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Zhang Y, Liu H, Nakagawa Y, Nagasaka Y, Ding T, Tang SY, Yalikun Y, Goda K, Li M. Enhanced CRISPR/Cas12a-based quantitative detection of nucleic acids using double emulsion droplets. Biosens Bioelectron 2024; 257:116339. [PMID: 38688231 DOI: 10.1016/j.bios.2024.116339] [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: 03/04/2024] [Revised: 04/05/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Pairing droplet microfluidics and CRISPR/Cas12a techniques creates a powerful solution for the detection and quantification of nucleic acids at the single-molecule level, due to its specificity, sensitivity, and simplicity. However, traditional water-in-oil (W/O) single emulsion (SE) droplets often present stability issues, affecting the accuracy and reproducibility of assay results. As an alternative, water-in-oil-in-water (W/O/W) double emulsion (DE) droplets offer superior stability and uniformity for droplet digital assays. Moreover, unlike SE droplets, DE droplets are compatible with commercially available flow cytometry instruments for high-throughput analysis. Despite these advantages, no study has demonstrated the use of DE droplets for CRISPR-based nucleic acid detection. In our study, we conducted a comparative analysis to assess the performance of SE and DE droplets in quantitative detection of human papillomavirus type 18 (HPV18) DNA based on CRISPR/Cas12a. We evaluated the stability of SEs and DEs by examining size variation, merging extent, and content interaction before and after incubation at different temperatures and time points. By integrating DE droplets with flow cytometry, we achieved high-throughput and high-accuracy CRISPR/Cas12a-based quantification of target HPV18 DNA. The DE platform, when paired with CRISPR/Cas12a and flow cytometry techniques, emerges as a reliable tool for absolute quantification of nucleic acid biomarkers.
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Affiliation(s)
- Yang Zhang
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia; School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Hangrui Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Yuta Nakagawa
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yuzuki Nagasaka
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tianben Ding
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Shi-Yang Tang
- School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK
| | - Yaxiaer Yalikun
- Division of Materials Science, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan; Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA; Institute of Technological Sciences, Wuhan University, Hubei, 430072, China
| | - Ming Li
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia; School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, NSW, 2052, Australia.
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2
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Song K, Hwang SJ, Jeon Y, Yoon Y. The Biomedical Applications of Biomolecule Integrated Biosensors for Cell Monitoring. Int J Mol Sci 2024; 25:6336. [PMID: 38928042 PMCID: PMC11204277 DOI: 10.3390/ijms25126336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Cell monitoring is essential for understanding the physiological conditions and cell abnormalities induced by various stimuli, such as stress factors, microbial invasion, and diseases. Currently, various techniques for detecting cell abnormalities and metabolites originating from specific cells are employed to obtain information on cells in terms of human health. Although the states of cells have traditionally been accessed using instrument-based analysis, this has been replaced by various sensor systems equipped with new materials and technologies. Various sensor systems have been developed for monitoring cells by recognizing biological markers such as proteins on cell surfaces, components on plasma membranes, secreted metabolites, and DNA sequences. Sensor systems are classified into subclasses, such as chemical sensors and biosensors, based on the components used to recognize the targets. In this review, we aim to outline the fundamental principles of sensor systems used for monitoring cells, encompassing both biosensors and chemical sensors. Specifically, we focus on biosensing systems in terms of the types of sensing and signal-transducing elements and introduce recent advancements and applications of biosensors. Finally, we address the present challenges in biosensor systems and the prospects that should be considered to enhance biosensor performance. Although this review covers the application of biosensors for monitoring cells, we believe that it can provide valuable insights for researchers and general readers interested in the advancements of biosensing and its further applications in biomedical fields.
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Affiliation(s)
| | | | | | - Youngdae Yoon
- Department of Environmental Health Science, Konkuk University, Seoul 05029, Republic of Korea; (K.S.); (S.-J.H.)
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3
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Shen Q, Song G, Lin H, Bai H, Huang Y, Lv F, Wang S. Sensing, Imaging, and Therapeutic Strategies Endowing by Conjugate Polymers for Precision Medicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2310032. [PMID: 38316396 DOI: 10.1002/adma.202310032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/29/2024] [Indexed: 02/07/2024]
Abstract
Conjugated polymers (CPs) have promising applications in biomedical fields, such as disease monitoring, real-time imaging diagnosis, and disease treatment. As a promising luminescent material with tunable emission, high brightness and excellent stability, CPs are widely used as fluorescent probes in biological detection and imaging. Rational molecular design and structural optimization have broadened absorption/emission range of CPs, which are more conductive for disease diagnosis and precision therapy. This review provides a comprehensive overview of recent advances in the application of CPs, aiming to elucidate their structural and functional relationships. The fluorescence properties of CPs and the mechanism of detection signal amplification are first discussed, followed by an elucidation of their emerging applications in biological detection. Subsequently, CPs-based imaging systems and therapeutic strategies are illustrated systematically. Finally, recent advancements in utilizing CPs as electroactive materials for bioelectronic devices are also investigated. Moreover, the challenges and outlooks of CPs for precision medicine are discussed. Through this systematic review, it is hoped to highlight the frontier progress of CPs and promote new breakthroughs in fundamental research and clinical transformation.
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Affiliation(s)
- Qi Shen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Gang Song
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongrui Lin
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Haotian Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yiming Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
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4
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Hussein Z, Nour MAY, Kozlova AV, Kolpashchikov DM, Komissarov AB, El-Deeb AA. DNAzyme Nanomachine with Fluorogenic Substrate Delivery Function: Advancing Sensitivity in Nucleic Acid Detection. Anal Chem 2023; 95:18667-18672. [PMID: 38079240 DOI: 10.1021/acs.analchem.3c04420] [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: 12/27/2023]
Abstract
We have developed a hook-equipped DNA nanomachine (HDNM) for the rapid detection of specific nucleic acid sequences without a preamplification step. HDNM efficiently unwinds RNA structures and improves the detection sensitivity. Compared to the hookless system, HDNM offers an 80-fold and 13-fold enhancement in DNA and RNA detection, respectively, reducing incubation time from 3 to 1 h.
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Affiliation(s)
- Zain Hussein
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Anastasia V Kozlova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816, United States
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32816, United States
- National Center for Forensic Science, University of Central Florida, Orlando, Florida 32816, United States
| | - Andrey B Komissarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russian Federation
| | - Ahmed A El-Deeb
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
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5
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Wu Z, Yu L, Shi W, Ma J. Argonaute protein-based nucleic acid detection technology. Front Microbiol 2023; 14:1255716. [PMID: 37744931 PMCID: PMC10515653 DOI: 10.3389/fmicb.2023.1255716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023] Open
Abstract
It is vital to diagnose pathogens quickly and effectively in the research and treatment of disease. Argonaute (Ago) proteins are recently discovered nucleases with nucleic acid shearing activity that exhibit specific recognition properties beyond CRISPR-Cas nucleases, which are highly researched but restricted PAM sequence recognition. Therefore, research on Ago protein-mediated nucleic acid detection technology has attracted significant attention from researchers in recent years. Using Ago proteins in developing nucleic acid detection platforms can enable efficient, convenient, and rapid nucleic acid detection and pathogen diagnosis, which is of great importance for human life and health and technological development. In this article, we introduce the structure and function of Argonaute proteins and discuss the latest advances in their use in nucleic acid detection.
