1
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Liu J, Li X, Wu Y, Zhang X, Wang X, Yuan L, Zhao Y, Liu M. A multifunctional DNA tetrahedron for imaging, gene therapy, and chemotherapy-phototherapy combination: Binding affinity and anticancer activity. Int J Biol Macromol 2024; 280:135713. [PMID: 39293631 DOI: 10.1016/j.ijbiomac.2024.135713] [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: 03/06/2024] [Revised: 08/26/2024] [Accepted: 09/13/2024] [Indexed: 09/20/2024]
Abstract
Imaging, silencing cancer-related microRNA, and chemotherapy-phototherapy (CTPT) combination therapy are crucial for cancer diagnosis and drug resistance overcoming. In this study, we designed a multifunctional DNA tetrahedron (MB-MUC1-TD) for the targeted delivery of combined daunorubicin (DAU) + toluidine blue O (TBO). The detection limit of miRNA-21 was determined to be 0.91 nM. The intercalation of DAU and TBO into MB-MUC1-TD was proved by spectroscopic and calorimetric methods. The thermodynamic parameters for the interactions of DAU and/or TBO with MB-MUC1-TD confirmed high drug loading. The first addition of TBO in the ternary system achieved a higher loading of both drugs and a more stable complex structure. Deoxyribonuclease I (DNase I) accelerated the release of DAU and/or TBO loaded in MB-MUC1-TD. Confocal laser scanning microscope demonstrated that MB-MUC1-TD exhibited good imaging ability for miRNA-21 to accurately identify cancer cells, and DAU/TBO was predominantly distributed within the nucleus of cancer cells. In vitro cytotoxicity showed better gene therapy efficacy of MB on MCF-7 cells, better biocompatibility of loaded DAU and TBO on LO2 cells, and stronger synergistic cytotoxicity of DAU + TBO on MCF-7/ADR cells. This study may establish a theoretical foundation for co-loading CTPT combination drugs based on multifunctional DNA nanostructures.
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Affiliation(s)
- Jie Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Xinyu Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Yushu Wu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Xinpeng Zhang
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Xiangtai Wang
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Lixia Yuan
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Yanna Zhao
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Min Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China; School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China.
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2
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Song Y, Mao C, Zhang W, Deng D, Chen H, Sun P, Liu M, Feng C, Luo L. Catalytic hairpin assembly-based AIEgen/graphene oxide nanocomposite for fluorescence-enhanced and high-precision spatiotemporal imaging of microRNA in living cells. Biosens Bioelectron 2024; 259:116416. [PMID: 38797033 DOI: 10.1016/j.bios.2024.116416] [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: 04/02/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
The low abundance, heterogeneous expression, and temporal changes of miRNA in different cellular locations pose significant challenges for both the detection sensitivity of miRNA liquid biopsy and intracellular imaging. In this work, we report an intelligently assembled biosensor based on catalytic hairpin assembly (CHA) and aggregation-induced emission (AIE), named as catalytic hairpin aggregation-induced emission (CHAIE), for the ultrasensitive detection and intracellular imaging of miRNA-155. To achieve such goal, tetraphenylethylene-N3 (TPE-N3) is used as AIE luminogen (AIEgen), while graphene oxide is introduced to quench the fluorescence. When the target miRNA is present, CHA reaction is triggered, causing the AIEgen to self-assemble with the hairpin DNA. This will restrict the intramolecular rotation of the AIEgen and produce a strong AIE fluorescence. Interestingly, CHAIE does not require any enzyme or expensive thermal cycling equipment, and therefore provides a rapid detection. Under optimal conditions, the proposed biosensor can determine miRNA in the concentration range from 2 pM to 200 nM within 30 min, with the detection limit of 0.42 pM. The proposed CHAIE biosensor in this work offers a low background signal and high sensitivity, making it applicable for highly precise spatiotemporal imaging of target miRNA in living cells.
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Affiliation(s)
- Yuchen Song
- College of Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Changqing Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Wenjiao Zhang
- College of Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Dongmei Deng
- College of Sciences, Shanghai University, Shanghai, 200444, PR China.
| | - Huinan Chen
- College of Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Pei Sun
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Meiyin Liu
- College of Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China.
| | - Liqiang Luo
- College of Sciences, Shanghai University, Shanghai, 200444, PR China.
