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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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2
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Ultra-wide, attomolar-level limit detection of CD44 biomarker with a silanized optical fiber biosensor. Biosens Bioelectron 2022; 208:114217. [DOI: 10.1016/j.bios.2022.114217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/02/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022]
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3
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Gundagatti S, Srivastava S. Development of Electrochemical Biosensor for miR204-Based Cancer Diagnosis. Interdiscip Sci 2022; 14:596-606. [PMID: 35471629 DOI: 10.1007/s12539-022-00508-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
With increase in cancer burden worldwide and poor survival rates due to delayed diagnosis, it is pertinent to develop a device for early diagnosis. We report an electrochemical biosensor for quantification of miRNA-204 (miR-204) biomarker that is dysregulated in most of the cancers. The proposed methodology uses the gold nanoparticles-modified carbon screen-printed electrode for immobilization of single-stranded DNA probe against miR-204. Colloidal gold nanoparticles were synthesized using L-glutamic acid as reducing agent. Nanoparticles were characterized by UV-visible spectroscopy and transmission electron microscopy. Spherical gold nanoparticles were of 7-28 nm in size. Biosensor fabricated using these nanoparticles was characterized by cyclic voltammetry after spiking 0.1 fg/mL-0.1 µg/mL of miR-204 in fetal bovine serum. Response characteristics of the miR-204 biosensor displayed high sensitivity of 8.86 µA/µg/µL/cm2 with wide detection range of 15.5 aM to 15.5 nM. The low detection limit makes it suitable for early diagnosis and screening of cancer.
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Affiliation(s)
- Shilpa Gundagatti
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, U.P., India
| | - Sudha Srivastava
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, U.P., India.
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4
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Wang C, Wang W, Xu Y, Zhao X, Li S, Qian Q, Mi X. Tetrahedral DNA Framework-Programmed Electrochemical Biosenors with Gold Nanoparticles for Ultrasensitive Cell-Free DNA Detection. NANOMATERIALS 2022; 12:nano12040666. [PMID: 35214994 PMCID: PMC8879424 DOI: 10.3390/nano12040666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/16/2022]
Abstract
Tumor-associated cell-free DNA (cfDNA) is a dynamic biomarker for genetic analysis, early diagnosis and clinical treatment of cancers. However, its detection has limitations because of its low abundance in blood or other complex bodily fluids. Herein, we developed an ultrasensitive cfDNA electrochemical biosensor (E-cfDNA sensor) based on tetrahedral DNA framework (TDF)-modified gold nanoparticles (Au NPs) with an interface for cfDNA detection. By accurately controlling the numbers of base pairs on each DNA framework, three types of TDFs were programmed: 26 base pairs of TDF; 17 base pairs of TDF; and 7 base pairs of TDF (TDF-26, TDF-16 and TDF-7, respectively). We also combined the TDF with hybridization chain reaction (HCR) to achieve signal amplification. Under optimal conditions, we detected the breast cancer susceptibility gene 1 (BRCA-1), a representative cfDNA closely related to breast cancer. An ultra-low detection limit of 1 aM with a linear range from 1 aM to 1 pM by TDF-26 was obtained, which was superior to the existing methods. Each type of TDF has excellent discrimination ability, which can distinguish single mismatch. More significantly, we also detected BRCA-1 in mimic serum samples, demonstrating that the E-cfDNA sensor has potential use in clinical research.
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Affiliation(s)
- Chenguang Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (C.W.); (Y.X.); (S.L.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- Shanghai Pudong New District Zhoupu Hospital, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China;
| | - Yi Xu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (C.W.); (Y.X.); (S.L.); (Q.Q.)
| | - Xiaoshuang Zhao
- State Key Laboratory of Functional Material for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China;
| | - Shuainan Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (C.W.); (Y.X.); (S.L.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuling Qian
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (C.W.); (Y.X.); (S.L.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianqiang Mi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; (C.W.); (Y.X.); (S.L.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Functional Material for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China;
- CAS Center for Excellence in Superconducting Electronics (CENSE), Shanghai 200050, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
- Correspondence:
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5
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Cheng X, Yin W. Probing Biosensing Interfaces With Single Molecule Localization Microscopy (SMLM). Front Chem 2021; 9:655324. [PMID: 33996750 PMCID: PMC8117217 DOI: 10.3389/fchem.2021.655324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/16/2021] [Indexed: 11/23/2022] Open
Abstract
Far field single molecule localization microscopy (SMLM) has been established as a powerful tool to study biological structures with resolution far below the diffraction limit of conventional light microscopy. In recent years, the applications of SMLM have reached beyond traditional cellular imaging. Nanostructured interfaces are enriched with information that determines their function, playing key roles in applications such as chemical catalysis and biological sensing. SMLM enables detailed study of interfaces at an individual molecular level, allowing measurements of reaction kinetics, and detection of rare events not accessible to ensemble measurements. This paper provides an update to the progress made to the use of SMLM in characterizing nanostructured biointerfaces, focusing on practical aspects, recent advances, and emerging opportunities from an analytical chemistry perspective.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory for Modern Optical Instrumentations, National Engineering Research Center of Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Wei Yin
- Core Facilities, School of Medicine, Zhejiang University, Hangzhou, China
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Mono-dispersed nano-hydroxyapatite based MRI probe with tetrahedral DNA nanostructures modification for in vitro tumor cell imaging. Anal Chim Acta 2020; 1138:141-149. [PMID: 33161975 DOI: 10.1016/j.aca.2020.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 12/24/2022]
Abstract
Taking advantage of the superior biocompatibility, good stability in a wide pH and temperature range, as well as its strong affinity with DNA of hydroxyapatite (HAp), tetrahedral DNA nanostructures (TDNs) conjugated with AS1411 aptamer (anti-nucleolin overexpressed on tumor cell membranes) were employed as affinity ligands to construct a novel mono-dispersed HAp based probe with Gd3+ doping (Apt-TDNs-GdHAp) for MR imaging. The adsorption of TDNs on the nano-HAp surface facilely accomplished the construction of the Apt-TDNs-GdHAp probes. Meanwhile, the use of hydrophilic TDNs not only favored the phase-transfer from the oil phase to the aqueous phase, but also enhanced the mono-dispersion of this probe due to the well-ordered distribution of TDNs on the surface of nano-HAp. Moreover, Apt-TDNs-GdHAp probe with a better mono-dispersion and crystalinity achieved twice higher longitudinal relaxivity (r1 value) than that of GdHAp synthesized by microwave-assisted method (Microwave-GdHAp), exhibiting much more excellent T1-weighted imaging performance. With the introduction of TDNs, the stability and the tumor-targeting accessibility were also greatly improved, showing its great potential for further bio-applications.