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Affiliation(s)
- Zhiyun Wu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Li Yu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Institute of Stem Cell, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Weifeng Shi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Jinhong Ma
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
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6
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Wang HN, Vo-Dinh T. Cascade Amplified Plasmonics Molecular Biosensor for Sensitive Detection of Disease Biomarkers. BIOSENSORS 2023; 13:774. [PMID: 37622860 PMCID: PMC10452163 DOI: 10.3390/bios13080774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Recent advances in molecular technologies have provided various assay strategies for monitoring biomarkers, such as miRNAs for early detection of various diseases and cancers. However, there is still an urgent unmet need to develop practical and accurate miRNA analytical tools that could facilitate the incorporation of miRNA biomarkers into clinical practice and management. In this study, we demonstrate the feasibility of using a cascade amplification method, referred to as the "Cascade Amplification by Recycling Trigger Probe" (CARTP) strategy, to improve the detection sensitivity of the inverse Molecular Sentinel (iMS) nanobiosensor. The iMS nanobiosensor developed in our laboratory is a unique homogeneous multiplex bioassay technique based on surface-enhanced Raman scattering (SERS) detection, and was used to successfully detect miRNAs from clinical samples. The CARTP strategy based on the toehold-mediated strand displacement reaction is triggered by a linear DNA strand, called the "Recycling Trigger Probe" (RTP) strand, to amplify the iMS SERS signal. Herein, by using the CARTP strategy, we show a significantly improved detection sensitivity with the limit of detection (LOD) of 45 fM, which is 100-fold more sensitive than the non-amplified iMS assay used in our previous report. We envision that the further development and optimization of this strategy ultimately will allow multiplexed detection of miRNA biomarkers with ultra-high sensitivity for clinical translation and application.
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Affiliation(s)
- Hsin-Neng Wang
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC 27708, USA;
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Tuan Vo-Dinh
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC 27708, USA;
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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7
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Xie S, Zhu C, Yang L, Li H, Zhu H, Nie Z, Lei C. Programmable Proteolysis-Activated Transcription for Highly Sensitive Ratiometric Electrochemical Detection of Viral Protease. Anal Chem 2023. [PMID: 37410966 DOI: 10.1021/acs.analchem.3c01720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Viral proteases play a crucial role in viral infection and are regarded as promising targets for antiviral drug development. Consequently, biosensing methods that target viral proteases have contributed to the study of virus-related diseases. This work presents a ratiometric electrochemical sensor that enables highly sensitive detection of viral proteases through the integration of target proteolysis-activated in vitro transcription and the DNA-functionalized electrochemical interface. In particular, each viral protease-mediated proteolysis triggers the transcription of multiple RNA outputs, leading to amplified ratiometric signals on the electrochemical interface. Using the NS3/4A protease of the hepatitis C virus as a model, this method achieves robust and specific NS3/4A protease sensing with sub-femtomolar sensitivity. The feasibility of this sensor was demonstrated by monitoring NS3/4A protease activities in virus-infected cell samples with varying viral loads and post-infection times. This study provides a new approach to analyzing viral proteases and holds the potential for developing direct-acting antivirals and novel therapies for viral infections.
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Affiliation(s)
- Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Cong Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Lijuan Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Huiyi Li
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
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8
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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9
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Shang X, Yan Y, Li J, Zhou X, Xiang X, Huang R, Li X, Ma C, Nie X. A turn-on fluorescent strategy for alkaline phosphatase detection based on enzyme-assisted signal amplification. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 286:121939. [PMID: 36219964 DOI: 10.1016/j.saa.2022.121939] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/09/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
As a representative biochemical indicator, alkaline phosphatase (ALP) is of great importance in indicating and diagnosing clinical diseases. Herein, we developed a signal-on fluorescence sensing method for sensitive ALP activity detection based on the enzyme-assisted target recycling (EATR) technique. In this method, a two-step signal amplification process is designed. In the presence of ALP, the 3' phosphate group of an ss-DNA is removed explicitly by ALP, thus releasing free 3'-OH. Terminal deoxynucleotidyl transferase (TdT) can subsequently extend this substrate to generate poly(A) tails, converting the trace-level ALP information into multiple sequences and achieving the first-time amplification. A poly(T) Taqman probe labeled with FAM and BHQ1 provides the second one under the assistance of T7 exonuclease (T7 Exo) through alternate hybridization and degradation of ds-DNA regions. The previously quenched fluorescence is recovered due to the departure of FAM/BHQ1 during the cleavage of T7 Exo. Thus, taking advantage of template-free TdT-mediated polymerization and T7 Exo-based EATR, this strategy shows a sensitive LOD at 0.0074 U/L (S/N = 3) and a linear range of 0.01-8 U/L between ALP concentration and fluorescence intensity. To further verify the specificity and accuracy in practical application, we challenged it in a set of co-existing interference and biological environments and have gained satisfying results. The proposed method successfully quantified the ALP levels in clinical human serum samples, suggesting its applicability in practical application. Moreover, we have used this method to investigate the inhibition effects of Na3VO4. Above all, the proposed assay is sensitive, facile, and cost-effective for ALP determining, holding a promising perspective and excellent potential in clinical diagnosis and drug screening.
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Affiliation(s)
- Xueling Shang
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Ying Yan
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Jian Li
- Department of Blood Transfusion, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Xi Zhou
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Xinying Xiang
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Rong Huang
- Department of Blood Transfusion, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Xisheng Li
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Xinmin Nie
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha 410013, China; Hunan Engineering Technology Research Center of Optoelectronic Health Detection, Changsha 410013, China.
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Kim D, Lee J, Han J, Lim J, Lim EK, Kim E. A highly specific and flexible detection assay using collaborated actions of DNA-processing enzymes for identifying multiple gene expression signatures in breast cancer. Analyst 2023; 148:316-327. [PMID: 36484412 DOI: 10.1039/d2an01672a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most nucleic acid biosensors employ nucleic acid-processing enzymes to bind, degrade, splice, synthesize, and modify nucleic acids. Utilizing their unique substrate preference, binding mode, and catalytic activity is of great importance in designing nucleic acid biosensors. Combination with DNA-processing enzymes enables them to transform into a new generation of molecular diagnostics tools with enhanced selectivity and sensitivity and reduced reaction time. Here, we report an isothermal amplification strategy by coemploying a structure-specific endonuclease (flap endonuclease 1, FEN1) and a strand-displacing DNA polymerase (Bst DNA polymerase) to detect long RNA targets. This approach couples the FEN1-driven invasive cleavage reaction with toehold-mediated rolling circle amplification (iFEN-tRCA), enabling the highly selective and rapid detection of long RNA targets and offering a detection limit below 10 pM within 1 h. We used two targets, such as human epidermal growth factor receptor 2 (HER2, encoded by ERBB2) and dopamine- and cyclic AMP-regulated phosphoprotein (DARPP, encoded by PPP1R1B), associated with prognosis or response to anticancer therapy. We demonstrated the feasibility and quantitative capability of the iFEN-tRCA assay by assessing the expression of two RNA transcripts (ERBB2 and PPP1R1B) with total RNA extracts purified from human breast cancer cells. Therefore, we envision that the developed assay will provide a suitable prognostic and diagnostic tool for identifying appropriate patients for HER2-targeted therapy and predicting the clinical outcome and occurrence of metastasis relapse in breast cancer.