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3
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Zhu H, Chen S, Lan F, Li W, Ji T, Zhang L, Guo Y, Pan W, Luo S, Xie R. Sensitive electrochemical biosensor for rapid detection of sEV-miRNA based turbo-like localized catalytic hairpin assembly. Anal Chim Acta 2024; 1311:342704. [PMID: 38816166 DOI: 10.1016/j.aca.2024.342704] [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: 03/20/2024] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 06/01/2024]
Abstract
Small extracellular vesicle-associated microRNAs (sEV-miRNAs) have emerged as critical biomarkers for cancer diagnosis, yet the rapid detection of these low-abundance molecules in clinical samples remains a formidable challenge. Herein, a simple turbo-like localized catalytic hairpin assembly (TL-CHA) was proposed for sEV-miR-1246 measurement. This electrochemical sensor achieves dual localization through the ingeniously use of AuNPs and DNA nanowires, which provides rich sites for CHA cascade amplification, significantly enhancing the effective reaction and amplify the detection response. Leveraging this innovative design, this biosensor demonstrated the ability to detect sEV-miRNA at concentrations as low as 5.24 aM in a time frame of 30 min. The precision of the measurements was validated through reverse transcription quantitative polymerase chain reaction. Furthermore, the sensor was used for analyzing plasma samples from gastric cancer patients yielded AUC values of 0.973 for all stages and 0.945 for early stages. This demonstrates the sensor's robust performance in both the staging diagnosis and early screening of gastric cancer. Therefore, this platform has great potential for the clinical cancer diagnosis.
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Affiliation(s)
- Huiqin Zhu
- Department of Clinical Laboratory, YunFu People's Hospital, Yunfu, Guangdong, 527300, PR China; YunFu Key Laboratory of Brain Diseases Research, YunFu People's Hospital, Yunfu, 527300, PR China
| | - Siting Chen
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, PR China; Pathology Department, Affiliated Qingyuan Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong, 511518, PR China
| | - Fei Lan
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, PR China
| | - Wenbin Li
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, PR China
| | - Tingting Ji
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, PR China
| | - Lifeng Zhang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, PR China
| | - Yuhang Guo
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, PR China
| | - Weilun Pan
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, PR China.
| | - Shihua Luo
- Center for Clinical Laboratory Diagnosis and Research, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, PR China; Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi of Guangxi Higher Education Institutions, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, PR China.
| | - Rongzhang Xie
- Department of Clinical Laboratory, YunFu People's Hospital, Yunfu, Guangdong, 527300, PR China; YunFu Key Laboratory of Brain Diseases Research, YunFu People's Hospital, Yunfu, 527300, PR China.
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4
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Na H, Koo BI, Park JC, Lim J, Kim Y, Chung HJ, Nam YS. Live-Cell Imaging of MicroRNA Expression via Photoinduced Electron Transfer Controlled by Catalytic Hairpin Assembly. Adv Healthc Mater 2024:e2401483. [PMID: 38889395 DOI: 10.1002/adhm.202401483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/14/2024] [Indexed: 06/20/2024]
Abstract
MicroRNAs (miRNAs) serve as emerging biomarkers for a range of diseases, and their quantitative analysis draws increasing attention. Yet, current invasive methods limit continuous tracking within living cells. To overcome this, a nonenzymatic DNA-based nanoprobe is developed for dynamic, noninvasive miRNA tracking via live-cell imaging. This probe features a unique hairpin DNA structure with five guanines that act as internal quenchers, suppressing fluorescence from an attached fluorophore via photoinduced electron transfer. Target miRNA initiates toehold-mediated strand displacement, restoring, and amplifying the fluorescence signal. Additionally, by introducing a single mismatch to the hairpin DNA, the nanoprobe's sensitivity is significantly enhanced, lowering the detection limit to about 60 pM without compromising specificity. To optimize intracellular delivery for prolonged monitoring, the nanoprobe is encapsulated within multilamellar lipid nanovesicles, fluorescently labeled for dual-wavelength ratiometric analysis. The proposed nanoprobe demonstrates a significant advance in live-cell miRNA detection, promising enhanced in situ analysis for a better understanding of miRNAs' pathophysiological function.