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Jiang J, Yu Y, Zhang H, Cai C. Electrochemical aptasensor for exosomal proteins profiling based on DNA nanotetrahedron coupled with enzymatic signal amplification. Anal Chim Acta 2020; 1130:1-9. [PMID: 32892927 DOI: 10.1016/j.aca.2020.07.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/22/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022]
Abstract
Exosomes are extracellular nanovesicles for transferring and delivering membrane and cytosolic molecules between cells. Detection and profiling of exosomal proteins can provide direct information on disease progression, which is important to the early diagnosis and monitoring of diseases. Herein, a well-designed electrochemical aptasensor was fabricated for the profiling of cancerous exosomal proteins based on DNA nanotetrahedron (NTH) coupled with Au nanoparticles (NPs) and enzymatic signal amplification. In this assay, the aptamer modified DNA NTHs were used as the recognition and capture unit, Au NPs-DNA conjugates coupled with horseradish peroxidase were used to realize signal amplification. This aptasensor achieves a detection limit down to 1.66 × 104 particles/mL for HepG2 liver cancer exosomes. In addition, the analysis of plasma-derived exosomes in HepG2 liver cancer bearing mice at different cancer stages was also achieved. More importantly, the aptasensor can be used to profile four kinds of exosomal proteins by using the corresponding aptamer. The proposed electrochemical aptasensor may be served as a potential platform for exosome detection and exosomal proteins profiling.
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Affiliation(s)
- Juqian Jiang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, National and Local Joint Engineering Research Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210097, PR China
| | - Yongqi Yu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, National and Local Joint Engineering Research Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210097, PR China
| | - Hui Zhang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, National and Local Joint Engineering Research Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210097, PR China.
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, National and Local Joint Engineering Research Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210097, PR China
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8
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Yousefi F, Movahedpour A, Shabaninejad Z, Ghasemi Y, Rabbani S, Sobnani-Nasab A, Mohammadi S, Hajimoradi B, Rezaei S, Savardashtaki A, Mazoochi M, Mirzaei H. Electrochemical-Based Biosensors: New Diagnosis Platforms for Cardiovascular Disease. Curr Med Chem 2020; 27:2550-2575. [DOI: 10.2174/0929867326666191024114207] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 02/05/2023]
Abstract
One of the major reasons for mortality throughout the world is cardiovascular diseases.
Therefore, bio-markers of cardiovascular disease are of high importance to diagnose and manage procedure.
Detecting biomarkers provided a promising procedure in developing bio-sensors. Fast, selective,
portable, accurate, inexpensive, and sensitive biomarker sensing instruments will be necessary for
detecting and predicting diseases. One of the cardiac biomarkers may be ordered as C-reactive proteins,
lipoprotein-linked phospho-lipase, troponin I or T, myoglobin, interleukin-6, interleukin-1, tumor necrosis
factor alpha, LDL and myeloperoxidase. The biomarkers are applied to anticipate cardio-vascular
illnesses. Initial diagnoses of these diseases are possible by several techniques; however, they are laborious
and need costly apparatus. Current researches designed various bio-sensors for resolving the respective
issues. Electrochemical instruments and the proposed bio-sensors are preferred over other
methods due to its inexpensiveness, mobility, reliability, repeatability. The present review comprehensively
dealt with detecting biomarkers of cardiovascular disease through electro-chemical techniques.
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Affiliation(s)
- Fatemeh Yousefi
- Department of Biological Sciences, Faculty of Genetics, Tarbiat Modares University, Tehran, Iran
| | - Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Shabaninejad
- Department of Biological Sciences, Faculty of Nanotechnology, Tarbiat Modares University, Tehran, Iran
| | - Younes Ghasemi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shahram Rabbani
- Research Center for Advanced Technologies in Cardiovascular Medicine, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Sobnani-Nasab
- Social Determinants of Health (SDH) Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Soheila Mohammadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Behzad Hajimoradi
- Cardiology Department of Shohaday-e-Tajrish Hospital Shahid Beheshti University of Medical Sciences (SBMU), Tehran, Iran
| | - Samaneh Rezaei
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Majid Mazoochi
- Department of Cardiology, Cardiac Electrophysiology Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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9
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Immobilization Techniques for Aptamers on Gold Electrodes for the Electrochemical Detection of Proteins: A Review. BIOSENSORS-BASEL 2020; 10:bios10050045. [PMID: 32354207 PMCID: PMC7277302 DOI: 10.3390/bios10050045] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The development of reliable biosensing platforms plays a key role in the detection of proteins in clinically and environmentally derived samples for diagnostics, as well as for process monitoring in biotechnological productions. For this purpose, the biosensor has to be stable and reproducible, and highly sensitive to detect potentially extremely low concentrations and prevent the nonspecific binding of interfering compounds. In this review, we present an overview of recently published (2017–2019) immobilization techniques for aptamers on gold electrodes for the electrochemical detection of proteins. These include the direct immobilization of thiolated aptamers and the utilization of short linkers, streptavidin/biotin interaction, as well as DNA nanostructures and reduced graphene oxide as immobilization platforms. Applied strategies for signal amplification and the prevention of biofouling are additionally discussed, as they play a crucial role in the design of biosensors. While a wide variety of amplification strategies are already available, future investigations should aim to establish suitable antifouling strategies that are compatible with electrochemical measurements. The focus of our review lies on the detailed discussion of the underlying principles and the presentation of utilized chemical protocols in order to provide the reader with promising ideas and profound knowledge of the subject, as well as an update on recent discoveries and achievements.
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10
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DNA framework-engineered electrochemical biosensors. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1130-1141. [PMID: 32253588 DOI: 10.1007/s11427-019-1621-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/04/2020] [Indexed: 02/07/2023]
Abstract
Self-assembled DNA nanostructures have shown remarkable potential in the engineering of biosensing interfaces, which can improve the performance of various biosensors. In particular, by exploiting the structural rigidity and programmability of the framework nucleic acids with high precision, molecular recognition on the electrochemical biosensing interface has been significantly enhanced, leading to the development of highly sensitive and specific biosensors for nucleic acids, small molecules, proteins, and cells. In this review, we summarize recent advances in DNA framework-engineered biosensing interfaces and the application of corresponding electrochemical biosensors.
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Tan X, Broses LJ, Zhou M, Day KC, Liu W, Li Z, Weizer AZ, Munson KA, Khaing Oo MK, Day ML, Fan X. Multiparameter urine analysis for quantitative bladder cancer surveillance of orthotopic xenografted mice. LAB ON A CHIP 2020; 20:634-646. [PMID: 31922156 DOI: 10.1039/c9lc01006h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The human-derived orthotopic xenograft mouse model is an effective platform for performing in vivo bladder cancer studies to examine tumor development, metastasis, and therapeutic effects of drugs. To date, the surveillance of tumor progression in real time for orthotopic bladder xenografts is highly dependent on semi-quantitative in vivo imaging technologies such as bioluminescence. While these imaging technologies can estimate tumor progression, they are burdened with requirements such as anesthetics, specialized equipment, and genetic modification of the injected cell line. Thus, a convenient and non-invasive technology to quantitatively monitor the growth of bladder cancer in orthotopic xenografts is highly desired. In this work, using a microfluidic chemiluminescent ELISA platform, we have successfully developed a rapid, multiparameter urine-based and non-invasive biomolecular prognostic technology for orthotopic bladder cancer xenografts. This method consists of two steps. First, the concentrations of a panel of four urinary biomarkers are quantified from the urine of mice bearing orthotopic bladder xenografts. Second, machine learning and principal component analysis (PCA) algorithms are applied to analyze the urinary biomarkers, and subsequently, a score is assigned to indicate the tumor growth. With this methodology, we have quantitatively monitored the orthotopic growth of human bladder cancer that was inoculated with low, medium, and high cancer cell numbers. We also employed this method and performed a proof of principle experiment to examine the in vivo therapeutic efficacy of the EGFR inhibitor, dacomitinib.
