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Yang H, Chen D, Zhang Y, Yuan P, Xie N, Dai Z. MiRNA and mRNA-Controlled Double-Cascaded Amplifying Circuit Nanosensor for Accurate Discrimination of Breast Cancers in Living Cells, Animals, and Organoids. Anal Chem 2024; 96:4154-4162. [PMID: 38426698 DOI: 10.1021/acs.analchem.3c05085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Metastasis is the leading cause of death in patients with breast cancer. Detecting high-risk breast cancer, including micrometastasis, at an early stage is vital for customizing the right and efficient therapies. In this study, we propose an enzyme-free isothermal cascade amplification-based DNA logic circuit in situ biomineralization nanosensor, HDNAzyme@ZIF-8, for simultaneous imaging of multidimensional biomarkers in live cells. Taking miR-21 and Ki-67 mRNA as the dual detection targets achieved sensitive logic operations and molecular recognition through the cascade hybridization chain reaction and DNAzyme. The HDNAzyme@ZIF-8 nanosensor has the ability to accurately differentiate breast cancer cells and their subtypes by comparing their relative fluorescence intensities. Of note, our nanosensor can also achieve visualization within breast cancer organoids, faithfully recapitulating the functional characteristics of parental tumor. Overall, the combination of these techniques offers a universal strategy for detecting cancers with high sensitivity and holds vast potential in clinical cancer diagnosis.
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Affiliation(s)
- Huihui Yang
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
| | - Dong Chen
- Department of Thyroid and Breast Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Yanfei Zhang
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Peixiu Yuan
- College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Ni Xie
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
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2
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Xia Y, Rao R, Xiong M, He B, Zheng B, Jia Y, Li Y, Yang Y. CRISPR-Powered Strategies for Amplification-Free Diagnostics of Infectious Diseases. Anal Chem 2024. [PMID: 38451204 DOI: 10.1021/acs.analchem.3c04363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Affiliation(s)
- Yupiao Xia
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruotong Rao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengqiu Xiong
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Bangshun He
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Bingxin Zheng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanwei Jia
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Hubei 430074, China
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3
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Li B, Ashrafizadeh M, Jiao T. Biomedical application of metal-organic frameworks (MOFs) in cancer therapy: Stimuli-responsive and biomimetic nanocomposites in targeted delivery, phototherapy and diagnosis. Int J Biol Macromol 2024; 260:129391. [PMID: 38242413 DOI: 10.1016/j.ijbiomac.2024.129391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
The nanotechnology is an interdisciplinary field that has become a hot topic in cancer therapy. Metal-organic frameworks (MOFs) are porous materials and hybrid composites consisted of organic linkers and metal cations. Despite the wide application of MOFs in other fields, the potential of MOFs for purpose of cancer therapy has been revealed by the recent studies. High surface area and porosity, significant drug loading and encapsulation efficiency are among the benefits of using MOFs in drug delivery. MOFs can deliver genes/drugs with selective targeting of tumor cells that can be achieved through functionalization with ligands. The photosensitizers and photo-responsive nanostructures including carbon dots and gold nanoparticles can be loaded in/on MOFs to cause phototherapy-mediated tumor ablation. The immunogenic cell death induction and increased infiltration of cytotoxic CD8+ and CD4+ T cells can be accelerated by MOF platforms in providing immunotherapy of tumor cells. The stimuli-responsive MOF platforms responsive to pH, redox, enzyme and ion can accelerate release of therapeutics in tumor site. Moreover, MOF nanocomposites can be modified ligands and green polymers to improve their selectivity and biocompatibility for cancer therapy. The application of MOFs for the detection of cancer-related biomarkers can participate in the early diagnosis of patients.
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Affiliation(s)
- Beixu Li
- School of Policing Studies, Shanghai University of Political Science and Law, Shanghai 201701, China; Shanghai Fenglin Forensic Center, Shanghai 200231, China; State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Department of Pathology, University of Maryland, Baltimore, MD 21201, USA
| | - Milad Ashrafizadeh
- Department of General Surgery, Institute of Precision Diagnosis and Treatment of Digestive System Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055, China; International Association for Diagnosis and Treatment of Cancer, Shenzhen, Guangdong 518055, China; Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250000, China.
| | - Taiwei Jiao
- Department of Gastroenterology and Endoscopy, The First Hospital of China Medical University, 155 North Nanjing St, Shenyang 110001, China.