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Affiliation(s)
- Hyebin Na
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Bon Il Koo
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jae Chul Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jiwoo Lim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Jung Chung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yoon Sung Nam
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
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5
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Wu Z, Zhao S. Three-Way Junction-Assisted Rolling Circle Amplification Integrated with trans-Cleavage of Cas12a for Sensitive and Reliable Detection of miRNA. Appl Biochem Biotechnol 2024; 196:3115-3125. [PMID: 37624508 DOI: 10.1007/s12010-023-04691-8] [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] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
MicroRNAs (miRNAs) serve a crucial role in numerous biological processes, such as acute pancreatitis development. Due to its low abundance and high similarity among homogeneous family members, sensitive and reliable detection of microRNA remains a formidable challenge. By combining the three-way junction-assisted rolling circle amplification (RCA) with the trans-cleavage of Cas12a, we propose a novel fluorescent technique for sensitive miRNA detection. In order to increase the amplification efficiency of RCA-based methods, catalytic hairpin amplification (CHA) is incorporated into the RCA process, playing the roles of specific target recognition and three-way junction formation. Consequently, the method demonstrated a six-orders-of-magnitude detection range and a LOD as low as 27 aM, making it a promising method for the early diagnosis of various diseases.
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Affiliation(s)
- Zhiquan Wu
- Emergency and Critical Care Center, The Third Affiliated Hospital of Chongqing Medical University, Chongqing City, 401120, China
| | - Shuqi Zhao
- Department of Hematology, The Third Affiliated Hospital of Chongqing Medical University, Shuanghu Branch Road, Yubei District, Chongqing City, 401120, China.
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6
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Bai Y, Xu P, Li S, Wang D, Zhang K, Zheng D, Yue D, Zhang G, He S, Li Y, Zou H, Deng Y. Signal amplification strategy of DNA self-assembled biosensor and typical applications in pathogenic microorganism detection. Talanta 2024; 272:125759. [PMID: 38350248 DOI: 10.1016/j.talanta.2024.125759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
Biosensors have emerged as ideal analytical devices for various bio-applications owing to their low cost, convenience, and portability, which offer great potential for improving global healthcare. DNA self-assembly techniques have been enriched with the development of innovative amplification strategies, such as dispersion-to-localization of catalytic hairpin assembly, and dumbbell hybridization chain reaction, which hold great significance for building biosensors capable of realizing sensitive, rapid and multiplexed detection of pathogenic microorganisms. Here, focusing primarily on the signal amplification strategies based on DNA self-assembly, we concisely summarized the strengths and weaknesses of diverse isothermal nucleic acid amplification techniques. Subsequently, both single-layer and cascade amplification strategies based on traditional catalytic hairpin assembly and hybridization chain reaction were critically explored. Furthermore, a comprehensive overview of the recent advances in DNA self-assembled biosensors for the detection of pathogenic microorganisms is presented to summarize methods for biorecognition and signal amplification. Finally, a brief discussion is provided about the current challenges and future directions of DNA self-assembled biosensors.
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Affiliation(s)
- Yuxin Bai
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Pingyao Xu
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Shi Li
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Kaijiong Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Dongming Zheng
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Daifan Yue
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Guiji Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Shuya He
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Yan Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China.
| | - Haimin Zou
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China.
| | - Yao Deng
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China.
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7
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Zhang L, Zhao H, Yang H, Su X. Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection. Biosens Bioelectron 2023; 239:115622. [PMID: 37611449 DOI: 10.1016/j.bios.2023.115622] [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: 05/29/2023] [Revised: 08/03/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
DNA-based enzyme-free signal amplification strategies are widely employed to detect biomarkers in low abundance. To enhance signal amplification, localized DNA reaction units which increases molecular collision probability is commonly utilized. However, the current understanding of the structure-function relationships in localized DNA signal amplification probes is limited, leading to unsatisfied performance. In this study, we introduced a coarse-grained molecular model to simulate the dynamic behavior of two DNA reaction units within a DNA enzyme-free signal amplification circuit called Localized Catalytic Hairpin Assembly (LCHA). We investigated the impact of localized distance and flexibility on reaction performance. The most efficient LCHA probe guided by simulation exhibits sensitivity 28 times greater that of free CHA, with a detection limit of miR-21 reaching 16 pM, while the least effective LCHA probe demonstrated a modest improvement of only 7 times. We successfully employed the optimized probe to differentiate cancer cells from normal cells based on their miR-21 expression levels, showcasing its quantification ability. By elucidating the mechanistic insights and structure-function relationship in our work, we aim to contribute valuable information that can save users' time and reduce costs when designing localized DNA probes. With a comprehensive understanding of how the localization affects probe performance, researchers can now make more informed and efficient decisions during the design process. This work would find broad applications of DNA nanotechnology in biosensing, biocomputing, and bionic robots.
