1
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Huang Q, Wang K, Wang Y. Highly sensitive miRNA-21 detection with enzyme-free cascade amplification biosensor. Talanta 2024; 273:125928. [PMID: 38508125 DOI: 10.1016/j.talanta.2024.125928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/17/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
In this study, we present an enzyme-free fluorescence biosensor for the highly sensitive detection of miRNA-21, a crucial biomarker in clinical diagnosis. Our innovative approach combines catalytic hairpin assembly (CHA) and entropy-driven amplification into a cascade amplification strategy. MicroRNA initiates the catalytic hairpin assembly reaction, liberating the trigger region needed for the entropy-driven amplification reaction. This triggers a series of strand displacement reactions, resulting in the separation of the fluorescence resonance energy transfer pair and an amplified fluorescence signal from FAM. Our cascade amplification strategy achieves ultra-sensitive microRNA detection, with an impressive limit of detection (LOD) of 1.3 fM, approximately 100-fold lower than CHA alone. Additionally, we successfully applied this biosensor for microRNA quantification in human serum and cell lysates, demonstrating its practicality and potential for early diagnosis.
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Affiliation(s)
- Qiuyan Huang
- School of Chemistry and Enviromental Engineering, Changchun University of Science and Technology, Changchun, 130022, China
| | - Kun Wang
- Department of Physics, New York University, New York, NY, 10003, USA
| | - Yuan Wang
- School of Chemistry and Enviromental Engineering, Changchun University of Science and Technology, Changchun, 130022, China.
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2
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DNA walker for signal amplification in living cells. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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3
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Zhang H, Yao S, Sheng R, Wang J, Li H, Fu Y, Li J, Zhang X, Zhao C. A cascade amplification strategy for ultrasensitive Salmonella typhimurium detection based on DNA walker coupling with CRISPR-Cas12a. J Colloid Interface Sci 2022; 625:257-263. [PMID: 35717841 DOI: 10.1016/j.jcis.2022.06.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 11/18/2022]
Abstract
Salmonella typhimurium (S. typhimurium) infection is one of leading causes of severe foodborne illness, which poses grievous threats to public health. Thus, the detection with ultra-sensitivity is highly demanded for timely prevention and diagnosis of S. typhimurium. In this study, we developed a novel detection machinery based on DNA walker and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas12a technologies. Mechanistically, the S. typhimurium specific sequence triggers Nt.AlwI nicking endonuclease and produces particular signaling nucleotide, which further activates Cas12a for strong fluorescence signal output. This cascade amplification strategy exhibits excellent specificity and successfully decreases the limit of detection (LOD) of DNA walker by 2,000 folds to 5 CFU/mL. Collectively, this combinatorial approach offers great promises to effectively reduce foodborne diseases by ultrasensitive detection of S. typhimurium. As a proof of concept, this innovative design also shows prominent potential in detections of other biomolecules, cells and pathogens.
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Affiliation(s)
- Haijiao Zhang
- College of Life and Health Science, Northeastern University, Shenyang 110819, PR China
| | - Shuo Yao
- School of Public Health, Jilin University, Changchun 130021, PR China
| | - Ren Sheng
- College of Life and Health Science, Northeastern University, Shenyang 110819, PR China; College of Sciences, Northeastern University, Shenyang 110004, PR China
| | - Juan Wang
- School of Public Health, Jilin University, Changchun 130021, PR China
| | - Hang Li
- School of Public Health, Jilin University, Changchun 130021, PR China
| | - Yanli Fu
- School of Public Health, Jilin University, Changchun 130021, PR China
| | - Juan Li
- School of Public Health, Jilin University, Changchun 130021, PR China
| | - Xi Zhang
- College of Sciences, Northeastern University, Shenyang 110004, PR China.
| | - Chao Zhao
- School of Public Health, Jilin University, Changchun 130021, PR China.