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Liu B, Li Y, Du L, Zhang F, Liu Y, Sun J, Zhang Q, Li C, Li X, Xue Q. "One-to-many" signal-output strategy-based CRISPR/Cas12a system for sensitive label-free fluorescence detection of HBV-DNA. Spectrochim Acta A Mol Biomol Spectrosc 2024; 304:123338. [PMID: 37683439 DOI: 10.1016/j.saa.2023.123338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/22/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]
Abstract
Although CRISPR/Cas12a systems significantly enhance the analytical accuracy and flexibility of fluorescent biosensors, their sensitivity is limited by traditional "one-to-one" mediation types and ineffective signal-output turnover routes. Herein, we demonstrate a "one-to-many" signal-output strategy-based CRISPR/Cas12a systems resembling a "seaweed" to enhance the sensitivity. Based on dendrimer DNA from high-dimensional hybridization chain (HCR) of three hairpin-free DNA building blocks, the 3D magnetic DNA machine was created. The HBV-DNA initiates the rolling circle amplification (RCA) reaction and produces DNA nanowires to activate the CRISPR/Cas12a system. The trans-cleavage of the "seaweed root" by CRISPR/Cas12a system left dendrimer DNA in solution, thus, adding SYBR Green I (SG I) to the high-density DNA duplexes, achieving multiple-turnover label-free fluorescence signal output demonstrated and a low LOD (1.502 pM). However, in the absence of target, the blocked RCA failed to activate the CRISPR/Cas12a system, resulting in complete separation from substrate and negligible fluorescence signals. Moreover, the mandatory RCA-based pre-amplification of the DNA activator could efficiently trigger the multiple-turnover trans-cleavage activity of Cas12a. it can cleave one single-stranded linker of "seaweed-like" DNA machine, thereby releasing massive DNA duplex-enriched dendrimer DNA with a "one-to-many" signal-output turnover. By coupling the periodically extended Cas12a activator generated by RCA with hyperbranched DNA duplex by high-dimensional HCR, compact 3D extension structures were formed, achieving high-density fluorescence distribution in focal volume, avoiding signal dilution and ensuring high enhancement. Additionally, spiked recoveries in physiological media exceeded 95%, demonstrating the potential application of such platforms in clinical diagnosis.
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Affiliation(s)
- Bingxin Liu
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, PR China
| | - Yanli Li
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, PR China
| | - Lei Du
- Shandong Public Health Clinical Center, Shandong University, Jinan 250010, P. R. China
| | - Fengqi Zhang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, PR China
| | - Yeling Liu
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, PR China
| | - Jiuming Sun
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, PR China
| | - Qi Zhang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, PR China
| | - Chenzhong Li
- Biomedical Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Avenue, Longgang District, Shenzhen 518172, China
| | - Xia Li
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, PR China.
| | - Qingwang Xue
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, PR China.
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Li T, Cheng N. Sensitive and Portable Signal Readout Strategies Boost Point-of-Care CRISPR/Cas12a Biosensors. ACS Sens 2023; 8:3988-4007. [PMID: 37870387 DOI: 10.1021/acssensors.3c01338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Point-of-care (POC) detection is getting more and more attention in many fields due to its accuracy and on-site test property. The CRISPR/Cas12a system is endowed with excellent sensitivity, target identification specificity, and signal amplification ability in biosensing because of its unique trans-cleavage ability. As a result, a lot of research has been made to develop CRISPR/Cas12a-based biosensors. In this review, we focused on signal readout strategies and summarized recent sensitivity-improving strategies in fluorescence, colorimetric, and electrochemical signaling. Then we introduced novel portability-improving strategies based on lateral flow assays (LFAs), microfluidic chips, simplified instruments, and one-pot design. In the end, we also provide our outlook for the future development of CRISPR/Cas12a biosensors.
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Affiliation(s)
- Tong Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Nan Cheng
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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Dong JX, Zhang SM, Li YL, Zhang X, Fan YJ, Su M, Wang ZG, Li H, Shen SG, Gao ZF, Wei Q, Xia F. Photocontrollable DNA Walker-Based Molecular Circuit for the Tunable Detection of MicroRNA-21 Using Metal-Organic Frameworks as Label-Free Fluorescence Tags. Anal Chem 2023; 95:16744-16753. [PMID: 37929302 DOI: 10.1021/acs.analchem.3c03913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Tunable detection of microRNA is crucial to meet the desired demand for sample species with varying concentrations in clinical settings. Herein, we present a DNA walker-based molecular circuit for the detection of miRNA-21 (miR-21) with tunable dynamic ranges and sensitivity levels ranging from fM to pM. The phosphate-activated fluorescence of UiO-66-NH2 metal-organic framework nanoparticles was used as label-free fluorescence tags due to their competitive coordination effect with the Zr atom, which significantly inhibited the ligand-to-metal charge transfer. To achieve a tunable detection performance for miR-21, the ultraviolet sensitive o-nitrobenzyl was induced as a photocleavable linker, which was inserted at various sites between the loop and the stem of the hairpin probe to regulate the DNA strand displacement reaction. The dynamic range can be precisely regulated from 700- to 67,000-fold with tunable limits of detection ranging from 2.5 fM to 36.7 pM. Impressively, a Boolean logic tree and complex molecular circuit were constructed for logic computation and cancer diagnosis in clinical blood samples. This intelligent biosensing method presents a powerful solution for converting complex biosensing systems into actionable healthcare decisions and will facilitate early disease diagnosis.