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Affiliation(s)
- Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hongyang Zhao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huixiao Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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8
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Ma H, Chen L, Lv J, Yan X, Li Y, Xu G. The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology. Chem Commun (Camb) 2023; 59:10330-10342. [PMID: 37615403 DOI: 10.1039/d3cc02597g] [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: 08/25/2023]
Abstract
DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.
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Affiliation(s)
- Hongmin Ma
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Long Chen
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Jingnan Lv
- The Second Affiliated People's Hospital of Soochow University, Suzhou 215008, China
| | - Xiaoyu Yan
- Guang'an Vocational & Technical College, Sichuan 638000, China
| | - Yonghao Li
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Guoxin Xu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
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9
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Shao M, Guo Q. Sensitive analysis of miRNAs via primer exchange reaction integrated with hairpin catalytic reaction. Anal Biochem 2023; 672:115170. [PMID: 37127114 DOI: 10.1016/j.ab.2023.115170] [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: 03/06/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) can serve as potential biological targets for early screening, targeted therapy, and prognosis in ovarian cancer (OC). However, sensitive and reliable quantification and identification of miRNA remain a huge challenge. Herein, we proposed a simple and reliable approach for the ultra-sensitive detection of miRNA by integrating endonuclease-III (Exo-III) assisted signal recycle, primer exchange reaction (PER), and hairpin catalytic reaction (HCR). In this method, target miRNA specifically binds with toehold sequence to form a blunt 3' terminus in the detection probe (dumbbell probe) that can be recognized by Exo-III, and to initiate subsequent signal amplifications. Based on this, the approach is successfully utilized in detecting OC related miRNAs with high sensitivity (limit of detection for miRNA-211 was 13 aM) and stability. By simply changing the toehold sequence in detection probe, the established approach can be easily extended to other miRNA detection. We believe that the platform is robust in detecting OS related biomarkers and is promising in renovating cancer diagnostic tools.
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Affiliation(s)
- Meili Shao
- Department of Obstetrics, Northwest Women's and Children's Hospital, Xi'an, Shaanxi, 710061, China
| | - Qian Guo
- Xijing Hospital affiliated to Air Force Medical University, Xi'an, Shaanxi, 710032, China.
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10
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Fu X, Chen Z, Ma W, Zhang H, Mo W, Li J, Yang M. Entropy-driven dynamic self-assembled DNA dendrimers for colorimetric detection of African swine fever virus. Anal Bioanal Chem 2023; 415:1675-1685. [PMID: 36715708 DOI: 10.1007/s00216-023-04562-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/04/2023] [Accepted: 01/20/2023] [Indexed: 01/31/2023]
Abstract
Herein, we subtly engineered an amplified colorimetric biosensor for the cyclic detection of African swine fever virus DNA (ASFV-DNA), which associated the branched catalytic hairpin assembly (bCHA) amplification with G-quadruplex DNAzyme activity through triplex DNA formation. Firstly, a Y-shaped hairpin trimer was constructed for the dynamic self-assembly of DNA dendrimers. Then, in the presence of ASFV-DNA, the signal strand CP was opened, exposing the toehold regions, which would trigger the CHA cascade reaction between hairpin trimers. In the CHA cascade reaction, H1, H2, and H3 opened and bound in sequence, eventually forming the structure of DNA dendrimers. Subsequently, the obtained bCHA product was specifically recognized by the GGG repeat sequences of L1 and L2, then amplified by the synergistic effect of triplex DNA and the formation of asymmetric split G-quadruplex. Benefiting from the amplification properties of bCHA and the high peroxidase-like catalytic activity of asymmetrically split G-quadruplex DNAzymes, it could achieve effective colorimetric signal output in the presence of ASFV-DNA by means of triplex DNA formation. Under the optimal experimental conditions, this biosensor exhibited excellent sensitivity with a detection limit of 1.8 pM. Further, it was applied to the content detection of simulated samples of African swine fever, and the recoveries were 98.9 ~ 103.2%. This method has the advantages of simple operation, good selectivity, and high sensitivity, which is expected to be used for highly sensitive detection of actual samples of African swine fever virus.