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Affiliation(s)
- Xiaotian Tan
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Luke J Broses
- Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA. and Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Menglian Zhou
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Kathleen C Day
- Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA. and Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wenyi Liu
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Ziqi Li
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Alon Z Weizer
- Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA. and Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katherine A Munson
- Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA. and Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Mark L Day
- Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA. and Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xudong Fan
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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Wang X, Wu J, Mao W, He X, Ruan L, Zhu J, Shu P, Zhang Z, Jiang B, Zhang X. A tetrahedral DNA nanostructure-decorated electrochemical platform for simple and ultrasensitive EGFR genotyping of plasma ctDNA. Analyst 2020; 145:4671-4679. [PMID: 32458862 DOI: 10.1039/d0an00591f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In this study, we propose an on-site electrochemical platform for sensitive simultaneous genotyping of the two major EGFR mutations (19del and L858R) through plasma ctDNA based on tetrahedral DNA nanostructure decorated screen-printed electrodes.
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13
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Wang L, Wen Y, Yang X, Xu L, Liang W, Zhu Y, Wang L, Li Y, Li Y, Ding M, Ren S, Yang Z, Lv M, Zhang J, Ma K, Liu G. Ultrasensitive Electrochemical DNA Biosensor Based on a Label-Free Assembling Strategy Using a Triblock polyA DNA Probe. Anal Chem 2019; 91:16002-16009. [PMID: 31746200 DOI: 10.1021/acs.analchem.9b04757] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Multiblock DNA probe attracted a large amount of scientific attention, for the development of multitarget biosensor and improved specificity/sensitivity. However, the development of multiblock DNA probes highly relied on the chemical synthesis of organic linkers or nanomaterials, which limited their practicability and biological compatibility. In this work, we developed a label-free assembling strategy using a triblock DNA capture probe, which connects two DNA probes with its intrinsic polyA fragment (probe-PolyA-probe, PAP). The middle polyA segment has a high affinity to the gold electrode surface, leading to excellent reproducibility, stability, and regeneration of our biosensor. Two flanking capture probes were tandemly co-assembled on the electrode surface with consistent spatial relationship and exactly the same amount. When combined with the target DNA, the hybridization stability was improved, because of the strong base stacking effect of two capture probes. The sensitivity of our biosensor was proved to be 10 fM, with a wide analysis range between 10 fM to 1 nM. Our PAP-based biosensor showed excellent specificity when facing mismatched DNA sequences. Even single nucleotide polymorphisms can be distinguished by each probe. The excellent practicability of our biosensor was demonstrated by analyzing genomic DNA both with and without PCR amplification.
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Affiliation(s)
- Lele Wang
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Yanli Wen
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Xue Yang
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Li Xu
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Wen Liang
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Ying Zhu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , People's Republic of China.,Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , People's Republic of China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , People's Republic of China.,Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , People's Republic of China
| | - Yan Li
- Division of Chemical Metrology and Analytical Science , National Institute of Metrology of China , Beijing 102200 , People's Republic of China
| | - Yuan Li
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Min Ding
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Shuzhen Ren
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Zhenzhou Yang
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
| | - Min Lv
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , People's Republic of China.,Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , People's Republic of China
| | - Jichao Zhang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , People's Republic of China.,Shanghai Advanced Research Institute , Chinese Academy of Sciences , Shanghai 201210 , People's Republic of China
| | - Kang Ma
- Division of Chemical Metrology and Analytical Science , National Institute of Metrology of China , Beijing 102200 , People's Republic of China
| | - Gang Liu
- Laboratory of Biometrology, Division of Chemistry , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , People's Republic of China
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Wang R, Zhu X, Xing Y, Memon AG, Shi H, Zhou X. Multitag-Regulated Cascade Reaction: A Generalizable Ultrasensitive MicroRNA Biosensing Approach for Cancer Prognosis. ACS APPLIED MATERIALS & INTERFACES 2019; 11:36444-36448. [PMID: 31525882 DOI: 10.1021/acsami.9b14452] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ultrasensitive PCR-free microRNA (miR) analysis based on biosensors with enzyme-free nucleic acid amplification and reusable surface has great clinical significance in cancer prognosis. However, building such a biosensing strategy has long been challenging due to uncontrollable miR-triggered cascade amplifiers and insufficient sensing surface regeneration capability. To meet the challenge, for the first time, a general approach, named enzyme-free multitag-regulated cascade reaction (MCR), is developed to fabricate reliable trace miR biosensors. As a proof of concept, miR let-7a is detected on an evanescent wave fluorescent optical-fiber biosensing platform. The size and morphology of well-formed MCR assemblies (∼1 μm in length) are characterized by atomic force microscopy. This MCR method achieves a 30 000-fold improved sensitivity (detection limit 0.8 fM) compared to the MCR-free system and can detect abnormal urinary miR levels in lung cancer patients. Moreover, the biosensor is robust enough to be reused for over 100 cycles, which greatly reduces the cost of single detection. In sum, MCR is developed as a generalizable ultrasensitive miR biosensing approach for cancer prognosis, which opens a broad field for facile enzyme-free biosensing applications by nucleic acid assembling regulation.
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Affiliation(s)
- Ruoyu Wang
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
| | - Xiyu Zhu
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
| | - Yunpeng Xing
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
| | - Abdul Ghaffar Memon
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
| | - Hanchang Shi
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health School of Environment , Tsinghua University , Beijing 100084 , China
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15
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Sadighbayan D, Sadighbayan K, Khosroushahi AY, Hasanzadeh M. Recent advances on the DNA-based electrochemical biosensing of cancer biomarkers: Analytical approach. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.07.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Wang Q, Wen Y, Li Y, Liang W, Li W, Li Y, Wu J, Zhu H, Zhao K, Zhang J, Jia N, Deng W, Liu G. Ultrasensitive Electrochemical Biosensor of Bacterial 16S rRNA Gene Based on polyA DNA Probes. Anal Chem 2019; 91:9277-9283. [PMID: 31198030 DOI: 10.1021/acs.analchem.9b02175] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Traditional microbiology analysis is usually hindered by the long time-cost and lack of portability in many urgent situations. In this work, we developed a novel electrochemical DNA biosensor (E-biosensor) for sensitive analysis of the 16S rRNA gene of five bacteria, using a consecutive adenine (polyA) probe. The polyA probe consists of a polyA tail and a recognition part. The polyA tail can combine onto the gold surface with improved controllability of the surface density, by conveniently changing the length of polyA. The recognition part of the capture probe together with two biotin-labeled reporter probes hybridize with the target DNA and form a stable DNA-tetramer sandwich structure, and then avidin-HRP enzyme was added to produce a redox current signal for the following electrochemical detection. Finally, we realized sensitive quantification of artificial target DNA with a limit of detection (LOD) of 10 fM, and excellent selectivity and reusability were also demonstrated. Importantly, the detection capability was equally good when facing bacterial genomic DNA, due to the base-stacking force of our multireporter-probe system, which can help to break the second structure and stabilize the probe-target complexes. Our biosensor was constructed on a 16-channel electrode chip without any polymerase chain reaction (PCR) process needed, which took a significant step toward a portable bacteria biosensor.