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Affiliation(s)
- Dain Kim
- Department of Bioengineering & Nano-bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon 22012, Republic of Korea.
| | - Jiyoung Lee
- Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Jueun Han
- Department of Chemistry, Incheon National University, Incheon 22012, Republic of Korea
| | - Jaewoo Lim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Eun-Kyung Lim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea. .,Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon 34113, Republic of Korea.,School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Eunjung Kim
- Department of Bioengineering & Nano-bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon 22012, Republic of Korea. .,Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
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11
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Ning Y, Wang X, Liu S, Li L, Lu F. A graphene-oxide-based aptasensor for fluorometric determination of chloramphenicol in milk and honey samples utilizing exonuclease III-assisted target recycling and Nb.BbvCI-powered DNA walker cascade amplification. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114449. [PMID: 38321668 DOI: 10.1016/j.ecoenv.2022.114449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2024]
Abstract
Herein, a graphene oxide (GO)-based fluorescence aptasensor was developed for the sensitive and selective detection of chloramphenicol (CAP), based on exonuclease III (Exo III)-assisted target recycling and Nb.BbvCI-driven DNA walker cascade amplification. Interactions between CAP, hairpin1(HP1), hairpin2 (HP2), and 3'-amino modified hairpin3 (HP3) labeled with carboxyfluorescein (FAM) and covalently coupled to GO enabled efficient CAP detection. CAP was quantitatively assayed by measuring fluorescence at excitation/emission wavelengths of 480/514 nm, resulting from the accumulation of released FAM. A good linear range of 1 fM to 1 nM and a limit of detection (LOD) of 0.875 fM (signal-to-noise (S/N)= 3) were achieved. This aptasensor can distinguish the CAP from interference antibiotics with good specificity and selectivity, even if the concentration of the interfering substance is ten-fold higher than the target concentration. Moreover, the developed fluorescence aptasensor was successfully applied for the detection of CAP in spiked milk and honey samples. Thus, this method is potentially applicable for assaying CAP in foods and provides a promising strategy for the development of fluorescence aptasensors for environmental sample analysis.
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Affiliation(s)
- Yi Ning
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, PR China
| | - Xiaoqi Wang
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, PR China
| | - Shiwu Liu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, PR China
| | - Ling Li
- Experimental Center of molecular biology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, PR China
| | - Fangguo Lu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, PR China.
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12
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Li X, Wang Y, Tang H, Yang B, Zhao Y, Wu P. Evaluation of the sequence-dependent relative activity of APE1 for optimal biosensing design. Biosens Bioelectron 2022; 214:114539. [DOI: 10.1016/j.bios.2022.114539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
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13
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Ratiometric fluorescent detection of miRNA-21 via pH-regulated adsorption of DNA on polymer dots and exonuclease III-assisted amplification. Anal Chim Acta 2022; 1232:340450. [DOI: 10.1016/j.aca.2022.340450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/12/2022] [Accepted: 09/25/2022] [Indexed: 11/01/2022]
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14
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Reed MA, Gerasimova YV. Single-tube isothermal label-free fluorescent sensor for pathogen detection based on genetic signatures. Front Chem 2022; 10:951279. [PMID: 36118306 PMCID: PMC9475119 DOI: 10.3389/fchem.2022.951279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
We report on a single-tube biosensor for real-time detection of bacterial pathogens with multiplex capabilities. The biosensor consists of two DNA probes, which bind to the complementary fragment of a bacterial RNA to form a three-way junction (3WJ) nucleic acid structure. One of the probes encodes a fluorescent light-up RNA aptamer under T7 promoter. It allows for generation of multiple aptamer copies due to elongation and transcription of the 3WJ structure in the presence of the complementary target. The aptamer coordinates and thereby enhances fluorescence of a cognate fluorogenic dye, allowing for fluorescent detection of the RNA target. Multiple aptamer copies can be produced from a single target-dependent 3WJ structure allowing for amplification and visual observation of the signal. The limit of detection depended on the assay time and was found to be 1.7 nM or 0.6 nM for 30-min or 60-min assay, respectively, when N-methylmesoporphyrin IX (NMM) was used as a fluorescent indicator. The sensor is excellent in analyzing folded RNA targets and differentiating between closely related sequences due to the multicomponent character of the target-interrogating probe. Response to unamplified samples of total bacterial RNA from Mycobacterium tuberculosis complex or Escherichia coli was observed with excellent selectivity within 30 min under isothermal conditions at 50°C in a one-tube one-step assay. Several bacterial species can be detected in multiplex by utilizing biosensors with the template strands encoding different light-up aptamers. The isothermal one-tube-one-step format of the assay and the possibility to monitor the signal visually makes it amenable to use in a point-of-care scenario.
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15
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Bioanalytical methods encompassing label-free and labeled tuberculosis aptasensors: A review. Anal Chim Acta 2022; 1234:340326. [DOI: 10.1016/j.aca.2022.340326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/12/2022] [Accepted: 08/24/2022] [Indexed: 11/22/2022]
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16
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Zheng C, Hu X, Sun S, Zhu L, Wang N, Zhang J, Huang G, Wang Y, Huang X, Wang L, Shen Z. Hairpin allosteric molecular beacons-based cascaded amplification for effective detection of lung cancer-associated microRNA. Talanta 2022; 244:123412. [DOI: 10.1016/j.talanta.2022.123412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 02/07/2022] [Accepted: 03/25/2022] [Indexed: 12/25/2022]
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17
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Wang X, Liu S, Xiao R, Hu J, Li L, Ning Y, Lu F. Graphene-oxide-based bioassay for the fluorometric determination of agrC gene transcription in methicillin-resistant Staphylococcus aureus that uses nicking-enzyme-assisted target recycling and a hybridization chain reaction. Talanta 2022; 250:123714. [PMID: 35779362 DOI: 10.1016/j.talanta.2022.123714] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/18/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022]
Abstract
Herein, we report the development of a graphene-oxide-based (GO-based) fluorescent bioassay for determining agrC gene transcription (mRNA) in methicillin-resistant Staphylococcus aureus (MRSA). The design is based on nicking-enzyme-assisted (Nb.BbvcI-assisted) target recycling amplification (NATR) and a hybridization chain reaction (HCR). The system consists of a helper probe (HP), a molecular beacon (MB) probe, four hairpins, and endonuclease Nb.BbvcI, which plays a role in target recycling and signal amplification. In the absence of the target, all of the carboxyfluorescein-labeled (FAM-labeled) hairpins are adsorbed through π-stacking interactions onto the surface of GO, resulting in FAM signal quenching. When the target is added, three nucleic acid chains hybridize together to form a triple complex that is recognized by Nb.BbvCI. The MB probe is then cleaved by Nb.BbvCI to generate an HP/target complex and two new DNA fragments; the former is hybridized to another MB probe and enters the next round of reaction. The two newly reproduced DNA fragments induce a HCR with the assistance of hairpins 1-4 to create double-stranded DNA (dsDNA) products. These dsDNA products are repelled by GO and generate strong fluorescence at excitation/emission wavelengths of 480/514 nm. Importantly, synergy between FAM and the dsDNA-SYBR Green I duplex structure led to significantly amplified fluorescence and enhanced sensitivity. The bioassay showed a detection limit of 7.5 fM toward the target and a good linearity in the 10 fM to 100 pM range. The developed method was applied to monitor biofilm formation and study the mechanism of drug action, with satisfactory results obtained.
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Affiliation(s)
- Xiaoqi Wang
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China
| | - Shiwu Liu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China
| | - Rong Xiao
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China
| | - Jue Hu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China
| | - Ling Li
- Experimental Center of Molecular Biology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China
| | - Yi Ning
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China.
| | - Fangguo Lu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, People's Republic of China.
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18
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Hu P, Dong Y, Yao C, Yang D. Construction of branched DNA-based nanostructures for diagnosis, therapeutics and protein engineering. Chem Asian J 2022; 17:e202200310. [PMID: 35468254 DOI: 10.1002/asia.202200310] [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: 03/26/2022] [Revised: 04/23/2022] [Indexed: 11/08/2022]
Abstract
Branched DNA with multibranch-like anisotropic topology serves as a promising and powerful building block in constructing multifunctional-integrated nanomaterials in a programmable and controllable manner. Recently, a series of branched DNA-based functional nanomaterials were developed by elaborate molecular design. In this review, we focused on the construction of branched DNA-based nanostructures for biological and biomedical applications. First, the molecular design and synthesis method of branched DNA monomer were briefly described. Then, the construction strategies of branched DNA-based nanostructures were categorially discussed, including target-triggered polymerization, enzymatic extension and hybrid assembly. Finally, the biological and biomedical applications including diagnosis, therapeutics and protein engineering were summarized. We envision that the review will contribute to the further development of branched DNA-based nanomaterials with great application potential in the field of biomedicine, thus building a new bridge between material chemistry and biomedicine.