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Affiliation(s)
- Xin Fu
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China.
| | - Zhoujie Chen
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Wenjie Ma
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - He Zhang
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China.
| | - Wenhao Mo
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Jinyan Li
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
| | - Mei Yang
- State Key Laboratory of Environmental Catalysis and Waste Recycling, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, 411104, China
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11
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Kou Q, Wang L, Zhang L, Ma L, Fu S, Su X. Simulation-Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2205191. [PMID: 36287076 DOI: 10.1002/smll.202205191] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/30/2022] [Indexed: 06/16/2023]
Abstract
DNA-based nanodevices equipped with localized modules have been promising probes for biomarker detection. Such devices heavily rely on the intramolecular hybridization reaction. However, there is a lack of mechanistic insights into this reaction that limits the sensing speed and sensitivity. A coarse-grained model is utilized to simulate the intramolecular hybridization of localized DNA circuits (LDCs) not only optimizing the performance, but also providing mechanistic insights into the hybridization reaction. The simulation guided-LDCs enable the detection of multiple biomarkers with high sensitivity and rapid speed showing good consistency with the simulation. Fluorescence assays demonstrate that the simulation-guided LDC shows an enhanced sensitivity up to 9.3 times higher than that of the same probes without localization. The detection limits of ATP, miRNA, and APE1 reach 0.14 mM, 0.68 pM, and 0.0074 U mL-1 , respectively. The selected LDC is operated in live cells with good success in simultaneously detecting the biomarkers and discriminating between cancer cells and normal cells. LDC is successfully applied to detect the biomarkers in cancer tissues from patients, allowing the discrimination of cancer/adjacent/normal tissues. This work herein presents a design workflow for DNA nanodevices holding great potential for expanding the applications of DNA nanotechnology in diagnostics and therapeutics.
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Affiliation(s)
- Qiaoni Kou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Lei Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Liang Ma
- Clinical Laboratory, China-Japan Friendship Hospital, Beijing, 100029, P. R. China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
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12
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Li G, Ge S, Niu P, Zhang J, Mao Y, Wang Y, Sun A. Simultaneous detection of circulating tumor DNAs using a SERS-based lateral flow assay biosensor for point-of-care diagnostics of head and neck cancer. BIOMEDICAL OPTICS EXPRESS 2022; 13:4102-4117. [PMID: 36032568 PMCID: PMC9408245 DOI: 10.1364/boe.463612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/17/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Circulating tumor DNA (ctDNA) has recently emerged as an ideal target for biomarker analytes. Thus, the development of rapid and ultrasensitive ctDNA detection methods is essential. In this study, a high-throughput surface-enhanced Raman scattering (SERS)-based lateral flow assay (LFA) strip is proposed. The aim of this method is to achieve accurate quantification of TP53 and PIK3CA E545K, two types of ctDNAs associated with head and neck squamous cell carcinoma (HNSCC), particularly for point-of-care testing (POCT). Raman reporters and hairpin DNAs are used to functionalize the Pd-Au core-shell nanorods (Pd-AuNRs), which serve as the SERS probes. During the detection process, the existence of targets could open the hairpins on the surface of Pd-AuNRs and trigger the first step of catalytic hairpin assembly (CHA) amplification. The next stage of CHA amplification is initiated by the hairpins prefixed on the test lines, generating numerous "hot spots" to enhance the SERS signal significantly. By the combination of high-performing SERS probes and a target-specific signal amplification strategy, TP53 and PIK3CA E545K are directly quantified in the range of 100 aM-1 nM, with the respective limits of detection (LOD) calculated as 33.1 aM and 20.0 aM in the PBS buffer and 37.8 aM and 23.1 aM in human serum, which are significantly lower than for traditional colorimetric LFA methods. The entire detection process is completed within 45 min, and the multichannel design realizes the parallel detection of multiple groups of samples. Moreover, the analytical performance is validated, including reproducibility, uniformity, and specificity. Finally, the SERS-LFA biosensor is employed to analyze the expression levels of TP53 and PIK3CA E545K in the serum of patients with HNSCC. The results are verified as consistent with those of qRT-PCR. Thus, the SERS-LFA biosensor can be considered as a noninvasive liquid biopsy assay for clinical cancer diagnosis.