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Affiliation(s)
- Jiang Xue Dong
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Materials Science, Hebei University, Baoding 071002, P. R. China
| | - Sai Mei Zhang
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Materials Science, Hebei University, Baoding 071002, P. R. China
| | - Yan Lei Li
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Xu Zhang
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Materials Science, Hebei University, Baoding 071002, P. R. China
| | - Ya Jie Fan
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Materials Science, Hebei University, Baoding 071002, P. R. China
| | - Ming Su
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Materials Science, Hebei University, Baoding 071002, P. R. China
| | - Zhen Guang Wang
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Materials Science, Hebei University, Baoding 071002, P. R. China
| | - Hui Li
- Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, School of Eco-Environment, Hebei University, Baoding 071002, P. R. China
| | - Shi Gang Shen
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Materials Science, Hebei University, Baoding 071002, P. R. China
| | - Zhong Feng Gao
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
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Wang C, Feng X, Shang S, Liu H, Song Z, Zhang H. Adsorption of methyl orange from aqueous solution with lignin-modified metal-organic frameworks: Selective adsorption and high adsorption capacity. Bioresour Technol 2023; 388:129781. [PMID: 37730139 DOI: 10.1016/j.biortech.2023.129781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
The lignin-based metal-organic framework (UIO-g-NL) was prepared by a Schiff base reaction of aminated lignin and the zirconium cluster-based MOF (UIO-66-NH2) as an adsorbent of methyl orange (MO). The results showed that UIO-g-NL maintained the original crystal structure and aminated lignin was successfully introduced after functionalization. UIO-g-NL selectively adsorbed MO from a mixed solution 50 mg/L MO and 50 mg/L methylene blue (MB), with an adsorption efficiency of nearly 100%. In a mixed solution 250 mg/L MB and 250 mg/L MO, UIO-g-NL adsorbed both dyes with 1120.70 mg/g for MB and 961.54 mg/g for MO. Hydrogen bonding, π-π and NH-π interactions, and electrostatic attraction contribute to the MO adsorption by UIO-g-NL. In the MO/MB mixture, MO adsorption by UIO-g-NL follows the pseudo-second-order kinetic and Freundlich isotherm models, which is an endothermic, spontaneous, and feasible adsorption process. Furthermore, the MO adsorption efficiency of UIO-g-NL remained high (>90%) after six re-use cycles.
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Affiliation(s)
- Chao Wang
- Institute of Chemical Industry of Forest Products, CAF, National Engineering Lab. for Biomass Chemical Utilization, Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, Key Lab. of Biomass Energy and Material, Jiangsu Province, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Xuezhen Feng
- Institute of Chemical Industry of Forest Products, CAF, National Engineering Lab. for Biomass Chemical Utilization, Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, Key Lab. of Biomass Energy and Material, Jiangsu Province, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Shibin Shang
- Institute of Chemical Industry of Forest Products, CAF, National Engineering Lab. for Biomass Chemical Utilization, Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, Key Lab. of Biomass Energy and Material, Jiangsu Province, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - He Liu
- Institute of Chemical Industry of Forest Products, CAF, National Engineering Lab. for Biomass Chemical Utilization, Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, Key Lab. of Biomass Energy and Material, Jiangsu Province, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Zhanqian Song
- Institute of Chemical Industry of Forest Products, CAF, National Engineering Lab. for Biomass Chemical Utilization, Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, Key Lab. of Biomass Energy and Material, Jiangsu Province, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Haibo Zhang
- Institute of Chemical Industry of Forest Products, CAF, National Engineering Lab. for Biomass Chemical Utilization, Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, Key Lab. of Biomass Energy and Material, Jiangsu Province, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China.