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Affiliation(s)
- Qian Wang
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China.,Department of Chemistry, College of Chemistry and Materials Science , Shanghai Normal University , 100 Guilin Road , Shanghai 200234 , P. R. China
| | - Yanli Wen
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Yan Li
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Wen Liang
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Wen Li
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Yuan Li
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Jiahuan Wu
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Huichen Zhu
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Keke Zhao
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Jun Zhang
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
| | - Nengqin Jia
- Department of Chemistry, College of Chemistry and Materials Science , Shanghai Normal University , 100 Guilin Road , Shanghai 200234 , P. R. China
| | - Wangping Deng
- Chinese Center for Disease Control and Prevention , National Institute of Parasitic Diseases , 207 Rui Jin Er Road , Shanghai 200025 , P. R. China
| | - Gang Liu
- Laboratory of Biometrology , Shanghai Institute of Measurement and Testing Technology , 1500 Zhang Heng Road , Shanghai 201203 , P. R. China
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17
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Abstract
Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.
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Affiliation(s)
- Hong Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Jing Liu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Jing-Juan Xu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi, China.
| | - Hong-Yuan Chen
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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18
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Campuzano S, Pedrero M, Yáñez-Sedeño P, Pingarrón JM. Antifouling (Bio)materials for Electrochemical (Bio)sensing. Int J Mol Sci 2019; 20:E423. [PMID: 30669466 PMCID: PMC6358752 DOI: 10.3390/ijms20020423] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/13/2019] [Accepted: 01/16/2019] [Indexed: 12/20/2022] Open
Abstract
(Bio)fouling processes arising from nonspecific adsorption of biological materials (mainly proteins but also cells and oligonucleotides), reaction products of neurotransmitters oxidation, and precipitation/polymerization of phenolic compounds, have detrimental effects on reliable electrochemical (bio)sensing of relevant analytes and markers either directly or after prolonged incubation in rich-proteins samples or at extreme pH values. Therefore, the design of antifouling (bio)sensing interfaces capable to minimize these undesired processes is a substantial outstanding challenge in electrochemical biosensing. For this purpose, efficient antifouling strategies involving the use of carbon materials, metallic nanoparticles, catalytic redox couples, nanoporous electrodes, electrochemical activation, and (bio)materials have been proposed so far. In this article, biomaterial-based strategies involving polymers, hydrogels, peptides, and thiolated self-assembled monolayers are reviewed and critically discussed. The reported strategies have been shown to be successful to overcome (bio)fouling in a diverse range of relevant practical applications. We highlight recent examples for the reliable sensing of particularly fouling analytes and direct/continuous operation in complex biofluids or harsh environments. Opportunities, unmet challenges, and future prospects in this field are also pointed out.
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Affiliation(s)
- Susana Campuzano
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - María Pedrero
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Paloma Yáñez-Sedeño
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - José M Pingarrón
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
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19
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Sensitive and label-free electrochemical lead ion biosensor based on a DNAzyme triggered G-quadruplex/hemin conformation. Biosens Bioelectron 2018; 115:91-96. [DOI: 10.1016/j.bios.2018.04.054] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 01/01/2023]
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20
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Campuzano S, Yáñez-Sedeño P, Pingarrón JM. Tailoring Sensitivity in Electrochemical Nucleic Acid Hybridization Biosensing: Role of Surface Chemistry and Labeling Strategies. ChemElectroChem 2018. [DOI: 10.1002/celc.201800667] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Susana Campuzano
- Departamento de Química Analítica, Facultad de CC. Químicas; Universidad Complutense de Madrid; E-28040 Madrid Spain
| | - Paloma Yáñez-Sedeño
- Departamento de Química Analítica, Facultad de CC. Químicas; Universidad Complutense de Madrid; E-28040 Madrid Spain
| | - José Manuel Pingarrón
- Departamento de Química Analítica, Facultad de CC. Químicas; Universidad Complutense de Madrid; E-28040 Madrid Spain
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21
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Abstract
Nucleic acids have been actively exploited to develop various exquisite nanostructures due to their unparalleled programmability. Especially, framework nucleic acids (FNAs) with tailorable functionality and precise addressability hold great promise for biomedical applications. In this review, we summarize recent progress of FNA-enabled biosensing in homogeneous solutions, on heterogeneous surfaces, and inside cells. We describe the strategies to translate the structural order and rigidity of FNAs to interfacial engineering with high controllability, and approaches to realize multiplexing for highly parallel in vitro detection. We also envision the marriage of the currently available FNA tool sets with other emerging technologies to develop a new generation of biosensors for precision diagnosis and bioimaging.
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Affiliation(s)
- Fan Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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22
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Li L, Wang L, Xu Q, Xu L, Liang W, Li Y, Ding M, Aldalbahi A, Ge Z, Wang L, Yan J, Lu N, Li J, Wen Y, Liu G. Bacterial Analysis Using an Electrochemical DNA Biosensor with Poly-Adenine-Mediated DNA Self-Assembly. ACS APPLIED MATERIALS & INTERFACES 2018; 10:6895-6903. [PMID: 29383931 DOI: 10.1021/acsami.7b17327] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The spatial arrangement of DNA probes on the electrode surface is of critical significance for the performance of electrochemical biosensors. However, rational control of the probe surface remains challenging. In this work, we develop a capture probe carrying a poly-adenine anchoring block to construct a programmable self-assembled monolayer for a "sandwich-type" electrochemical biosensor. We show that with a co-assembling strategy using a polyA capture probe and 6-mercapto-1-hexanol, the density of the probes on the gold electrode can be simply adjusted by the length of polyA. The electron-transfer effect and thus the hybridization efficiency can as well be optimized by tuning the polyA length. As a result, we obtained an excellent biosensor performance with a limit of detection as low as 5 fM for a synthetic DNA target. We demonstrate the practicability of this system by analyzing a PCR product from Escherichia coli genomic DNA (0.2 pg/μL). On the basis of the ideal electrochemical interface, our polyA-based biosensor exhibited excellent reusability and stability, which is important for potential applications in the onsite analysis for a wide range of targets.
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Affiliation(s)
- Lanying Li
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology , Shanghai 201203, China
| | - Lele Wang
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology , Shanghai 201203, China
| | - Qin Xu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology , Shanghai 201203, China
| | - Li Xu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology , Shanghai 201203, China
| | - Wen Liang
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology , Shanghai 201203, China
| | - Yan Li
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology , Shanghai 201203, China
| | - Min Ding
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology , Shanghai 201203, China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia
| | - Zhilei Ge
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Science , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Science , Shanghai 201800, China
| | - Juan Yan
- College of Food Science & Technology Shanghai Ocean University , Shanghai 201306, China
| | - Na Lu
- School of Materials Engineering, Shanghai University of Engineering Science , Shanghai 201620, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Science , Shanghai 201800, China
| | - Yanli Wen
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology , Shanghai 201203, China
| | - Gang Liu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology , Shanghai 201203, China
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23
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Yang F, Zuo X, Fan C, Zhang XE. Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing. Natl Sci Rev 2018. [DOI: 10.1093/nsr/nwx134] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.
