is also sensitive and selective for miR-21 when applied to crude extractions from MCF-7 cancer cell line at room temperature, with the results showing high fluorescence signals for the MCF-7 samples while showing much less signals for samples that did not contain miR-21. Thus, this new smart probe system constitutes a homogeneous, mix-and-read detection technique that can provide reliable diagnostics of miR-21 cancer biomarker at room temperature.
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40
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Wang X, Tang S, Ye S, Cheng Z, Xu J, Li BW, Chen Z. Ultrasensitive quantitation of circulating miR-195-5p with triple strand displacement amplification cascade. Talanta 2022; 242:123300. [PMID: 35180536 DOI: 10.1016/j.talanta.2022.123300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/31/2022] [Accepted: 02/05/2022] [Indexed: 01/14/2023]
Abstract
Circulating miR-195-5p has been proposed as a promising peripheral biomarker for the diagnosis, prognosis and severity assessment of various diseases. However, the demand for its sensitive and convenient quantification has not been met yet. Herein, we proposed a one-pot isothermal approach, in which the target signal acquisition, amplification and conversion (fluorescence read-out) system was integrated by a triple strand displacement amplification (SDA) cascade. Using this triple SDA strategy, miR-195-5p can be at least detected at 1 aM, and the linear dynamic range (from 100 aM to 1 pM) is wide enough to meet the detection needs of clinical miRNA level. A proof-of-principle study, using this novel methodology to directly analyze the spiking serum samples with different levels of miR-195-5p, demonstrated the potential of circulating miR-195-5p detection for clinical point-of-care assay. This one-pot isothermal triple SDA approach, we believe, will be a simple and feasible tool for ultrasensitive quantification of circulating miR-195-5p, and may promote the wide application of this potential biomarker in non-invasive clinical diagnosis.
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Affiliation(s)
- Xuzhi Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuzhi Tang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shengnan Ye
- Department of Otorhinolaryngology, Fujian Institute of Otorhinolaryngology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Zhou Cheng
- Breast Cancer Institute, Department of Breast Surgery, The Affiliated Union Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Jianhua Xu
- The School of Pharmacy, Fujian Medical University, Fuzhou, Fujian, 350004, China
| | - Bo-Wen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China.
| | - Zhuo Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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41
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Chen S, Zhao J, Sakharov IY, Xu J, Xu C, Zhao S. An ultrasensitive multivariate signal amplification strategy based on microchip platform tailored for simultaneous quantification of multiple microRNAs in single cell. Biosens Bioelectron 2022; 203:114053. [PMID: 35121443 DOI: 10.1016/j.bios.2022.114053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) play a very important regulatory role in life activities. Abnormal expression levels of miRNAs in cells are associated with various diseases, especially human cancer. Nevertheless, accurate detection of the copy numbers of various miRNA molecules in single cell is still a great challenge. In this study, an intracellular multivariate signal amplification strategy based on microchip platform was proposed, and an ultrasensitive single-cell analysis method was established for simultaneous quantification of absolute copy numbers of multiple miRNAs in a single cell. Using miRNA-21 and miRNA-141 as the analytical models of miRNAs, the detection limits of 1.0 and 2.0 fM were obtained. Based on the developed method, an analysis of 600 randomly acquired different types of cells was performed. The distribution of absolute copy numbers of miRNA-21 and miRNA-141 in six types of cells was obtained. It was found that the number of copies of miRNA-21 and miRNA-141 in different types of cancer cells showed different expression characteristics. The study results can help us more accurately understand cell-to-cell heterogeneity and the relationship between different miRNAs and different types of cancer at the single cell level.
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Affiliation(s)
- Shengyu Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin, 541004, China
| | - Jingjin Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin, 541004, China.
| | - Ivan Yu Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Jiayao Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin, 541004, China
| | - Chunhuan Xu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin, 541004, China
| | - Shulin Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Science, Guangxi Normal University, Guilin, 541004, China.
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42
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Xue C, Huang H, Wang L, Liao W, Jiang H, Wu ZS. Swelling of Serum-Stable DNA Nanoparticles upon Target-Induced Conformational Rearrangement of Sensing Probes for the Signal-On Detection of Cancer-Related Genes. Anal Chem 2022; 94:2749-2756. [PMID: 35099191 DOI: 10.1021/acs.analchem.1c03598] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nuclease-resistant assay probes are of significant importance for biochemical analysis and disease diagnosis. In this contribution, a reconfigurable lipidic moiety-attached DNA nanoparticle (LDN) is constructed from a cholesterol-conjugated multifunctional hairpin-type DNA probe (Chol-DP) by hydrophobicity-mediated self-assembly. The LDN holds high serum stability and displays a low false-positive signal even in a complex biological milieu. The hydrophobic cholesterol moiety enables the hydrophobicity-mediated assembly, while hydrophilic DNA sequence serves as a recognition element and a polymerization template. The initiator-activated strand displacement amplification (SDA) reaction can convert the hairpin-shaped probe into rigid double-stranded DNA (dsDNA), causing the conformational rearrangement-based LDN swelling that can be used to reliably and fluorescently signal the cancer-related p53 gene. The size increase and structural reconfiguration are confirmed by dynamic light scattering (DLS) analysis and confocal microscopy imaging, respectively. Target p53 is specifically detected down to 10 pM. The whole assay process involved only several simple mixing steps. Recovery test and blind test further confirm the feasibility of the use of the LDN for the detection of target DNA in a complex biological milieu, indicating a promising nanotool for biomedical applications.