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Zhao J, He C, Long Y, Lei J, Liu H, Hou J, Hou C, Huo D. 3D DNAzyme walker based electrochemical biosensor for attomolar level microRNA-155 detection. Anal Chim Acta 2023; 1276:341642. [PMID: 37573120 DOI: 10.1016/j.aca.2023.341642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
Abstract
Herein, an ultrasensitive electrochemical biosensor for microRNA-155 (miR-155) detection based on the powerful catalytic and continuous walking signal amplification capability of 3D DNAzyme walker and the gold nanoparticles/graphene aerogels carbon fiber paper-based (AuNPs/GAs/CFP) flexible sensing electrode with excellent electrochemical performance was successfully constructed. In a proof-of-concept experiment, in the presence of miR-155, the DNAzyme strands anchored on the streptavidin-modified magnetic beads (MBs) silenced by locked strands can be activated, thus generating the walking arm of the 3D DNAzyme walker. Meanwhile, the substrate strands modified with Fe-MOF-NH2 nanoparticles were evenly distributed on the surface of MBs and served as tracks of the 3D DNAzyme walker. Once the DNAzyme strand was activated, the catalytic site in the substrate strand can be cleaved in the presence of Mn2+, and a large number of stumps modified with Fe-MOF-NH2 nanoparticles (output@Fe-MOF-NH2) will be generated during the continuous and efficient walking cleavage of the DNAzyme walker, driving the recognition-catalysis-release cycle process for signal amplification. Immediately afterwards, the signal was read out through the base complementary pairing of capture probe (PS) immobilized on the surface of the paper-based flexible sensing electrode AuNPs/GAs/CFP and signal probes output@Fe-MOF-NH2, thus achieving the quantitative detection of miR-155. Under optimal experimental conditions, the designed 3D DNAzyme walker-based biosensor exhibited a relatively lower limit of detection (LOD) of 56.23 aM, with a linear range of 100 aM to 100 nM. Overall, the proposed 3D DNAzyme walker biosensor exhibited good interference and reproducibility, demonstrating a promising future in the field of clinical disease diagnosis.
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Affiliation(s)
- Jiaying Zhao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Congjuan He
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Yanyi Long
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China
| | - Jincan Lei
- Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing, 401331, PR China
| | - Huan Liu
- Chongqing Institute for Food and Drug Control, Chongqing, 401121, PR China
| | - Jingzhou Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Postdoctoral Research Station, Chongqing University, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing, 401331, PR China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, 400044, PR China; Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing, 401331, PR China.
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9
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Wang H, Li YL, Fan YJ, Dong JX, Ren X, Ma H, Wu D, Gao ZF, Wei Q, Xia F. DNA Tile and Invading Stacking Primer-Assisted CRISPR-Cas12a Multiple Amplification System for Entropy-Driven Electrochemical Detection of MicroRNA with Tunable Sensitivity. Anal Chem 2023; 95:13659-13667. [PMID: 37623910 DOI: 10.1021/acs.analchem.3c02603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Conventional electrochemical detection of microRNA (miRNA) encounters issues of poor sensitivity and fixed dynamic range. Here, we report a DNA tile and invading stacking primer-assisted CRISPR-Cas12a multiple amplification strategy to construct an entropy-controlled electrochemical biosensor for the detection of miRNA with tunable sensitivity and dynamic range. To amplify the signal, a cascade amplification of the CRISPR-Cas12a system along with invading stacking primer signal amplification (ISPSA) was designed to detect trace amounts of miRNA-31 (miR-31). The target miR-31 could activate ISPSA and produce numerous DNAs, triggering the cleavage of the single-stranded linker probe (LP) that connects a methylene blue-labeled DNA tile with a DNA tetrahedron to form a Y-shaped DNA scaffold on the electrode. Based on the decrease of current, miR-31 can be accurately and efficiently detected. Impressively, by changing the loop length of the LP, it is possible to finely tune the entropic contribution while keeping the enthalpic contribution constant. This strategy has shown a tunable limit of detection for miRNA from 0.31 fM to 0.56 pM, as well as a dynamic range from ∼2200-fold to ∼270,000-fold. Moreover, it demonstrated satisfactory results in identifying cancer cells with a high expression of miR-31. Our strategy broadens the application of conventional electrochemical biosensing and provides a tunable strategy for detecting miRNAs at varying concentrations.