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Affiliation(s)
- Fan Yang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, CAS Excellence Center for Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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24
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Wan Y, Xu L, Zhuo N, Lu X. A novel DNA sensor based on C 60NPs-PAMAM-PtPNPs to detect VKORC1 gene for guiding rational clinical therapy with warfarin. Anal Chim Acta 2018; 1009:39-47. [PMID: 29422130 DOI: 10.1016/j.aca.2018.01.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 12/24/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022]
Abstract
Reports have indicated that warfarin is the most widely prescribed anticoagulant. However, traditionally prescribed doses for each patient may be too low or too high. The therapeutic effect is often hindered by a lack of evidence-based medical information. Herein, our aim is to provide this information. To accomplish this challenge, we report the development of a novel assay based on biotinylated tetrahedral DNA as a capture probe and fullerene (C60)-based nanomaterial as a redox probe using an ultrasensitivity assay with the Vitamin K epoxide reductase complex, subunit 1 (VKORC1). Platinum porous nanoparticles (PtPNPs) were modified on amino-terminated polyamidoamine (PAMAM)-functionalized C60 nanoparticles (C60NPs). The resultant C60NPs-PAMAM-PtPNPs were used as a redox probe. In this design, C60 exhibited excellent redox activity that was triggered by tetraoctylammonium bromide (TOAB). To improve the immobilization of the tetrahedral DNA capture probe, avidin was introduced during the fabrication of the biosensor because it can provide more active sites for the immobilization capture probe. The free-standing probe on top of the tetrahedral DNA served as a receptor to hybridize with target DNA directly. Different pulse voltammetry (DPV) was applied to record the electrochemical signals, which increased linearly with the target DNA. Under optimal conditions, the prepared biosensor showed a wide linear relationship, from 1 pM to 10 nM, with detection limits of 0.33 pM. This strategy demonstrates a new avenue for the determination of tumour-related mutated nucleotides in biosamples.
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Affiliation(s)
- Yongxian Wan
- Department of Orthopedics, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lili Xu
- Department of Rehabilitation Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Naiqiang Zhuo
- Department of Orthopedics, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiaobo Lu
- Department of Orthopedics, Affiliated Hospital of Southwest Medical University, Luzhou, China
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25
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Kilic T, Erdem A, Ozsoz M, Carrara S. microRNA biosensors: Opportunities and challenges among conventional and commercially available techniques. Biosens Bioelectron 2018; 99:525-546. [DOI: 10.1016/j.bios.2017.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 12/19/2022]
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26
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Borghei YS, Hosseini M, Ganjali MR. Fluorometric determination of microRNA via FRET between silver nanoclusters and CdTe quantum dots. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2512-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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27
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Zhu X, Wang R, Zhou X, Shi H. Free-Energy-Driven Lock/Open Assembly-Based Optical DNA Sensor for Cancer-Related microRNA Detection with a Shortened Time-to-Result. ACS APPLIED MATERIALS & INTERFACES 2017; 9:25789-25795. [PMID: 28707877 DOI: 10.1021/acsami.7b06579] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Quantification of cancer biomarker microRNAs (miRs) by exquisitely designed biosensors with a short time-to-result is of great clinical significance. With immobilized capture probes (CPs) and fluorescent-labeled signal probes (SPs), surface-involved sandwich-type (SST) biosensors serve as powerful tools for rapid, highly sensitive, and selective detection of miR in complex matrices as opposed to the conventional techniques. One key challenge for such SST biosensors is the existence of false-negative signals when the amount of miRs exceeds SPs in solution phase for a surface with a limited number of CP. To meet this challenge, a dynamic lock/open DNA assembly was designed to rationally program the pathway for miR/SP hybrids. Based on secondary structure analysis and free-energy assessment, a "locker" strand that partially hybridizes with target miR by two separated short arms was designed to stabilize target miR, preventing possible false-negative signals. The strategy was demonstrated on a fiber-based fluorescent DNA-sensing platform. CP/miR/SP sandwiches formed on the fiber surface would generate fluorescent signals for quantitative analysis. The developed SST biosensor was able to detect miR Hsa let-7a with a detection limit of 24 pM. The applicability of this free-energy-driven lock/open assembly-based optical DNA sensor was further confirmed with spiked human urine and serum samples.
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Affiliation(s)
- Xiyu Zhu
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University , Beijing 100084, China
| | - Ruoyu Wang
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University , Beijing 100084, China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University , Beijing 100084, China
| | - Hanchang Shi
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University , Beijing 100084, China
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28
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Xu L, Liang W, Wen Y, Wang L, Yang X, Ren S, Jia N, Zuo X, Liu G. An ultrasensitive electrochemical biosensor for the detection of mecA gene in methicillin-resistant Staphylococcus aureus. Biosens Bioelectron 2017; 99:424-430. [PMID: 28810233 DOI: 10.1016/j.bios.2017.08.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
Abstract
Electrochemical DNA biosensor has unique advantages for on-site pathogenic microorganism detection, yet the detection of long DNA towards genome DNA (gDNA) analysis remains challenge. In this work, we report a novel electrochemical biosensor for the ultrasensitive analysis of mecA DNA on methicillin-resistant Staphylococcus aureus (MRSA) genome, using a multi-signal probes (MSP) system. The MSP consists of 7 biotin-labelled signal probes that will combine to the target DNA in a prehybridization step, and then the complex will be captured by a DNA tetrahedron structure probe (TSP) on the electrode surface. Then, after the introduction of the streptavidin-labelled HRP enzyme, a catalysis current signal is detected that is found to be corresponding to the concentration of the target DNA. MSP in this work plays a critical role not only for the signal amplification through bringing 7 biotins, but also dramatically improves the accessibility of the target sequence embedded in the double-strand DNA molecules and complex second structures. The 3-D DNA TSP here provides steady support and optimized surface density for the very "large" complex of MSP system and gDNA, as a base of the capture probe. Finally, as low as 10fM synthetic target DNA was successfully detected, which is at least 3 magnitudes lower than that using single signal probe. Most importantly, we demonstrated the practicability of our analysis method by analyzing a 57fM MRSA gDNA sample showing excellent selectivity, and the reliability of the analysis was also demonstrated by digital PCR.
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Affiliation(s)
- Li Xu
- Laboratory of biometrology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China
| | - Wen Liang
- Laboratory of biometrology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China
| | - Yanli Wen
- Laboratory of biometrology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China
| | - Lele Wang
- Laboratory of biometrology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China
| | - Xue Yang
- Department of Chemistry, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, PR China
| | - Shuzhen Ren
- Laboratory of biometrology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China
| | - Nengqin Jia
- Department of Chemistry, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, PR China
| | - Xiaolei Zuo
- Division of Physical Biology&Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, PR China
| | - Gang Liu
- Laboratory of biometrology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China.