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Affiliation(s)
- Pin Hu
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Yuhang Dong
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Chi Yao
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Dayong Yang
- Tianjin University, Chemistry Department, Room 328, Building 54, 300350, Tianjin, CHINA
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19
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Wang X, Xuan T, Huang W, Li X, Lai G. Endonuclease-driven DNA walking for constructing a novel colorimetric and electrochemical dual-mode biosensing method. Anal Chim Acta 2022; 1208:339835. [DOI: 10.1016/j.aca.2022.339835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022]
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20
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Liu L, Hong F, Liu H, Zhou X, Jiang S, Šulc P, Jiang JH, Yan H. A localized DNA finite-state machine with temporal resolution. SCIENCE ADVANCES 2022; 8:eabm9530. [PMID: 35333578 PMCID: PMC8956261 DOI: 10.1126/sciadv.abm9530] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/02/2022] [Indexed: 05/21/2023]
Abstract
The identity and timing of environmental stimulus play a pivotal role in living organisms in programming their signaling networks and developing specific phenotypes. The ability to unveil history-dependent signals will advance our understanding of temporally regulated biological processes. Here, we have developed a two-input, five-state DNA finite-state machine (FSM) to sense and record the temporally ordered inputs. The spatial organization of the processing units on DNA origami enables facile modulation of the energy landscape of DNA strand displacement reactions, allowing precise control of the reactions along predefined paths for different input orders. The use of spatial constraints brings about a simple, modular design for the FSM with a minimum set of orthogonal components and confers minimized leaky reactions and fast kinetics. The FSM demonstrates the capability of sensing the temporal orders of two microRNAs, highlighting its potential for temporally resolved biosensing and smart therapeutics.
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Affiliation(s)
- Lan Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Fan Hong
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Hao Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Xu Zhou
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Petr Šulc
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Corresponding author. (H.Y.); (J.-H.J.)
| | - Hao Yan
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Corresponding author. (H.Y.); (J.-H.J.)
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21
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Wu H, Ma X, Chu Y, Qi X, Zou B, Liu Y, Zhou G. Digital Nucleic Acid Signal Amplification Platform for Highly Sensitive DNA Mutation Analysis. Anal Chem 2022; 94:3858-3864. [PMID: 35212518 DOI: 10.1021/acs.analchem.1c04765] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Digital nucleic acid analysis technology has shown great application potential due to its excellent performance. However, most current digital nucleic acid detection methods are based on PCR or other template amplification strategies. Here, we present an alternative analysis platform based on digital nucleic acid signal amplification in droplets termed dNASA. Using a bead-based controllable extension bridged cascade signal amplification reaction, we achieved an ultralow background, high efficiency, and highly specific nucleic acid signal amplification analysis. As a "proof of concept", we demonstrated the feasibility of the proposed dNASA platform in single-base DNA mutation analysis using artificially synthesized samples. This platform provides innovative ideas for the field of digital nucleic acid analysis.
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Affiliation(s)
- Haiping Wu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, China Pharmaceutical University, Nanjing 210009, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yunlong Liu
- State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China
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22
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Park HJ, Jung C, Yoo TH. Development of one-step isothermal methods to detect RNAs using hairpin-loop signal converters and proximity proteolysis reaction. Biosens Bioelectron 2022; 197:113769. [PMID: 34773751 DOI: 10.1016/j.bios.2021.113769] [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: 08/27/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Ribonucleic acids (RNAs) provide valuable information for biological systems and act as important indicators of disease states. RNAs are diverse in size and structure, and various strategies have been proposed for the detection of nucleic acids; however, developing them into point-of-care (POC) tests has been challenging as most of them consist of complex time-consuming steps. Here, we propose a strategy to assay RNAs using a hairpin-loop (HP) converter and proximity proteolysis reaction (PPR). Interaction between the loop part of HP and its target exposes a single strand of nucleotides, which acts as the template for PPR. A pair of protease and zymogen-conjugated nucleic acids associates with the adjacent regions of the template, resulting in an enhanced proteolysis reaction between protease and zymogen. The activated zymogen then generates a color signal through the hydrolysis of a chromogenic substrate. The combination of HP converter and PPR allowed the same pair of protease- and zymogen-nucleic acids to be used for different RNAs. Guidelines were provided for designing HP converters based on computational analyses and experimental characterizations. This strategy using an HP converter and PPR has been successfully applied to develop simple isothermal methods for the detection of various RNAs, including several microRNAs and KRAS mRNA, in the picomolar range in 1 h. The simplicity of designing HP converters and the beneficial properties of PPR as POC tests would enable the development of novel methods to detect RNAs under low-resource conditions.
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Affiliation(s)
- Hyeon Ji Park
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea.
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23
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MUTO Y, ZAKO T. Signal-amplified Colorimetric Biosensors Using Gold Nanoparticles. BUNSEKI KAGAKU 2021. [DOI: 10.2116/bunsekikagaku.70.661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yu MUTO
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University
| | - Tamotsu ZAKO
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University
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24
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Qu H, Fan C, Chen M, Zhang X, Yan Q, Wang Y, Zhang S, Gong Z, Shi L, Li X, Liao Q, Xiang B, Zhou M, Guo C, Li G, Zeng Z, Wu X, Xiong W. Recent advances of fluorescent biosensors based on cyclic signal amplification technology in biomedical detection. J Nanobiotechnology 2021; 19:403. [PMID: 34863202 PMCID: PMC8645109 DOI: 10.1186/s12951-021-01149-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022] Open
Abstract
The cyclic signal amplification technology has been widely applied for the ultrasensitive detection of many important biomolecules, such as nucleic acids, proteins, enzymes, adenosine triphosphate (ATP), metal ions, exosome, etc. Due to their low content in the complex biological samples, traditional detection methods are insufficient to satisfy the requirements for monitoring those biomolecules. Therefore, effective and sensitive biosensors based on cyclic signal amplification technology are of great significance for the quick and simple diagnosis and treatment of diseases. Fluorescent biosensor based on cyclic signal amplification technology has become a research hotspot due to its simple operation, low cost, short time, high sensitivity and high specificity. This paper introduces several cyclic amplification methods, such as rolling circle amplification (RCA), strand displacement reactions (SDR) and enzyme-assisted amplification (EAA), and summarizes the research progress of using this technology in the detection of different biomolecules in recent years, in order to provide help for the research of more efficient and sensitive detection methods.