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4
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Zhao LD, Yang X, Zhong X, zhuo Y. Advances in Electrochemiluminescence Biosensors Based on DNA Walkers. Chempluschem 2022; 87:e202200070. [DOI: 10.1002/cplu.202200070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/19/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Li-Dan Zhao
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - Xia Yang
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - Xia Zhong
- Southwest University College of Chemistry and Chemical Engineering CHINA
| | - ying zhuo
- Southwest University College of Chemistry and Chemical Engineering No.2 Tiansheng RoadBeiBei District 400715 Chongqing CHINA
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5
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Xu M, Tang D. Recent advances in DNA walker machines and their applications coupled with signal amplification strategies: A critical review. Anal Chim Acta 2021; 1171:338523. [PMID: 34112433 DOI: 10.1016/j.aca.2021.338523] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 02/08/2023]
Abstract
DNA walkers, a type of dynamic nanomachines, have become the subject of burgeoning research in the field of biology. These walkers are powered by driving forces based on strand displacement reactions, protein enzyme/DNAzyme reactions and conformational transitions. With the unique properties of high directionality, flexibility and efficiency, DNA walkers move progressively and autonomously along multiple dimensional tracks, offering abundant and promising applications in biosensing, material assembly and synthesis, and early cancer diagnosis. Notably, DNA walkers identified as signal amplifiers can be combined with various amplification approaches to enhance signal transduction and amplify biosensor sensing signals. Herein, we systematically and comprehensively review the walking principles of various DNA walkers and the recent progress on multiple dimensional tracks by presenting representative examples and an insightful discussion. We also summarized and categorized the diverse signal amplification strategies with which DNA walkers have coupled. Finally, we outline the challenges and future trends of DNA walker machines in emerging analytical fields.
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Affiliation(s)
- Mingdi Xu
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou 350108, People's Republic of China; Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
| | - Dianping Tang
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
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6
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Wang W, Peng Y, Wu J, Zhang M, Li Q, Zhao Z, Liu M, Wang J, Cao G, Bai J, Gao Z. Ultrasensitive Detection of 17β-Estradiol (E2) Based on Multistep Isothermal Amplification. Anal Chem 2021; 93:4488-4496. [PMID: 33651609 DOI: 10.1021/acs.analchem.0c04681] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
17β-Estradiol (E2) can cause an adverse effect on the human endocrine system even at the nanomolar level. Measurements of very low levels of E2 remain a critical challenge due to insufficient sensitivity. In this study, a multistep isothermal amplification fluorescence strategy was constructed, which could realize the exponential amplification of target E2. Specifically, strand displacement reaction (SDA), rolling circle amplification (RCA), and multiprimed rolling circle amplification (MRCA) were combined in a series to quantify trace complementary strand of E2 (cDNA). The E2 aptamer and cDNA were hybridized and modified on the magnetic beads. E2 could bind to its aptamer and cause the release of the cDNA. Then, cDNA would combine with the template DNA, initiating the SDA-RCA-MRCA. The molecular beacons, possessing low background signal, whose fluorescence was quenched in the state of chain folding, could be specifically recognized by the long single-stranded DNA (L-ssDNA) generated by the multistep isothermal amplification triggered by cDNA, and then the fluorescence of the molecular beacons could be restored. Therefore, the E2 could be quantitatively detected by the recovery fluorescence intensity. The fluorescence value showed a good linear relationship with the concentration of E2 in the range of 0.001836-183.6 nM, and the limit of detection (LOD) was as low as 63.09 fM. In addition, the recovery rates of this method spiked in milk and water were 80.8-107.0%, respectively. This method has the advantage of multistep isothermal amplification to obtain abundant fluorescence signals, which may provide a new possibility for highly sensitive detection of other small-molecule targets.
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Affiliation(s)
- Weiya Wang
- Department of Public Health and Management, Binzhou Medical University, Yantai 264003, People's Republic of China.,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Jin Wu
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Man Zhang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Qiaofeng Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Zunquan Zhao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Mingzhu Liu
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Jiu Wang
- Department of Public Health and Management, Binzhou Medical University, Yantai 264003, People's Republic of China
| | - Gaofang Cao
- Department of Public Health and Management, Binzhou Medical University, Yantai 264003, People's Republic of China
| | - Jialei Bai
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
| | - Zhixian Gao
- Department of Public Health and Management, Binzhou Medical University, Yantai 264003, People's Republic of China.,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, People's Republic of China
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7
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Li Y, Luo Z, Zhang C, Sun R, Zhou C, Sun C. Entropy driven circuit as an emerging molecular tool for biological sensing: A review. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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8
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Zhao Z, Chen Z, Liu D, Wang L, Liu S. Fuel strand-powered self-propelled electrochemical DNA machine for enzyme-free and distinctly amplified detection of nucleic acid with tunable performance. Biosens Bioelectron 2021; 171:112706. [DOI: 10.1016/j.bios.2020.112706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/17/2020] [Accepted: 10/06/2020] [Indexed: 12/24/2022]
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9
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Mao J, Chen X, Xu H, Xu X. DNAzyme-driven DNA walker biosensor for amplified electrochemical detection of T4 polynucleotide kinase activity and inhibition. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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10
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Kala D, Gupta S, Nagraik R, Verma V, Thakur A, Kaushal A. Diagnosis of scrub typhus: recent advancements and challenges. 3 Biotech 2020; 10:396. [PMID: 32834918 PMCID: PMC7431554 DOI: 10.1007/s13205-020-02389-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023] Open
Abstract
Scrub typhus is a mite-borne, acute febrile illness caused by the bacterium Orientia tsutsugamushi. It is a re-emerging infectious disease of the tsutsugamushi triangle. Scrub typhus is transmitted through bites of contaminated chiggers (larval stage). Diagnosis of scrub typhus is challenging as its symptoms mimic with other acute febrile illnesses. Several methods are effectual for diagnosis of scrub typhus that includes enzyme-linked immunosorbent assay (ELISA), immunofluorescence assay (IFA), immunochromatographic test (ICT), Weil-Felix, polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP). Weil-Felix test was initially used for the diagnosis of scrub typhus in underdeveloped countries but not preferred due to a lack of both specificity and sensitivity. Other immuno-based methods like IFA and ELISA are most outrank for detection of scrub typhus due to their higher sensitivity and specificity, but not vigorous to lay bare the infection at early stages and need the convalescent sampling for verification of positive samples. On another deed, PCR based methods becoming acceptable over era due to its dexterity of early-stage diagnosis with higher specificity and sensitivity but lack its applicability in circumstances of scrub typhus due to the variegated genetic makeup of Orientia tsutsugamushi among its serotypes. The present review focused on various detection methods along with their advantages and disadvantages used in the diagnosis of scrub typhus. A comparison between available methods of diagnosis with challenges in the detection of scrub typhus is also summarized.