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Affiliation(s)
- Chang Xue
- 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 350108, China
| | - Hong Huang
- 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 350108, China
| | - Lei Wang
- 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 350108, China.,Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Wenqiang Liao
- 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 350108, China
| | - Hao Jiang
- 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 350108, China
| | - 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 350108, China
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43
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Hypersensitive detection of transcription factors by multiple amplification strategy based on molecular beacon. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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44
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Xue C, Wang L, Huang H, Wang R, Yuan P, Wu ZS. Stimuli-Induced Upgrade of Nuclease-Resistant DNA Nanostructure Composed of a Single Molecular Beacon for Detecting Mutant Genes. ACS Sens 2021; 6:4029-4037. [PMID: 34731570 DOI: 10.1021/acssensors.1c01423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As a kind of cell-free DNA in the bloodstream liberated from tumor cells, circulating tumor DNAs (ctDNAs) have been recognized as promising biomarkers in the field of early cancer diagnosis. However, robust, sensitive, and accurate detection of ctDNA in serum remains extremely challenging, especially toward the mutant KRAS gene, one of the most frequently mutated genes. Although DNA oligonucleotides as emerging practical signaling materials have been developed as sensitive and accurate tools, some intrinsic defects need to be overcome, such as fragility in complex biological environments. In this work, on the basis of the hydrophilicity-promoted assembly, a core/shell DNA nanostructure (DNS-MB) probe is constructed from only one hairpin-shaped probe (cholesterol-modified palindromic molecular beacon, Chol-PMB) for the amplification detection of KRAS mutation in serum without the need for any auxiliary probe. Chol-PMB is designed to recognize target DNA and serve as a polymerization primer and template, and thus target species can initiate polymerization-based strand displacement amplification (SDA). Moreover, target DNA is able to induce further aggregation of DNS-MB particles due to the enzymatic cross-linking effect, leading to a structural upgrade. The DNS-MB probe exhibits a detection limit of 50 fM and a wide quantitative range (from 50 fM to 160 nM). In addition, single nucleotide polymorphisms can be discriminated, such as mutant KRAS G12D (KRAS-M), providing a desirable platform for screening ctDNAs. More excitingly, because the termini of DNA components are hidden inward from nuclease attack, DNS-MB circumvents a false-positive signal even in freshly sampled serum and is suitable for application in the complex biological milieu. As a proof of concept, the DNS-MB probe is expected to provide useful insight into the development of simple and degradation-resistant DNA probes for substantially amplified detection of ctDNAs in complex serum, showing potential applications in the field of early tumor diagnosis.
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Affiliation(s)
- Chang Xue
- College of Chemical Engineering, 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 350108, China
| | - Lei Wang
- College of Chemical Engineering, 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 350108, China
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Hong Huang
- College of Chemical Engineering, 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 350108, China
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Pei Yuan
- College of Chemical Engineering, 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 350108, China
| | - Zai-Sheng Wu
- College of Chemical Engineering, 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 350108, China
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Martinez-Dominguez MV, Zottel A, Šamec N, Jovčevska I, Dincer C, Kahlert UD, Nickel AC. Current Technologies for RNA-Directed Liquid Diagnostics. Cancers (Basel) 2021; 13:5060. [PMID: 34680210 PMCID: PMC8534233 DOI: 10.3390/cancers13205060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
There is unequivocal acceptance of the variety of enormous potential liquid nucleic acid-based diagnostics seems to offer. However, the existing controversies and the increased awareness of RNA-based techniques in society during the current global COVID-19 pandemic have made the readiness of liquid nucleic acid-based diagnostics for routine use a matter of concern. In this regard-and in the context of oncology-our review presented and discussed the status quo of RNA-based liquid diagnostics. We summarized the technical background of the available assays and benchmarked their applicability against each other. Herein, we compared the technology readiness level in the clinical context, economic aspects, implementation as part of routine point-of-care testing as well as performance power. Since the preventive care market is the most promising application sector, we also investigated whether the developments predominantly occur in the context of early disease detection or surveillance of therapy success. In addition, we provided a careful view on the current biotechnology investment activities in this sector to indicate the most attractive strategies for future economic success. Taken together, our review shall serve as a current reference, at the interplay of technology, clinical use and economic potential, to guide the interested readers in this rapid developing sector of precision medicine.