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Affiliation(s)
- Guang Li
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225001, P. R., China
| | - Shengjie Ge
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225001, P. R., China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R., China
| | - Ping Niu
- Departments of Otolaryngology, Qingzhou People's Hospital, Qingzhou, 262500, P. R., China
| | - Jianyou Zhang
- Department of Anesthesiology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225001, P. R., China
| | - Yu Mao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R., China
| | - Youwei Wang
- Department of Neurosurgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225001, P. R., China
| | - Aidong Sun
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225001, P. R., China
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13
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Tian Z, Zhou C, Zhang C, Wu M, Duan Y, Li Y. Recent advances of catalytic hairpin assembly and its application in bioimaging and biomedicine. J Mater Chem B 2022; 10:5303-5322. [PMID: 35766024 DOI: 10.1039/d2tb00815g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic hairpin assembly (CHA) appears to be a particularly appealing nucleic acid circuit because of its powerful amplification capability, simple protocols, and enzyme-free and isothermal conditions, and can combine with various signal output modes for the biosensing of various analytes. Especially in the last five years, vast CHA related studies have sprung up. With the deep exploration of the CHA mechanism, some novel and excellent CHA strategies have been proposed; meanwhile the CHA cascade strategies with various amplification techniques further improve the analysis performance. Furthermore, diverse CHA based biosensors have been tactfully engineered and extensively employed in imaging applications in living cells and in vivo ascribed to its gentle reaction, efficient amplification and universality. Hence, we present a comprehensive and systematic summary of the progress in CHA and its application in bioimaging and biomedicine to date. At first, we introduced the mechanism and diversification of CHA in detail, including the newly developed CHA and its ingenious combination with a variety of other technologies. Concurrently, we summarized the latest application progress of different CHA strategies in bioimaging and biomedicine, highlighting the merits and drawbacks of representative approaches. Finally, we put forward some views on the challenges and prospects of CHA in bioimaging and biomedicine in the future.
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Affiliation(s)
- Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Chen Zhou
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Chuyan Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China.
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
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Lu X, Li D, Luo Z, Duan Y. A dual-functional fluorescent biosensor based on enzyme-involved catalytic hairpin assembly for the detection of APE1 and miRNA-21. Analyst 2022; 147:2834-2842. [PMID: 35621039 DOI: 10.1039/d2an00108j] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Both apurinic/apyrimidinic endonuclease 1 (APE1) and microRNA-21 (miRNA-21) have been reported to be related to tumors, enabling them to be the biomarkers of several cancers. This has led to the development of various biosensors to detect APE1 or miRNA-21. However, biosensors that focus on single target detection are subject to low accuracy. In this work, a fluorescent biosensor based on enzyme-involved catalytic hairpin assembly (CHA) for the detection of APE1 and miRNA-21 was developed, aimed at improving the accuracy of early-phase diagnosis of cancers. Two hairpin structured DNA probes (H1 and H2) were utilized to concatenate the enzyme-assisted circuit and CHA circuit in the system. The stem of H1 with a blunt end was modified with an AP site, while H2 was modified with 6-FAM at the 5' terminal and Dabcyl at the 3' terminal. In the presence of APE1, H1 was cleaved from the AP site to expose the toehold sequence. Then, miRNA-21 bound with the toehold sequence to initiate the CHA reaction between H1 and H2. The assembled product of CHA triggered the 6-FAM of H2 at a distance from Dabcyl, which recovered the fluorescence signal. It is worth noting that only under the co-stimulation of APE1 and miRNA-21 can the fluorescence signal be detected, indicating that the biosensor could work as an AND logic gate. The proposed dual-functional biosensor achieved a limit of detection (LOD) of 0.016 U mL-1 for APE1 and 0.25 nM for miRNA-21 and APE1, respectively, and also exhibits good selectivity and stability for the two biomarkers. Thus, the biosensor has great potential to be applied as a new platform for cancer diagnosis.