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29
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Zeng D, Wang Z, Meng Z, Wang P, San L, Wang W, Aldalbahi A, Li L, Shen J, Mi X. DNA Tetrahedral Nanostructure-Based Electrochemical miRNA Biosensor for Simultaneous Detection of Multiple miRNAs in Pancreatic Carcinoma. ACS APPLIED MATERIALS & INTERFACES 2017; 9:24118-24125. [PMID: 28660759 DOI: 10.1021/acsami.7b05981] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Specific and sensitive biomarker detection is essential to early cancer diagnosis. In this study, we demonstrate an ultrasensitive electrochemical biosensor with the ability to detect multiple pancreatic carcinoma (PC)-related microRNA biomarkers. By employing DNA tetrahedral nanostructure capture probes to enhance the detection sensitivity as well as a disposable 16-channel screen-printed gold electrode (SPGE) detection platform to enhance the detection efficiency, we were able to simultaneously detect four PC-related miRNAs: miRNA21, miRNA155, miRNA196a, and miRNA210. The detection sensitivity reached to as low as 10 fM. We then profiled the serum levels of the four miRNAs for PC patients and healthy individuals with our multiplexing electrochemical biosensor. Through the combined analyses of the four miRNAs, our results showed that PC patients could be discriminated from healthy controls with fairly high sensitivity. This multiplexing PCR-free miRNA detection sensor shows promising applications in early diagnosis of PC disease.
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Affiliation(s)
- Dongdong Zeng
- Shanghai Advanced Research Institute , Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai University of Medicine & Health Sciences , Shanghai 201318, China
| | - Zehua Wang
- Shanghai Advanced Research Institute , Chinese Academy of Sciences, Shanghai 201210, China
| | - Zhiqiang Meng
- Fudan University Shanghai Cancer Center , Shanghai 200032, China
| | - Peng Wang
- Fudan University Shanghai Cancer Center , Shanghai 200032, China
| | - Lili San
- Shanghai Advanced Research Institute , Chinese Academy of Sciences, Shanghai 201210, China
| | - Wei Wang
- Shanghai Pudong New District Zhoupu Hospital , Shanghai 201211, China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Li Li
- School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200241, China
| | - Juwen Shen
- School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200241, China
| | - Xianqiang Mi
- Shanghai Advanced Research Institute , Chinese Academy of Sciences, Shanghai 201210, China
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Isin D, Eksin E, Erdem A. Graphene oxide modified single-use electrodes and their application for voltammetric miRNA analysis. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 75:1242-1249. [DOI: 10.1016/j.msec.2017.02.166] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/24/2017] [Accepted: 02/28/2017] [Indexed: 01/16/2023]
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31
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Mandli J, Mohammadi H, Amine A. Electrochemical DNA sandwich biosensor based on enzyme amplified microRNA-21 detection and gold nanoparticles. Bioelectrochemistry 2017; 116:17-23. [PMID: 28342314 DOI: 10.1016/j.bioelechem.2017.03.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/01/2017] [Accepted: 03/12/2017] [Indexed: 01/03/2023]
Abstract
In this work, a novel electrochemical biosensor for miRNA-21 determination, involving a sandwich hybridization assay onto gold nanoparticles modified pencil graphite electrode (PGE) and enzyme signal amplification was reported. The thiol terminated capture probe 1 (SH-P1) was immobilized on the electrode through AuS interaction. In the presence of target miRNA-21, SH-P1 hybridized with the first part of the target, however, the second part hybridizes with a biotinylated probe P2 (B-P2). Then, a streptavidin-conjugated alkaline phosphatase was immobilized by a specific binding of avidin-B-P2. The enzyme catalyzed the electro-inactive α-naphtyl phosphate to an electro-active α-naphtol. The miRNA-21 detection was achieved through the changes of α-naphtol oxidation signals observed at +0.12V vs Ag/AgCl with Differential Pulse Voltammetry. Under the optimal detection conditions, the biosensor exhibited selective and sensitive detection with a linear range from 200pM to 388nM and the detection limit was 100pM (10fmol in 100μL).
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Affiliation(s)
- Jihane Mandli
- Laboratoire Génie des Procédés et Environnement, Faculté de Sciences et Techniques Mohammedia, University Hassan II of Casablanca, Morocco
| | - Hasna Mohammadi
- Laboratoire Génie des Procédés et Environnement, Faculté de Sciences et Techniques Mohammedia, University Hassan II of Casablanca, Morocco
| | - Aziz Amine
- Laboratoire Génie des Procédés et Environnement, Faculté de Sciences et Techniques Mohammedia, University Hassan II of Casablanca, Morocco.
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32
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Kamal Masud M, Islam MN, Haque MH, Tanaka S, Gopalan V, Alici G, Nguyen NT, Lam AK, Hossain MSA, Yamauchi Y, Shiddiky MJA. Gold-loaded nanoporous superparamagnetic nanocubes for catalytic signal amplification in detecting miRNA. Chem Commun (Camb) 2017; 53:8231-8234. [DOI: 10.1039/c7cc04789d] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A nonenzymatic, amplification-free, and sensitive method for microRNA detection is reported using Au@NPFe2O3NC nanocubes.
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33
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Xu F, Dong H, Cao Y, Lu H, Meng X, Dai W, Zhang X, Al-Ghanim KA, Mahboob S. Ultrasensitive and Multiple Disease-Related MicroRNA Detection Based on Tetrahedral DNA Nanostructures and Duplex-Specific Nuclease-Assisted Signal Amplification. ACS APPLIED MATERIALS & INTERFACES 2016; 8:33499-33505. [PMID: 27960393 DOI: 10.1021/acsami.6b12214] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A highly sensitive and multiple microRNA (miRNA) detection method by combining three-dimensional (3D) DNA tetrahedron-structured probes (TSPs) to increase the probe reactivity and accessibility with duplex-specific nuclease (DSN) for signal amplification for sensitive miRNA detection was proposed. Briefly, 3D DNA TSPs labeled with different fluorescent dyes for specific target miRNA recognition were modified on a gold nanoparticle (GNP) surface to increase the reactivity and accessibility. Upon hybridization with a specific target, the TSPs immobilized on the GNP surface hybridized with the corresponding target miRNA to form DNA-RNA heteroduplexes, and the DSN can recognize the formed DNA-RNA heteroduplexes to hydrolyze the DNA in the heteroduplexes to produce a specific fluorescent signal corresponding to a specific miRNA, while the released target miRNA strands can initiate another cycle, resulting in a significant signal amplification for sensitive miRNA detection. Different targets can produce different fluorescent signals, leading to the development of a sensitive detection for multiple miRNAs in a homogeneous solution. Under optimized conditions, the proposed assay can simultaneously detect three different miRNAs in a homogeneous solution with a logarithmic linear range spanning 5 magnitudes (10-12-10-16) and achieving a limit of detection down to attomolar concentrations. Meanwhile, the proposed miRNA assay exhibited the capability of discriminating single bases (three bases mismatched miRNAs) and showed good eligibility in the analysis of miRNAs extracted from cell lysates and miRNAs in cell incubation media, which indicates its potential use in biomedical research and clinical analysis.