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Affiliation(s)
- Hongke Qu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Mingjian Chen
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Qijia Yan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.,Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shanshan Zhang
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lei Shi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiayu Li
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Bo Xiang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Xu Wu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
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25
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Low SS, Ji D, Chai WS, Liu J, Khoo KS, Salmanpour S, Karimi F, Deepanraj B, Show PL. Recent Progress in Nanomaterials Modified Electrochemical Biosensors for the Detection of MicroRNA. MICROMACHINES 2021; 12:mi12111409. [PMID: 34832823 PMCID: PMC8618943 DOI: 10.3390/mi12111409] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/07/2021] [Accepted: 11/15/2021] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are important non-coding, single-stranded RNAs possessing crucial regulating roles in human body. Therefore, miRNAs have received extensive attention from various disciplines as the aberrant expression of miRNAs are tightly related to different types of diseases. Furthermore, the exceptional stability of miRNAs has presented them as biomarker with high specificity and sensitivity. However, small size, high sequence similarity, low abundance of miRNAs impose difficulty in their detection. Hence, it is of utmost importance to develop accurate and sensitive method for miRNA biosensing. Electrochemical biosensors have been demonstrated as promising solution for miRNA detection as they are highly sensitive, facile, and low-cost with ease of miniaturization. The incorporation of nanomaterials to electrochemical biosensor offers excellent prospects for converting biological recognition events to electronic signal for the development of biosensing platform with desired sensing properties due to their unique properties. This review introduces the signal amplification strategies employed in miRNA electrochemical biosensor and presents the feasibility of different strategies. The recent advances in nanomaterial-based electrochemical biosensor for the detection of miRNA were also discussed and summarized based on different types of miRNAs, opening new approaches in biological analysis and early disease diagnosis. Lastly, the challenges and future prospects are discussed.
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Affiliation(s)
- Sze Shin Low
- Research Centre of Life Science and Healthcare, China Beacons Institute, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China;
| | - Daizong Ji
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China;
| | - Wai Siong Chai
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen 518055, China;
| | - Jingjing Liu
- College of Automation Engineering, Northeast Electric Power University, Jilin 132012, China
- Correspondence: (J.L.); (P.L.S.)
| | - Kuan Shiong Khoo
- Faculty of Applied Sciences, UCSI University, UCSI Heights, Cheras 56000, Malaysia;
| | - Sadegh Salmanpour
- Department of Chemistry, Sari Branch, Islamic Azad University, Sari 1931848161, Iran;
| | - Fatemeh Karimi
- Department of Chemical Engineering, Quchan University of Technology, Quchan 9477177870, Iran;
| | - Balakrishnan Deepanraj
- Department of Mechanical Engineering, Jyothi Engineering College, Thrissur 679531, India;
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Selangor 43500, Malaysia
- Correspondence: (J.L.); (P.L.S.)
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26
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Liu H, You Y, Zhu Y, Zheng H. Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5103-5119. [PMID: 34664562 DOI: 10.1039/d1ay01275d] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.
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Affiliation(s)
- Hongyu Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Yuhao You
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Youzhuo Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
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27
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Elumalai M, Ipatov A, Carvalho J, Guerreiro J, Prado M. Dual colorimetric strategy for specific DNA detection by nicking endonuclease-assisted gold nanoparticle signal amplification. Anal Bioanal Chem 2021; 414:5239-5253. [PMID: 34374833 DOI: 10.1007/s00216-021-03564-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/05/2021] [Accepted: 07/19/2021] [Indexed: 11/30/2022]
Abstract
The continuous spread of invasive alien species, as zebra mussel (Dreissena polymorpha), is a major global concern and it is urgent to stop it. Early stages of an invasion are crucial and challenging; however, detection tools based on environmental DNA analysis are promising alternatives. We present an alternative DNA target amplification strategy for signal enhancement followed by dual-mode colorimetric naked eye and optical smartphone analysis for the early detection of zebra mussel environmental DNA. Target amplification was designed based on the nicking endonuclease probe cleavage upon probe and complementary target hybridization. The cleaved/intact probe interacts with DNA-modified nanoparticles for colorimetric detection. We have demonstrated that enzyme amplification strategy enhanced 12-fold the sensitivity by naked eye detection, achieving a detection limit of ~8 nM (4.48×1010 copies) in controlled conditions, whereas target in complex environmental samples allowed the detection of 22.5 nM (1.26×1011 copies). Competitive assays also showed that the system can discriminate specific zebra mussel DNA sequences from other DNA sequences. Additionally, smartphone analysis for DNA quantification further improved the sensitivity of its detection by 130-fold, more than 2 orders of magnitude, when applied to environmental samples. The limit of detection to 0.17 nM (9.52×108 copies) is based on RGB coordinates, which is especially relevant to monitor early aggregation stages, being more accurate and reducing naked eye detection subjectivity. DNA extracted from zebra mussel meat, zebra mussel contaminated river water, and non-contaminated river water samples were successfully tested. Dual-mode colorimetric detection is useful in field analysis without the need for expensive laboratory equipment.
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Affiliation(s)
- Monisha Elumalai
- Food Quality and Safety Research Group Av. Mestre José Veiga s/n, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Andrey Ipatov
- Food Quality and Safety Research Group Av. Mestre José Veiga s/n, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Joana Carvalho
- Food Quality and Safety Research Group Av. Mestre José Veiga s/n, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Joana Guerreiro
- Food Quality and Safety Research Group Av. Mestre José Veiga s/n, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.
| | - Marta Prado
- Food Quality and Safety Research Group Av. Mestre José Veiga s/n, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
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28
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Wu H, Wang H, Wu J, Han G, Liu Y, Zou P. A novel fluorescent aptasensor based on exonuclease-assisted triple recycling amplification for sensitive and label-free detection of aflatoxin B1. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125584. [PMID: 33743380 DOI: 10.1016/j.jhazmat.2021.125584] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Aflatoxins are the most toxic type of mycotoxins, which may cause serious carcinogenesis, teratogenesis, and mutagenesis to humans and animals. In this work, we demonstrate a novel label-free fluorescent aptasensor based on exonuclease-assisted triple recycling amplification for the sensitive detection of aflatoxin B1 (AFB1). With the close cooperation of T7 exonuclease and three elaborately designed hairpin probes, the target AFB1 can perform three consecutive cycles of amplification reactions. In this process, each hairpin probe is fully utilized, and the target AFB1, the secondary target and the tertiary target are recycled, thereby achieving a high amplification. Interestingly and importantly, the secondary and tertiary targets generated by amplification are also excellent DNA template sequences for silver nanoclusters (AgNCs). In the presence of NaBH4 and AgNO3, a great number of DNA-AgNCs are synthesized, thereby producing a strong fluorescent signal. Under optimal conditions, the developed aptasensor exhibited high sensitivity to AFB1 with a low detection limit of 0.19 pg mL-1 and a wide dynamic range of 1 × 10-6-1 μg mL-1. In addition, the aptasensor also performed well in the determination of AFB1 in real samples.
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Affiliation(s)
- Hao Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
| | - Hongyong Wang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Jun Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Guoqing Han
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Yaling Liu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
| | - Pei Zou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China; Jiangsu Kanion Pharmaceutical CO. LTD, Lianyungang 222001, China; State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Lianyungang 222001, China.
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29
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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30
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Wu H, Wu J, Wang H, Liu Y, Han G, Zou P. Sensitive and label-free chemiluminescence detection of malathion using exonuclease-assisted dual signal amplification and G-quadruplex/hemin DNAzyme. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:124784. [PMID: 33450635 DOI: 10.1016/j.jhazmat.2020.124784] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Malathion is one of the most commonly used organophosphorus pesticides that can cause serious harm to the ecological environment and human health. Herein, we demonstrated a label-free chemiluminescent aptasensor for the sensitive detection of malathion based on exonuclease-assisted dual signal amplification and G-quadruplex/hemin DNAzyme. Upon the addition of malathion, the aptamer probe specifically bound to the target to form a complex malathion-S3, leaving a duplex S1-S2. The complex malathion-S3 was digested by exonuclease I and the target was released. The released target was recycled to perform exonuclease I-assisted signal amplification. Furthermore, after treatment with exonuclease III, the duplex S1-S2 was converted into the secondary target ST. The secondary target ST interacted with the hairpin H1 to form a complex H1-ST, which was further digested by exonuclease III and released the secondary target. The released secondary target was recycled to perform exonuclease III-assisted signal amplification. After complete amplification, large numbers of G-quadruplex/hemin DNAzymes were generated. Under the optimal experimental conditions, the prepared aptasensor showed an excellent linear response to malathion with a detection limit of 0.47 pM. The relative standard deviations were in the range of 4.2-6.9%. Moreover, the aptasensor was successfully applied to detect malathion in spiked food and traditional Chinese medicine samples.