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Affiliation(s)
- Xiaoyong Lu
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P.R. China.
| | - Dan Li
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, Shaanxi, P.R. China.
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, Shaanxi, P.R. China.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-Resource and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P.R. China.
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15
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Sensitive detection of MiRNA and CircRNA through DSN enzyme cooperating NEase assisted dual signal amplification. Anal Biochem 2022; 654:114744. [DOI: 10.1016/j.ab.2022.114744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/16/2022] [Accepted: 05/18/2022] [Indexed: 11/23/2022]
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16
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Li J, Luo H. Nicking site enzyme assisted catalytic hairpin assembly based scaffold for sensitive monitoring of miRNA-21. Microchem J 2022. [DOI: 10.1016/j.microc.2021.107059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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17
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Catalytic hairpin assembly as cascade nucleic acid circuits for fluorescent biosensor: design, evolution and application. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Nie N, Tang W, Ding X, Guo X, Chen Y. DNAzyme based dual signal amplification strategy for ultrasensitive myocardial ischemia related MiRNA detection. Anal Biochem 2022; 640:114543. [PMID: 34973201 DOI: 10.1016/j.ab.2021.114543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 11/23/2022]
Abstract
Abnormal expression of microRNAs (miRNAs) is closely associated with a diverse of important biological processes, such as metastasis, myocardial ischemia and progression. Development of a facile and enzyme-free method for sensitive miRNA detection remains a huge challenge. Herein, we proposed a cross-catalytic circuit for trace miRNA detection by facilely integrating hairpin catalytic reaction (HCR) and DNAzyme biocatalyst through an ingenious feedback loop. The DNAzyme functional part was originally grafted in the designed hairpin structure probes, which would be released from hairpin structure probe and induce subsequent signal amplification after the recognition of target miRNA and the formation of double-strand DNA products. Through the dual signal amplification, the method exhibited a favorable detection sensitivity with a low of detection of 56 fM. These two indispensable catalytic reactions play vital roles in executing high-performance signal amplification, as demonstrated experimentally and theoretically.
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Affiliation(s)
- Na Nie
- Orthopedics Department, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, 401120, China
| | - Wei Tang
- Department of ICU, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, 401120, China
| | - Xinyue Ding
- Orthopedics Department, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, 401120, China
| | - Xiang Guo
- Orthopedics Department, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, 401120, China
| | - Yu Chen
- Department of ICU, The Third Affiliated Hospital of Chongqing Medical University (Gener Hospital), Chongqing, 401120, China.
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Zhang L, Wang M, Zhu Z, Chen S, Wu H, Yang Y, Che F, Li Q, Li H. A GD2-aptamer-mediated, self-assembling nanomedicine for targeted multiple treatments in neuroblastoma theranostics. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:732-748. [PMID: 34703655 PMCID: PMC8515170 DOI: 10.1016/j.omtn.2021.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023]
Abstract
Because current mainstream anti-glycolipid GD2 therapeutics for neuroblastoma (NB) have limitations, such as severe adverse effects, improved therapeutics are needed. In this study, we developed a GD2 aptamer (DB99) and constructed a GD2-aptamer-mediated multifunctional nanomedicine (ANM) with effective, precise, and biocompatible properties, which functioned both as chemotherapy and as gene therapy for NB. DB99 can bind to GD2+ NB tumor cells but has minimal cross-reactivity to GD2− cells. Furthermore, ANM is formulated by self-assembly of synthetic aptamers DB99 and NB-specific MYCN small interfering RNA (siRNA), followed by self-loading of the chemotherapeutic agent doxorubicin (Dox). ANM is capable of specifically recognizing, binding, and internalizing GD2+, but not GD2−, NB tumor cells in vitro. Intracellular delivery of ANM activates Dox release for chemotherapy and MYCN-siRNA-induced MYCN silencing. ANM specifically targets, and selectively accumulates in, the GD2+ tumor site in vivo and further induces growth inhibition of GD2+ tumors in vivo; in addition, ANM generates fewer or no side effects in healthy tissues, resulting in markedly longer survival with fewer adverse effects. These results suggest that the GD2-aptamer-mediated, targeted drug delivery system may have potential applications for precise treatment of NB.