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Affiliation(s)
- Fang Xu
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Haifeng Dong
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Yu Cao
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Huiting Lu
- School of Space and Environment, Beihang University , Beijing 100191, P. R. China
| | - Xiangdan Meng
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Wenhao Dai
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Khalid Abdullah Al-Ghanim
- Department of Zoology, College of Science, P.O. Box 2455, King Saud University , Riyadh 11451, Saudi Arabia
| | - Shahid Mahboob
- Department of Zoology, Government College University , Faisalabad, Pakistan
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Shuai HL, Huang KJ, Chen YX, Fang LX, Jia MP. Au nanoparticles/hollow molybdenum disulfide microcubes based biosensor for microRNA-21 detection coupled with duplex-specific nuclease and enzyme signal amplification. Biosens Bioelectron 2016; 89:989-997. [PMID: 27825521 DOI: 10.1016/j.bios.2016.10.051] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/30/2016] [Accepted: 10/18/2016] [Indexed: 11/16/2022]
Abstract
An ultrasensitive electrochemical biosensor for detecting microRNAs is fabricated based on hollow molybdenum disulfide (MoS2) microcubes. Duplex-specific nuclease, enzyme and electrochemical-chemical-chemical redox cycling are used for signal amplification. Hollow MoS2 microcubes constructed by ultrathin nanosheets are synthesized by a facile template-assisted strategy and used as supporting substrate. For biosensor assembling, biotinylated ssDNA capture probes are first immobilized on Au nanoparticles (AuNPs)/MoS2 modified electrode in order to combine with streptavidin-conjugated alkaline phosphatase (SA-ALP). When capture probes hybridize with miRNAs, duplex-specific nuclease cleaves the formative duplexes. At the moment, the biotin group strips from the electrode surface and SA-ALP is incapacitated to attach onto electrode. Then, ascorbic acids induce the electrochemical-chemical-chemical redox cycling to produce electrochemical response in the presence of ferrocene methanol and tris (2-carboxyethyl) phosphine. Under optimum conditions, the proposed biosensor shows a good linear relationship between the current variation and logarithm of the microRNAs concentration ranging from 0.1fM to 0.1pM with a detection limit of 0.086fM (S/N=3). Furthermore, the biosensor is successfully applied to detect target miRNA-21 in human serum samples.
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Affiliation(s)
- Hong-Lei Shuai
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Ke-Jing Huang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China; Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China.
| | - Ying-Xu Chen
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Lin-Xia Fang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Meng-Pei Jia
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, China
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35
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Shrestha P, Emura T, Koirala D, Cui Y, Hidaka K, Maximuck WJ, Endo M, Sugiyama H, Mao H. Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores. Nucleic Acids Res 2016; 44:6574-82. [PMID: 27387283 PMCID: PMC5001620 DOI: 10.1093/nar/gkw610] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 06/24/2016] [Indexed: 01/13/2023] Open
Abstract
DNA nanoassemblies have demonstrated wide applications in various fields including nanomaterials, drug delivery and biosensing. In DNA origami, single-stranded DNA template is shaped into desired nanostructure by DNA staples that form Holliday junctions with the template. Limited by current methodologies, however, mechanical properties of DNA origami structures have not been adequately characterized, which hinders further applications of these materials. Using laser tweezers, here, we have described two mechanical properties of DNA nanoassemblies represented by DNA nanotubes, DNA nanopyramids and DNA nanotiles. First, mechanical stability of DNA origami structures is determined by the effective density of Holliday junctions along a particular stress direction. Second, mechanical isomerization observed between two conformations of DNA nanotubes at 10–35 pN has been ascribed to the collective actions of individual Holliday junctions, which are only possible in DNA origami with rotational symmetric arrangements of Holliday junctions, such as those in DNA nanotubes. Our results indicate that Holliday junctions control mechanical behaviors of DNA nanoassemblies. Therefore, they can be considered as ‘mechanophores’ that sustain mechanical properties of origami nanoassemblies. The mechanical properties observed here provide insights for designing better DNA nanostructures. In addition, the unprecedented mechanical isomerization process brings new strategies for the development of nano-sensors and actuators.
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Affiliation(s)
- Prakash Shrestha
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Yunxi Cui
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - William J Maximuck
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
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36
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Controllable Molecule Transport and Release by a Restorable Surface-tethered DNA nanodevice. Sci Rep 2016; 6:28292. [PMID: 27384943 PMCID: PMC4935947 DOI: 10.1038/srep28292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/01/2016] [Indexed: 01/05/2023] Open
Abstract
In this paper, we report a novel surface-tethered DNA nanodevice that may present three states and undergo conformational changes under the operation of pH. Besides, convenient regulation on the electrode surface renders the construction and operation of this DNA nanodevice restorable. To make full use of this DNA nanodevice, ferrocene (Fc) has been further employed for the fabrication of the molecular device. On one hand, the state switches of the DNA nanodevice can be characterized conveniently and reliably by the obtained electrochemical signals from Fc. On the other hand, β-cyclodextrin-ferrocene (β-CD-Fc) host-guest system can be introduced by Fc, which functionalizes this molecular device. Based on different electrochemical behaviors of β-CD under different states, this DNA nanodevice can actualize directional loading, transporting and unloading of β-CD in nanoscale. Therefore, this DNA nanodevice bares promising applications in controllable molecular transport and release, which are of great value to molecular device design.
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37
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San L, Zeng D, Song S, Zuo X, Zhang H, Wang C, Wu J, Mi X. An electrochemical immunosensor for quantitative detection of ficolin-3. NANOTECHNOLOGY 2016; 27:254003. [PMID: 27183363 DOI: 10.1088/0957-4484/27/25/254003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Diabetes mellitus (DM) is one of the most common metabolic disorders in the world, of which more than 90% is type-2 diabetes mellitus (T2DM). There is a rather urgent need for reliable, sensitive and quick detection techniques in clinical application of T2DM. Ficolin-3 is a potential biomarker of T2DM, because serum ficolin-3 levels are associated with insulin resistance and predict the incidence of T2DM. Herein, a sandwich-type electrochemical immunosensor was developed for the detection of ficolin-3 in human serum. Cyclic voltammetry and the amperometric current versus time were used to characterize the performance of the immunosensor. Under optimal conditions, the detection limitation of ficolin-3 was 100 ng ml(-1) and the linear dynamic range was between 2 and 50 μg ml(-1). The method has ideal accuracy, excellent stability and selectivity and has wide application prospects in clinical research.