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Affiliation(s)
- Hao Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
| | - Jun Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Hongyong Wang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Yaling Liu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Guoqing Han
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Pei Zou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China; Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China.
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31
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Hsiao JC, Buryska T, Kim E, Howes PD, deMello AJ. Tuning DNA-nanoparticle conjugate properties allows modulation of nuclease activity. NANOSCALE 2021; 13:4956-4970. [PMID: 33629698 DOI: 10.1039/d0nr08668a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Enzyme-nanoparticle interactions can give rise to a range of new phenomena, most notably significant enzymatic rate enhancement. Accordingly, the careful study and optimization of such systems is likely to give rise to advanced biosensing applications. Herein, we report a systematic study of the interactions between nuclease enzymes and oligonucleotide-coated gold nanoparticles (spherical nucleic acids, SNAs), with the aim of revealing phenomena worthy of evolution into functional nanosystems. Specifically, we study two nucleases, an exonuclease (ExoIII) and an endonuclease (Nt.BspQI), via fluorescence-based kinetic experiments, varying parameters including enzyme and substrate concentrations, and nanoparticle size and surface coverage in non-recycling and a recycling formats. We demonstrate the tuning of nuclease activity by SNA characteristics and show that the modular units of SNAs can be leveraged to either accelerate or suppress nuclease kinetics. Additionally, we observe that the enzymes are capable of cleaving restriction sites buried deep in the oligonucleotide surface layer and that enzymatic rate enhancement occurs in the target recycling format but not in the non-recycling format. Furthermore, we demonstrate a new SNA phenomenon, we term 'target stacking', whereby nucleic acid hybridization efficiency increases as enzyme cleavage proceeds during the beginning of a reaction. This investigation provides important data to guide the design of novel SNAs in biosensing and in vitro diagnostic applications.
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Affiliation(s)
- Jeff C Hsiao
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
| | - Tomas Buryska
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
| | - Eunjung Kim
- Division of Bioengineering and Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Philip D Howes
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
| | - Andrew J deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
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32
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Liu L, Deng D, Wu D, Hou W, Wang L, Li N, Sun Z. Duplex-specific nuclease-based electrochemical biosensor for the detection of microRNAs by conversion of homogeneous assay into surface-tethered electrochemical analysis. Anal Chim Acta 2021; 1149:338199. [DOI: 10.1016/j.aca.2021.338199] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 02/07/2023]
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33
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Zhang Y, Zhu Y, Zeng Z, Zeng G, Xiao R, Wang Y, Hu Y, Tang L, Feng C. Sensors for the environmental pollutant detection: Are we already there? Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213681] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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34
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Liu M, Li H, Jia Y, Mak PI, Martins RP. SARS-CoV-2 RNA Detection with Duplex-Specific Nuclease Signal Amplification. MICROMACHINES 2021; 12:197. [PMID: 33672890 PMCID: PMC7918681 DOI: 10.3390/mi12020197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/23/2022]
Abstract
The emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a zoonotic pathogen, has led to the outbreak of coronavirus disease 2019 (COVID-19) pandemic and brought serious threats to public health worldwide. The gold standard method for SARS-CoV-2 detection requires both reverse transcription (RT) of the virus RNA to cDNA and then polymerase chain reaction (PCR) for the cDNA amplification, which involves multiple enzymes, multiple reactions and a complicated assay optimization process. Here, we developed a duplex-specific nuclease (DSN)-based signal amplification method for SARS-CoV-2 detection directly from the virus RNA utilizing two specific DNA probes. These specific DNA probes can hybridize to the target RNA at different locations in the nucleocapsid protein gene (N gene) of SARS-CoV-2 to form a DNA/RNA heteroduplex. DSN cleaves the DNA probe to release fluorescence, while leaving the RNA strand intact to be bound to another available probe molecule for further cleavage and fluorescent signal amplification. The optimized DSN amount, incubation temperature and incubation time were investigated in this work. Proof-of-principle SARS-CoV-2 detection was demonstrated with a detection sensitivity of 500 pM virus RNA. This simple, rapid, and direct RNA detection method is expected to provide a complementary method for the detection of viruses mutated at the PCR primer-binding regions for a more precise detection.
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Affiliation(s)
- Meiqing Liu
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China; (M.L.); (H.L.); (P.-I.M.); (R.P.M.)
| | - Haoran Li
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China; (M.L.); (H.L.); (P.-I.M.); (R.P.M.)
- Faculty of Science and Technology–ECE, University of Macau, Macau 999078, China
| | - Yanwei Jia
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China; (M.L.); (H.L.); (P.-I.M.); (R.P.M.)
- Faculty of Science and Technology–ECE, University of Macau, Macau 999078, China
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China; (M.L.); (H.L.); (P.-I.M.); (R.P.M.)
- Faculty of Science and Technology–ECE, University of Macau, Macau 999078, China
| | - Rui P. Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China; (M.L.); (H.L.); (P.-I.M.); (R.P.M.)
- Faculty of Science and Technology–ECE, University of Macau, Macau 999078, China
- On Leave from Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
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35
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Feng Z, Zhang W, Li L, Tu B, Ye W, Tang X, Wang H, Xiao X, Wu T. A cost-effective detection of low-abundance mutation with DNA three-way junction structure and lambda exonuclease. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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36
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Guo Y, Wang M, Shen F, Hu Z, Ding H, Yao W, Qian H. Sensitive detection of RNA based on concatenated self-fuelled strand displacement amplification and hairpin-AgNCs. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:447-452. [PMID: 33355546 DOI: 10.1039/d0ay01762k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Herein, a self-fuelled amplification strategy (SFAS) is proposed, in which two strand displacement amplification (SDA) processes were concatenated for the proliferation of ssDNA. The ssDNA then initiated a polymerase action and caused the destruction of hairpin-templated silver nanoclusters (AgNCs), resulting in decreased fluorescence for sensing miRNA-21. This SFAS-based sensor is less complicated in design and facile in operation, because of the easy concatenation of SDA and mutual enzymes used in the signal output process. The sensitivity of this SFAS-based miRNA sensor was 1.78 × 10-11 M with a linear relationship in the range 0.02-1.0 × 10-9 M, and the recoveries of this method ranged from 82.07% to 106.58% with an average RSD of 10.96%.
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Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology, National Centre for Technology Innovation on Fast Biological Detection of Grain Quality and Safety, School of Food Science and Technology, Jiangnan University, Wuxi, China.
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37
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Liu PF, Zhao KR, Liu ZJ, Wang L, Ye SY, Liang GX. Cas12a-based electrochemiluminescence biosensor for target amplification-free DNA detection. Biosens Bioelectron 2021; 176:112954. [PMID: 33412428 DOI: 10.1016/j.bios.2020.112954] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/16/2020] [Accepted: 12/28/2020] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas system have drawn increasing attention in accurate and sensitive nucleic acids detection. Herein, we reported a novel Cas12a-based electrochemiluminescence biosensor for target amplification-free human papilloma virus subtype (HPV-16) DNA detection. During this detection process, Cas12a employed its two-part recognition mechanism to improve the specificity and trans-cleavage capability to achieve signal amplification, while L-Methionine stabilized gold nanoclusters (Met-AuNCs) were served as high-efficiency ECL emitters to achieve ECL signal transition. Given the unique combination of Cas12a with ECL technique, the detection limit was determined as 0.48 pM and the whole detection could be completed within 70 min. We also validated the practical application of the proposed biosensor by using undiluted human blood samples, which gives impetus to the design of new generations of CRISPR/Cas detection system beyond the traditional ones with ultimate applications in sensing analysis and diagnostic technologies.