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Affiliation(s)
| | - Alja Zottel
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.); (I.J.)
| | - Neja Šamec
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.); (I.J.)
| | - Ivana Jovčevska
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.); (I.J.)
| | - Can Dincer
- FIT Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79110 Freiburg, Germany;
- Laboratory for Sensors, Department of Microsystems Engineering—IMTEK, University of Freiburg, 79110 Freiburg, Germany
| | - Ulf Dietrich Kahlert
- Clinic for Neurosurgery, Medical Faculty, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.V.M.-D.); (U.D.K.)
- Molecular and Experimental Surgery, Clinic of General-, Visceral-, Vascular-, and Transplant Surgery, University Hospital Magdeburg, 39120 Magdeburg, Germany
| | - Ann-Christin Nickel
- Clinic for Neurosurgery, Medical Faculty, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.V.M.-D.); (U.D.K.)
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Hong Q, Shen Y, Liu S, Zhang Y. Re-Examination of Plotting Analytical Response against Different Forms of Concentration. Anal Chem 2021; 93:11910-11914. [PMID: 34428023 DOI: 10.1021/acs.analchem.1c02683] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This perspective highlights the importance of examining the signal transformation mechanism before deciding to plot an analytical response against an appropriate form of concentration. Although sound in mathematical form and unprecedentedly successful in previous studies, the widely used linear and logarithmic fitting still have significant risks in concentration evaluation. Given the working principle of calibration curves, i.e., utilizing a limited number of experimental data points to predict the full-scale unknown data points, a reliable fitting should follow the signal transformation mechanism rather than merely the data statistics.
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Affiliation(s)
- Qing Hong
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, State Key Laboratory of Bioelectronics, School of Chemistry and Chemical Engineering, Medical School, Southeast University, Nanjing 211189, China
| | - Yanfei Shen
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, State Key Laboratory of Bioelectronics, School of Chemistry and Chemical Engineering, Medical School, Southeast University, Nanjing 211189, China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, State Key Laboratory of Bioelectronics, School of Chemistry and Chemical Engineering, Medical School, Southeast University, Nanjing 211189, China
| | - Yuanjian Zhang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, State Key Laboratory of Bioelectronics, School of Chemistry and Chemical Engineering, Medical School, Southeast University, Nanjing 211189, China
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Xue C, Luo M, Wang L, Li C, Hu S, Yu X, Yuan P, Wu ZS. Stimuli-Responsive Autonomous-Motion Molecular Machine for Sensitive Simultaneous Fluorescence Imaging of Intracellular MicroRNAs. Anal Chem 2021; 93:9869-9877. [PMID: 34232018 DOI: 10.1021/acs.analchem.1c01856] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNAzymes with enzymatic activity identified from random DNA pools by in vitro selection have recently attracted considerable attention. In this work, a DNAzyme-based autonomous-motion (AM) molecular machine is demonstrated for sensitive simultaneous imaging of different intracellular microRNAs (miRNAs). The AM molecular machine consists of two basic elements, one of which is a target-analogue-embedded double-stem hairpin substrate (TDHS) and the other is a locking-strand-silenced DNAzyme (LSDz). LSDz can be activated by target miRNA and catalytically cleave TDHS, generating Clv-TDHS and releasing free target analogue capable of triggering the next round of cleavage reaction. As such, the molecular machine can exert sustainable autonomous operation, producing an enhanced signal. Because the active target analogue comes from the machine itself and offers cyclical stimulation in a feedback manner, this target-induced autonomous cleavage circuit is termed a self-feedback circuit (SFC). The SFC-based molecular machine can be used to quantify miRNA-21 down to 10 pM without interference from nontarget miRNAs, indicating a substantial improvement in assay performance compared with its counterpart system without an SFC effect. Moreover, due to the enzyme-free process, the AM molecular machine is suitable for miRNA imaging in living cells, and the quantitative results are consistent with the gold standard PCR assay. More interestingly, the AM molecular machine can be used for the simultaneous fluorescence imaging of several intracellular miRNAs, enabling the accurate discrimination of cancerous cells (e.g., HeLa and MCF-7) from healthy cells. The SFC-based autonomous-motion machine is expected to be a promising tool for the research of molecular biology and early diagnosis of human diseases.