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Affiliation(s)
- Deepak Kala
- Amity Center of Nanotechnology, Amity University, Haryana, 122413 India
| | | | | | | | - Atul Thakur
- Amity Center of Nanotechnology, Amity University, Haryana, 122413 India
| | - Ankur Kaushal
- Amity Center of Nanotechnology, Amity University, Haryana, 122413 India
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11
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Hu Y, Wang Y, Yan J, Wen N, Xiong H, Cai S, He Q, Peng D, Liu Z, Liu Y. Dynamic DNA Assemblies in Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000557. [PMID: 32714763 PMCID: PMC7375253 DOI: 10.1002/advs.202000557] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/07/2020] [Indexed: 05/13/2023]
Abstract
Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer-aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli-triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.
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Affiliation(s)
- Yaqin Hu
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Ying Wang
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Jianhua Yan
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Nachuan Wen
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Hongjie Xiong
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Shundong Cai
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Qunye He
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Dongming Peng
- Department of Medicinal ChemistrySchool of PharmacyHunan University of Chinese MedicineChangshaHunan410013P. R. China
| | - Zhenbao Liu
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
- Molecular Imaging Research Center of Central South UniversityChangshaHunan410013P. R. China
| | - Yanfei Liu
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
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12
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Chen J, Luo Z, Sun C, Huang Z, Zhou C, Yin S, Duan Y, Li Y. Research progress of DNA walker and its recent applications in biosensor. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115626] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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13
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Fu Z, Lu YC, Lai JJ. Recent Advances in Biosensors for Nucleic Acid and Exosome Detection. Chonnam Med J 2019; 55:86-98. [PMID: 31161120 PMCID: PMC6536430 DOI: 10.4068/cmj.2019.55.2.86] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/19/2022] Open
Abstract
Biosensors are analytical devices for biomolecule detection that compromise three essential components: recognition moiety, transducer, and signal processor. The sensor converts biomolecule recognition to detectable signals, which has been applied in diverse fields such as clinical monitoring, in vitro diagnostics, food industry etc. Based on signal transduction mechanisms, biosensors can be categorized into three major types: optical biosensors, electrochemical biosensors, and mass-based biosensors. Recently, the need for faster, more sensitive detection of biomolecules has compeled researchers to develop various sensing techniques. In this review, the basic structure and sensing principles of biosensors are introduced. Additionally, the review discusses multiple recent works about nucleic acid and exosome sensing.
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Affiliation(s)
- Zirui Fu
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Yi-Cheng Lu
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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14
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Wang S, Ji Y, Fu H, Ju H, Lei J. A rolling circle amplification-assisted DNA walker triggered by multiple DNAzyme cores for highly sensitive electrochemical biosensing. Analyst 2019; 144:691-697. [DOI: 10.1039/c8an01892h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A DNA walker triggered by multiple DNAzyme cores was constructed with the assistance of rolling circle amplification for electrochemical biosensing.
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Affiliation(s)
- Sina Wang
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Yuhang Ji
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Haomin Fu
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- China
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15
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Wang K, Zhai FH, He MQ, Wang J, Yu YL, He RH. A simple enzyme-assisted cascade amplification strategy for ultrasensitive and label-free detection of DNA. Anal Bioanal Chem 2018; 411:4569-4576. [DOI: 10.1007/s00216-018-1422-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 02/07/2023]
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