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Affiliation(s)
- Peng-Fei Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China
| | - Kai-Ren Zhao
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China
| | - Zhi-Jun Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China
| | - Li Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China.
| | - Shu-Ying Ye
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Guo-Xi Liang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
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38
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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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39
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Lu L, Han X, Lin J, Zhang Y, Qiu M, Chen Y, Li M, Tang D. Ultrasensitive fluorometric biosensor based on Ti3C2 MXenes with Hg2+-triggered exonuclease III-assisted recycling amplification. Analyst 2021; 146:2664-2669. [DOI: 10.1039/d1an00178g] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Herein a fluorometric bioanalysis platform for mercury(ii) (Hg2+) detection was developed using two-dimensional MXenes (Ti3C2) as fluorescence quencher and Hg2+-induced exonuclease III-assisted target recycling strategy for efficient signal amplification.
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Affiliation(s)
- Liling Lu
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Department of Chemistry
- Fuzhou University
- Fuzhou 350116
| | - Xiao Han
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Department of Chemistry
- Fuzhou University
- Fuzhou 350116
| | - Jingwen Lin
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Department of Chemistry
- Fuzhou University
- Fuzhou 350116
| | - Yingxin Zhang
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Department of Chemistry
- Fuzhou University
- Fuzhou 350116
| | - Minghao Qiu
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Department of Chemistry
- Fuzhou University
- Fuzhou 350116
| | - Ying Chen
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Department of Chemistry
- Fuzhou University
- Fuzhou 350116
| | - Meijin Li
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Department of Chemistry
- Fuzhou University
- Fuzhou 350116
| | - Dianping Tang
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province)
- State Key Laboratory of Photocatalysis on Energy and Environment
- Department of Chemistry
- Fuzhou University
- Fuzhou 350116
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40
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Zhou Y, Yu S, Shang J, Chen Y, Wang Q, Liu X, Wang F. Construction of an Exonuclease III-Propelled Integrated DNAzyme Amplifier for Highly Efficient microRNA Detection and Intracellular Imaging with Ultralow Background. Anal Chem 2020; 92:15069-15078. [DOI: 10.1021/acs.analchem.0c03073] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yangjie Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Qing Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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41
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Lu J, Liang S, Tan L, Hu K, Zhao S, Tian J. Sensitive detection of microRNA using a label-free copper nanoparticle system with polymerase-based signal amplification. Anal Bioanal Chem 2020; 412:7179-7185. [PMID: 32785774 DOI: 10.1007/s00216-020-02850-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 11/25/2022]
Abstract
The abnormal expression of microRNAs (miRNAs) has been reported in many diseases, so it is of great interest to develop simple and accurate methods for the detection and analysis of miRNA expression. We have developed a novel biosensor to detect miRNAs. This method is based on a polymeric double-stranded DNA (dsDNA) copper nanoparticle (CuNP) template that is synthesised by a polymerase. When Cu2+ and ascorbic acid are added to the system, the dsDNA template (which is rich in A-T bases) promotes the formation of CuNPs, resulting in high fluorescence intensity. This system provides sensitive analysis of miRNA expression with a limit of detection down to 17.8 pmol/L, due to significant changes in the fluorescence signal of the system before and after the addition of the target. The linear range between F0-F and concentration of miR-122 is 80.0 pmol/L to 4.50 nmol/L, and the recovery rate in spiked HepG2 cell lysates is 93.33-102.53%. This method expands the applications of fluorescent DNA-CuNPs in the field of biosensor analysis, and can be used to detect and analyse any miRNA marker by changing the target recognition sequence. Graphical abstract A label-free dsDNA-CuNP-based and enzyme-assisted signal amplification method for microRNA is constructed.
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Affiliation(s)
- Jiangnan Lu
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China
| | - Shuping Liang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China
| | - Li Tan
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China
| | - Kun Hu
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China
| | - Shulin Zhao
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China
| | - Jianniao Tian
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Science of Guangxi Normal University, Guanxi, Guilin, 541004, China.
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42
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Tatulli G, Pompa PP. An amplification-free colorimetric test for sensitive DNA detection based on the capturing of gold nanoparticle clusters. NANOSCALE 2020; 12:15604-15610. [PMID: 32672272 DOI: 10.1039/d0nr03517c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
PCR-free or amplification-free strategies for DNA detection provide an interesting alternative to classical molecular biology techniques, opening new possibilities for on-site diagnostics. In this framework, we present herein an amplification-free colorimetric test for DNA detection, based on the capture of multiple gold nanoparticle (AuNP) clusters onto the surface of magnetic microbeads, leading to an increase of the plasmonic signal and, thus, of the overall sensitivity. Noteworthy, the assay allows the detection of as low as 15 attomoles of target DNA by simple visual inspection. The AuNP-cluster capturing mechanism was investigated by UV-vis, SEM, TEM, and EDX analysis. In a case study of E. coli contamination, the colorimetric test achieves a performance comparable to the reference instrumental PCR technique, enabling the naked-eye detection of 7.5 × 102 CFU μL-1.
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Affiliation(s)
- Giuseppina Tatulli
- Nanobiointeractions&Nanodiagnostics, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
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43
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Wu H, Wu J, Liu Y, Wang H, Zou P. Silver nanoclusters-based fluorescent biosensing strategy for determination of mucin 1: Combination of exonuclease I-assisted target recycling and graphene oxide-assisted hybridization chain reaction. Anal Chim Acta 2020; 1129:40-48. [PMID: 32891389 DOI: 10.1016/j.aca.2020.06.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/07/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
Abstract
A novel label-free fluorescent biosensing strategy was described for the sensitive detection of mucin 1 (MUC1). It consisted of an M-shaped aptamer probe for exonuclease I (Exo I)-assisted target recycling (EATR) amplification, and two AgNCs-hairpin probes for graphene oxide (GO)-assisted hybridization chain reaction (HCR) amplification. Based on the specificity of aptamer-target recognition, the addition of MUC1 caused a conformational change in the M-shaped aptamer probe, which was split into a MUC1-P3 complex and a P1-P2 duplex. Exo I then catalyzed the cleavage of aptamer sequence P3 from the MUC1-P3 complex and released the target MUC1. The released target MUC1 was free to bind with a new M-shaped probe to perform EATR amplification. Furthermore, the P1-P2 duplex with three single-stranded arms can act as a primer to initiate HCR between hairpin probes AgNCs-H1 and AgNCs-H2. In the process of HCR, two AgNCs-hairpins were autonomously cross-opened, generating long linear double-stranded nanowires containing large numbers of AgNCs. These nanowires cannot be quenched by GO due to the weak affinity between the long double-stranded DNA and GO, thereby retaining a strong fluorescent signal indicative of the concentration of MUC1. With these designs, in addition to an extremely low detection limit of 0.36 fg mL-1, the method exhibited an acceptable linear response to detect MUC1 from 1 fg mL-1 to 1 ng mL-1. Additionally, this method could be exerted with a high degree of success to detect MUC1 in diluted human serum with satisfactory results.
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Affiliation(s)
- Hao Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, China.
| | - Jun Wu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, China
| | - Yaling Liu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, China
| | - Hongyong Wang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, China
| | - Pei Zou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, 214063, China.