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Affiliation(s)
- Liyu Zhang
- Department of Neonatology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China.,Shaanxi Institute of Pediatric Diseases, Affiliated Children's hospital of Xi'an Jiaotong University, Xi'an 710002, Shaanixi, China
| | - Meng Wang
- Department of Emergency Surgery, Shaanxi Provincial People's Hospital, Xi'an 710068, Shaanxi, China
| | - Zeen Zhu
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Shengquan Chen
- Department of Neonatology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Haibin Wu
- Shaanxi Institute of Pediatric Diseases, Affiliated Children's hospital of Xi'an Jiaotong University, Xi'an 710002, Shaanixi, China
| | - Ying Yang
- Shaanxi Institute of Pediatric Diseases, Affiliated Children's hospital of Xi'an Jiaotong University, Xi'an 710002, Shaanixi, China
| | - Fengyu Che
- Shaanxi Institute of Pediatric Diseases, Affiliated Children's hospital of Xi'an Jiaotong University, Xi'an 710002, Shaanixi, China
| | - Qiao Li
- Department of clinical laboratory, Affiliated Children's hospital of Xi'an Jiaotong University, Xi'an 710002, China
| | - Hui Li
- Department of Neonatology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China.,Department of Neonatology, Affiliated Children's hospital of Xi'an Jiaotong University, Xi'an 710002, China
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20
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Liu Q, Liu M, Jin Y, Li B. Rapid and enzyme-free signal amplification for fluorescent detection of microRNA via localized catalytic hairpin assembly on gold nanoparticles. Talanta 2021; 242:123142. [DOI: 10.1016/j.talanta.2021.123142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/08/2021] [Accepted: 12/11/2021] [Indexed: 12/17/2022]
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21
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Wang L, Dai X, Feng Y, Zhao Q, Liu L, Xue C, Xiao L, Wang R. Dual Catalytic Hairpin Assembly-Based Automatic Molecule Machine for Amplified Detection of Auxin Response Factor-Targeted MicroRNA-160. Molecules 2021; 26:molecules26216432. [PMID: 34770841 PMCID: PMC8588017 DOI: 10.3390/molecules26216432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
MicroRNA160 plays a crucial role in plant development by negatively regulating the auxin response factors (ARFs). In this manuscript, we design an automatic molecule machine (AMM) based on the dual catalytic hairpin assembly (D-CHA) strategy for the signal amplification detection of miRNA160. The detection system contains four hairpin-shaped DNA probes (HP1, HP2, HP3, and HP4). For HP1, the loop is designed to be complementary to miRNA160. A fragment of DNA with the same sequences as miRNA160 is separated into two pieces that are connected at the 3′ end of HP2 and 5′ end of HP3, respectively. In the presence of the target, four HPs are successively dissolved by the first catalytic hairpin assembly (CHA1), forming a four-way DNA junction (F-DJ) that enables the rearrangement of separated DNA fragments at the end of HP2 and HP3 and serving as an integrated target analogue for initiating the second CHA reaction, generating an enhanced fluorescence signal. Assay experiments demonstrate that D-CHA has a better performance compared with traditional CHA, achieving the detection limit as low as 10 pM for miRNA160 as deduced from its corresponding DNA surrogates. Moreover, non-target miRNAs, as well as single-base mutation targets, can be detected. Overall, the D-CHA strategy provides a competitive method for plant miRNAs detection.
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Affiliation(s)
- Lei Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (L.W.); (X.D.); (Y.F.); (Q.Z.)
| | - Xing Dai
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (L.W.); (X.D.); (Y.F.); (Q.Z.)
| | - Yujian Feng
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (L.W.); (X.D.); (Y.F.); (Q.Z.)
| | - Qiyang Zhao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (L.W.); (X.D.); (Y.F.); (Q.Z.)
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China;
| | - Chang Xue
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Correspondence: (C.X.); (L.X.); (R.W.)
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (L.W.); (X.D.); (Y.F.); (Q.Z.)
- Correspondence: (C.X.); (L.X.); (R.W.)
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (L.W.); (X.D.); (Y.F.); (Q.Z.)
- Correspondence: (C.X.); (L.X.); (R.W.)
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