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Affiliation(s)
- Chang Xue
- College of Chemical Engineering, 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, 350108, China
| | - Mengxue Luo
- College of Chemical Engineering, 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, 350108, China
| | - Lei Wang
- College of Chemical Engineering, 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, 350108, China.,Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Congcong Li
- College of Chemical Engineering, 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, 350108, China
| | - Shuyao Hu
- College of Chemical Engineering, 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, 350108, China
| | - Xin Yu
- College of Chemical Engineering, 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, 350108, China
| | - Pei Yuan
- College of Chemical Engineering, 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, 350108, China
| | - Zai-Sheng Wu
- College of Chemical Engineering, 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, 350108, China
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Chen X, Deng Y, Cao G, Xiong Y, Huo D, Hou C. Ultra-sensitive MicroRNA-21 detection based on multiple cascaded strand displacement amplification and CRISPR/Cpf1 (MC-SDA/CRISPR/Cpf1). Chem Commun (Camb) 2021; 57:6129-6132. [PMID: 34038492 DOI: 10.1039/d1cc01938d] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
MicroRNA-21 (miR-21) has been considered as a potential biomarker for cancer diagnosis and prognosis due to its high expression in tumors. Here, an analytical method which integrates the multiple cascaded strand displacement amplification and CRISPR/Cpf1 (MC-SDA/CRISPR/Cpf1) was proposed to ultra-sensitively detect it.
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Affiliation(s)
- Xiaolong Chen
- 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, P. R. China.
| | - Yuanyi Deng
- 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, P. R. China.
| | - Gaihua Cao
- 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, P. R. China.
| | - Yifan Xiong
- 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, P. R. 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, P. R. China. and Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, P. R. 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, P. R. China. and Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, P. R. China
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49
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Wang D, Wang J. A sensitive and label-free electrochemical microRNA biosensor based on Polyamidoamine Dendrimer functionalized Polypyrrole nanowires hybrid. Mikrochim Acta 2021; 188:173. [PMID: 33893598 DOI: 10.1007/s00604-021-04824-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 04/06/2021] [Indexed: 01/09/2023]
Abstract
The potential of functionalized polypyrrole nanowires (PPyNWs) are demonstrated as a platform for lable-free miRNA detection using electrochemical impedance spectroscopy (EIS). MicroRNAs (miRNAs) detection methods and sensors are mainly challenged by very low concentrations in physiological samples and high similarity among family members. Herein, a sensitive and selective miRNA biosensor was constructed based on electrochemically synthesized PPyNWs, which were functionalized with polyamidoamine dendrimer (PAMAM) by an electro-oxidation method. The prepared PPyNWs/PAMAM hybrid combines the excellent electrical conductivity of conducting polymer PPyNWs with high surface to volume ratio of PAMAM. DNA probes were immobilized onto the PPyNWs/PAMAM hybrid for the construction of the miRNA biosensor. Using the sensitive EIS technique to monitor DNA/miRNA hybridization, the developed biosensor demonstrated excellent sensing performances, such as wide linear range (10-14 M-10-8 M) and low detection limit (0.34 × 10-14 M). Even more encouraging, the response sensitivity of the biosensor was 3.12 times higher than that of the bulk PPy-modified sensor, which proved that the microstructure of the PPy nanowires array can greatly improve the performance of the biosensor. An ultrasensitive and selective miRNA biosensor was constructed based on electrochemically synthesized polypyrrole nanowires array (PPyNWs), which were functionalized with polyamidoamine dendrimer (PAMAM) by an electro-oxidation method.
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Affiliation(s)
- Dongwei Wang
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Jiasheng Wang
- Qingdao Agricultural University, Qingdao, 266109, China.
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50
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Pu J, Liu M, Li H, Liao Z, Zhao W, Wang S, Zhang Y, Yu R. One-step enzyme-free detection of the miRNA let-7a via twin-stage signal amplification. Talanta 2021; 230:122158. [PMID: 33934803 DOI: 10.1016/j.talanta.2021.122158] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) play a significant role in diverse biological processes. The abnormal expression of miRNAs is related to the development of cancers and various diseases. It is of great importance to sensitively and accurately detect miRNAs for early disease diagnosis and treatment. Here, a new fluorescence strategy was initially proposed for the enzyme-free sensing of let-7a by combining the strand displacement reaction (SDR) with the hybridization chain reaction (HCR). The sensor was successfully applied to the detection of the let-7a gene with a wide linear range from 25 pM to 250 nM and a limit of detection (LOD) of 9.01 pM. The fluorescence intensity has a good linear relationship with the logarithm of the target concentration. In addition, the biosensor allowed for the highly sensitive detection of the target genes even in complex human serum samples. With simple operation yet improved detection capability for let-7a, the developed fluorescent biosensor thus shows great potential for early clinical diagnosis as well as biological research.
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Affiliation(s)
- Jiamei Pu
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Mingbin Liu
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Hongbo Li
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China.
| | | | - Weihua Zhao
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Suqin Wang
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Yun Zhang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, PR China.
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China.
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