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44
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Peng S, Tan Z, Chen S, Lei C, Nie Z. Integrating CRISPR-Cas12a with a DNA circuit as a generic sensing platform for amplified detection of microRNA. Chem Sci 2020; 11:7362-7368. [PMID: 33133487 PMCID: PMC7553042 DOI: 10.1039/d0sc03084h] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/17/2020] [Indexed: 12/16/2022] Open
Abstract
A generic sensing strategy that integrates CRISPR-Cas12a with a DNA circuit is proposed for amplified detection of microRNA.
CRISPR-based diagnostics (CRISPR-Dx) has shown great promise in molecular diagnostics, but its utility in the sensing of microRNA (miRNA) biomarkers is limited by sensitivity, cost and robustness. Here, we describe a CRISPR-Dx method for the sensitive and cost-effective detection of miRNAs by rationally integrating CRISPR-Cas12a with DNA circuits. In this work, a modular catalytic hairpin assembly (CHA) circuit is designed to convert and amplify each target into multiple programmable DNA duplexes, which serve as triggers to initiate the trans-cleavage activity of CRISPR-Cas12a for further signal amplification. Such rational integration provides a generic assay for the effectively amplified detection of miRNA biomarkers. By simply tuning the variable regions in the CHA modules, this assay achieves sub-femtomolar sensitivity for different miRNA biomarkers, which improves the detection limit of CRISPR-Dx in the analysis of miRNA by 3–4 orders of magnitude. With the usage of the proposed assay, the sensitive assessment of miR-21 levels in different cancer cell lines and clinical serum samples has been achieved, providing a generic method for the sensitive detection of miRNA biomarkers in molecular diagnosis.
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Affiliation(s)
- Shuang Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , P. R. China .
| | - Zhen Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , P. R. China .
| | - Siyu Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , P. R. China .
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , P. R. China .
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , P. R. China .
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45
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Huang Z, Lin Q, Ye X, Yang B, Zhang R, Chen H, Weng W, Kong J. Terminal deoxynucleotidyl transferase based signal amplification for enzyme-linked aptamer-sorbent assay of colorectal cancer exosomes. Talanta 2020; 218:121089. [PMID: 32797865 DOI: 10.1016/j.talanta.2020.121089] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022]
Abstract
Exosomes have received increasingly significant attention and have shown great clinical value as biomarkers for a number of diseases. However, there is still a lack of a highly sensitive and visualized method for the detection of exosomes in numerous samples simultaneously. Here, we developed a high-throughput, colorimetric and simple method to detect colorectal cancer (CRC) exosomes based on terminal deoxynucleotidyl transferase (TdT)-aided ultraviolet signal amplification. Anti-A33, a CRC exosomal protein marker, was selected as a capture probe, and a facility-prepared EpCAM (CRC exosomal protein) aptamer-Au-primer complex was used as a signal probe. After the CRC exosomes were captured onto the surface of 96-well plates, the primer was extended to the poly(biotin-adenine) chains with the help of TdT, resulting in an increase in the binding amount of avidin-modified horseradish peroxidase (Av-HRP) for H2O2-mediated oxidation of 3,3',5,5'-tetramethyl benzidine (TMB) in enzyme-linked aptamer-sorbent assay (ELASA). The results showed that the incorporation of ploy(biotin-A) enabled approximately 10.4-fold signal amplification. This approach achieved a linear range of 9.75 × 103-1.95 × 106 particles/μL for CRC cell-derived exosomes. The feasibility of the developed assay was evaluated using clinical serum samples. CRC patients (n = 16) could be clearly and successfully distinguished from healthy individuals (n = 9). Furthermore, this proposed platform holds considerable potential for the detection of different targets, simply by changing the aptamer and antibody.
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Affiliation(s)
- Zhipeng Huang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Qiuyuan Lin
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Xin Ye
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Bin Yang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Ren Zhang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai, 200438, China.
| | - Wenhao Weng
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, China.
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai, 200438, China.
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Duan R, Li T, Duan Z, Huang F, Xia F. Near-Infrared Light Activated Nucleic Acid Cascade Recycling Amplification for Spatiotemporally Controllable Signal Amplified mRNA Imaging. Anal Chem 2020; 92:5846-5854. [DOI: 10.1021/acs.analchem.9b05494] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ruilin Duan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Tao Li
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Zhijuan Duan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fujian Huang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, 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, China
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47
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Xing C, Chen Z, Zhang C, Wang J, Lu C. Construction of a Target-Initiated, Enzyme-Free DNA Cascade Circuit for Amplified Detection of Mercury. ACS APPLIED BIO MATERIALS 2020; 3:1853-1857. [DOI: 10.1021/acsabm.0c00142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Chao Xing
- Fujian Provincial Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, Minjiang University, Fuzhou 350108, P. R. China
| | - Ziyi Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China
| | - Cheng Zhang
- Fujian Provincial Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, Minjiang University, Fuzhou 350108, P. R. China
| | - Jun Wang
- Fujian Provincial Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors, Minjiang University, Fuzhou 350108, P. R. China
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China
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48
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49
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A carbon nanoparticle and DNase I-Assisted amplified fluorescent biosensor for miRNA analysis. Talanta 2020; 213:120816. [PMID: 32200921 DOI: 10.1016/j.talanta.2020.120816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/05/2020] [Accepted: 02/08/2020] [Indexed: 11/24/2022]
Abstract
Nucleic acid-based biosensors have become powerful tools in biomedical applications. But the stability issue seriously limits their wide applications. Fortunately, the emergence of carbon nanoparticles (CNPs), which can effectively protect DNA probes from enzymatic digestion and unspecific protein binding, provides a good solution. In this work, a DNase I-aided cyclic enzymatic amplification method (CEAM) for microRNA analysis has been developed based on the coupling use of nucleic acid probes with specific molecular recognition ability as well as CNPs with excellent biostability. The method is simple and sensitive, with a detection limit down to 3.2 pM. Furthermore, satisfactory results are achieved for miRNA analysis in breast cancer cell lysate, demonstrating the applicability in disease diagnosis. The ingenious combination of CNPs and nucleic acid probes can open a new chapter in the development of versatile analytical strategies that holds great potentials for clinical diagnosis, food safety, and environmental monitoring.
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50
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Hu Y, Tan C, Lin X, Lai Z, Zhang X, Lu Q, Feng N, Yang D, Weng L. Exonuclease III-Regulated Target Cyclic Amplification-Based Single Nucleotide Polymorphism Detection Using Ultrathin Ternary Chalcogenide Nanosheets. Front Chem 2020; 7:844. [PMID: 31921768 PMCID: PMC6913186 DOI: 10.3389/fchem.2019.00844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/19/2019] [Indexed: 12/30/2022] Open
Abstract
Herein, we report that the ternary chalcogenide nanosheet exhibits different affinity toward oligonucleotides with different lengths and efficiently quenches the fluorescence of dye-labeled DNA probes. Based on these findings, as a proof-of-concept application, the ternary chalcogenide nanosheet is used as a target cyclic amplification biosensor, showing high specificity in discriminating single-base mismatch. This simple strategy is fast and sensitive for the single nucleotide polymorphism detection. Ultralow detection limit of unlabeled target (250 fM) and high discrimination ratio (5%) in the mixture of perfect match (mutant-type) and single-base mismatch (wild-type) target are achieved. This sensing method is extensively compatible for the single nucleotide polymorphism detection in clinical samples, making it a promising tool for the mutation-based clinical diagnostic and genomic research.
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Affiliation(s)
- Yanling Hu
- School of Electrical and Control Engineering, Nanjing Polytechnic Institute, Nanjing, China.,Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Chaoliang Tan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xin Lin
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhuangchai Lai
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xiao Zhang
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qipeng Lu
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ning Feng
- Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Dongliang Yang
- Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China.,School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, China
| | - Lixing Weng
- Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
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