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Affiliation(s)
- Huan Wang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Nanxinzhuang West Road, Jinan 250022, P. R. China
| | - Yan Lei Li
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Nanxinzhuang West Road, Jinan 250022, P. R. China
| | - Ya Jie Fan
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Materials Science, Hebei University, Baoding 071002, P. R. China
| | - Jiang Xue Dong
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Materials Science, Hebei University, Baoding 071002, P. R. China
| | - Xiang Ren
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Nanxinzhuang West Road, Jinan 250022, P. R. China
| | - Hongmin Ma
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Nanxinzhuang West Road, Jinan 250022, P. R. China
| | - Dan Wu
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Nanxinzhuang West Road, Jinan 250022, P. R. China
| | - Zhong Feng Gao
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Nanxinzhuang West Road, Jinan 250022, P. R. China
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Nanxinzhuang West Road, Jinan 250022, P. R. China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, 388 Lumo Road, Wuhan 430074, P. R. China
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Ke X, Hu Y, Chen C, Hu T. A one-tube dual-readout biosensor for detection of nucleic acids and non-nucleic acids using CRISPR-ALP tandem assay. Analyst 2023; 148:4356-4364. [PMID: 37555739 DOI: 10.1039/d3an00918a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have been considered a next-generation molecular diagnosis tool. Single-readout mode has been extensively employed in massive CRISPR/Cas12a-based biosensors. In this work, we propose a one-tube dual-readout biosensor (CRISAT) for the first time for the detection of ultrasensitive nucleic acids and non-nucleic acids developed by harnessing CRISPR-ALP tandem assay. In the presence of a target, Cas12a is activated to randomly cut the single-stranded hyDNA sequence of MB@hyDNA-cALP, thus releasing abundant alkaline phosphatase (ALP) in the supernatant solution. By using 4-aminophenol phosphate as the substrate of ALP, p-aminophenol is produced, which then reacts with N-[3-(trimethoxysilyl)propyl]ethylenediamine or diethylenetriamine to generate silicon-containing polymer carbon dots (Si PCDs) or polymer carbon dots (PCDs) in situ, which can be observed by the naked eye or detected using a fluorescent device in the same solution. Using this strategy, a fluorescence and colorimetry dual-readout nanoplatform for CRISPR-based biosensors can be rationally developed. We ascertain the applicability of CRISAT by detecting the SARS-CoV-2 pseudovirus, achieving superior sensitivity and specificity. With simple modification of crRNAs, the CRISAT platform can also be employed to detect monkeypox virus (MPXV) and non-nucleic acids of adenosine triphosphate (ATP). This work shows great potential for the detection of nucleic acids and non-nucleic acids.
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Affiliation(s)
- Xinxin Ke
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China.
| | - Yi Hu
- Hefei National Lab for Physical Sciences at the Microscale and the Centers for Biomedical Engineering, University of Science and Technology of China, Hefei, 230027, China
| | - Chuanxia Chen
- School of Materials Science and Engineering, University of Jinan, Jinan, Shandong, 250022, China.
| | - Tao Hu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China.
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11
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Yu L, Wang Y, Sun Y, Tang Y, Xiao Y, Wu G, Peng S, Zhou X. Nanoporous Crystalline Materials for the Recognition and Applications of Nucleic Acids. Adv Mater 2023:e2305171. [PMID: 37616525 DOI: 10.1002/adma.202305171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Nucleic acid plays a crucial role in countless biological processes. Hence, there is great interest in its detection and analysis in various fields from chemistry, biology, to medicine. Nanoporous crystalline materials exhibit enormous potential as an effective platform for nucleic acid recognition and application. These materials have highly ordered and uniform pore structures, as well as adjustable surface chemistry and pore size, making them good carriers for nucleic acid extraction, detection, and delivery. In this review, the latest developments in nanoporous crystalline materials, including metal organic frameworks (MOFs), covalent organic frameworks (COFs), and supramolecular organic frameworks (SOFs) for nucleic acid recognition and applications are discussed. Different strategies for functionalizing these materials are explored to specifically identify nucleic acid targets. Their applications in selective separation and detection of nucleic acids are highlighted. They can also be used as DNA/RNA sensors, gene delivery agents, host DNAzymes, and in DNA-based computing. Other applications include catalysis, data storage, and biomimetics. The development of novel nanoporous crystalline materials with enhanced biocompatibility has opened up new avenues in the fields of nucleic acid analysis and therapy, paving the way for the development of sensitive, selective, and cost-effective diagnostic and therapeutic tools with widespread applications.
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Affiliation(s)
- Long Yu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yuhao Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuqing Sun
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongling Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuxiu Xiao
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Gaosong Wu
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Shuang Peng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
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Lu Z, Ni W, Liu N, Jin D, Li T, Li K, Zhang Y, Yao Q, Zhang GJ. CRISPR/Cas12a-based fluorescence biosensor for detection of exosomal miR-21 derived from lung cancer. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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