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Affiliation(s)
- Lili San
- Laboratory of System Biology, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, People's Republic of China. University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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38
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An electrochemical nanobiosensor for plasma miRNA-155, based on graphene oxide and gold nanorod, for early detection of breast cancer. Biosens Bioelectron 2016; 77:99-106. [DOI: 10.1016/j.bios.2015.09.020] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/29/2015] [Accepted: 09/10/2015] [Indexed: 11/20/2022]
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39
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Erdem A, Eksin E, Congur G. Indicator-free electrochemical biosensor for microRNA detection based on carbon nanofibers modified screen printed electrodes. J Electroanal Chem (Lausanne) 2015. [DOI: 10.1016/j.jelechem.2015.07.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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40
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Li L, Wen Y, Xu L, Xu Q, Song S, Zuo X, Yan J, Zhang W, Liu G. Development of mercury (II) ion biosensors based on mercury-specific oligonucleotide probes. Biosens Bioelectron 2015; 75:433-45. [PMID: 26356764 DOI: 10.1016/j.bios.2015.09.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/21/2015] [Accepted: 09/01/2015] [Indexed: 10/23/2022]
Abstract
Mercury (II) ion (Hg(2+)) contamination can be accumulated along the food chain and cause serious threat to the public health. Plenty of research effort thus has been devoted to the development of fast, sensitive and selective biosensors for monitoring Hg(2+). Thymine was demonstrated to specifically combine with Hg(2+) and form a thymine-Hg(2+)-thymine (T-Hg(2+)-T) structure, with binding constant even higher than T-A Watson-Crick pair in DNA duplex. Recently, various novel Hg(2+) biosensors have been developed based on T-rich Mercury-Specific Oligonucleotide (MSO) probes, and exhibited advanced selectivity and excellent sensitivity for Hg(2+) detection. In this review, we explained recent development of MSO-based Hg(2+) biosensors mainly in 3 groups: fluorescent biosensors, colorimetric biosensors and electrochemical biosensors.
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Affiliation(s)
- Lanying Li
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China
| | - Yanli Wen
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China
| | - Li Xu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China
| | - Qin Xu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China
| | - Shiping Song
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, PR China
| | - Xiaolei Zuo
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, PR China
| | - Juan Yan
- College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Pudong District, Shanghai 201306, PR China.
| | - Weijia Zhang
- College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Pudong District, Shanghai 201306, PR China
| | - Gang Liu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, PR China
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41
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A novel ultrasensitive electrochemical DNA sensor based on double tetrahedral nanostructures. Biosens Bioelectron 2015; 71:434-438. [DOI: 10.1016/j.bios.2015.04.065] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 04/09/2015] [Accepted: 04/20/2015] [Indexed: 12/30/2022]
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42
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Vaisocherová H, Šípová H, Víšová I, Bocková M, Špringer T, Laura Ermini M, Song X, Krejčík Z, Chrastinová L, Pastva O, Pimková K, Dostálová Merkerová M, Dyr JE, Homola J. Rapid and sensitive detection of multiple microRNAs in cell lysate by low-fouling surface plasmon resonance biosensor. Biosens Bioelectron 2015; 70:226-31. [DOI: 10.1016/j.bios.2015.03.038] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/05/2015] [Accepted: 03/16/2015] [Indexed: 12/31/2022]
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43
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Xing S, Jiang D, Li F, Li J, Li Q, Huang Q, Guo L, Xia J, Shi J, Fan C, Zhang L, Wang L. Constructing Higher-Order DNA Nanoarchitectures with Highly Purified DNA Nanocages. ACS APPLIED MATERIALS & INTERFACES 2015; 7:13174-9. [PMID: 25345465 DOI: 10.1021/am505592e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
DNA nanostructures have attracted great attention due to their precisely controllable geometry and great potential in various areas including bottom-up self-assembly. However, construction of higher-order DNA nanoarchitectures with individual DNA nanostructures is often hampered with the purity and quantity of these "bricks". Here, we introduced size exclusion chromatography (SEC) to prepare highly purified tetrahedral DNA nanocages in large scale and demonstrated that precise quantification of DNA nanocages was the key to the formation of higher-order DNA nanoarchitectures. We successfully purified a series of DNA nanocages with different sizes, including seven DNA tetrahedra with different edge lengths (7, 10, 13, 17, 20, 26, 30 bp) and one trigonal bipyramid with a 20-bp edge. These highly purified and aggregation-free DNA nanocages could be self-assembled into higher-order DNA nanoarchitectures with extraordinarily high yields (98% for dimer and 95% for trimer). As a comparison, unpurified DNA nanocages resulted in low yield of 14% for dimer and 12% for trimer, respectively. AFM images cleraly presented the characteristic structure of monomer, dimer and trimer, impling the purified DNA nanocages well-formed the designed nanoarchitectures. Therefore, we have demonstrated that highly purified DNA nanocages are excellent "bricks" for DNA nanotechnology and show great potential in various applications of DNA nanomaterials.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiaoyun Xia
- §College of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410004, China
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44
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An electrochemical microRNAs biosensor with the signal amplification of alkaline phosphatase and electrochemical–chemical–chemical redox cycling. Anal Chim Acta 2015; 878:95-101. [DOI: 10.1016/j.aca.2015.04.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/14/2023]
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45
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Simultaneous detection of two breast cancer-related miRNAs in tumor tissues using p19-based disposable amperometric magnetobiosensing platforms. Biosens Bioelectron 2015; 66:385-91. [DOI: 10.1016/j.bios.2014.11.047] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/17/2014] [Accepted: 11/25/2014] [Indexed: 11/21/2022]
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46
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Keshavarz M, Behpour M, Rafiee-pour HA. Recent trends in electrochemical microRNA biosensors for early detection of cancer. RSC Adv 2015. [DOI: 10.1039/c5ra01726b] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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47
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Krejcova L, Nguyen HV, Hynek D, Guran R, Adam V, Kizek R. Paramagnetic Particles and PNA Probe for Automated Separation and Electrochemical Detection of Influenza. Chromatographia 2014. [DOI: 10.1007/s10337-014-2737-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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48
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Torrente-Rodríguez RM, Campuzano S, López-Hernández E, Granados R, Sánchez-Puelles JM, Pingarrón JM. Direct Determination of miR-21 in Total RNA Extracted from Breast Cancer Samples Using Magnetosensing Platforms and the p19 Viral Protein as Detector Bioreceptor. ELECTROANAL 2014. [DOI: 10.1002/elan.201400317] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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49
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Kamiya Y, Asanuma H. Light-driven DNA nanomachine with a photoresponsive molecular engine. Acc Chem Res 2014; 47:1663-72. [PMID: 24617966 DOI: 10.1021/ar400308f] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CONSPECTUS: DNA is regarded as an excellent nanomaterial due to its supramolecular property of duplex formation through A-T and G-C complementary pairs. By simply designing sequences, we can create any desired 2D or 3D nanoarchitecture with DNA. Based on these nanoarchitectures, motional DNA-based nanomachines have also been developed. Most of the nanomachines require molecular fuels to drive them. Typically, a toehold exchange reaction is applied with a complementary DNA strand as a fuel. However, repetitive operation of the machines accumulates waste DNA duplexes in the solution that gradually deteriorate the motional efficiency. Hence, we are facing an "environmental problem" even in the nanoworld. One of the direct solutions to this problem is to use clean energy, such as light. Since light does not contaminate the reaction system, a DNA nanomachine run by a photon engine can overcome the drawback of waste that is a problem with molecular-fueled engines. There are several photoresponsive molecules that convert light energy to mechanical motion through the change of geometry of the molecules; these include spiropyran, diarylethene, stilbene, and azobenzene. Although each molecule has both advantages and drawbacks, azobenzene derivatives are widely used as "molecular photon engines". In this Account, we review light-driven DNA nanomachines mainly focusing on the photoresponsive DNAs that we have developed for the past decade. The basis of our method is installation of an azobenzene into a DNA sequence through a d-threoninol scaffold. Reversible hybridization of the DNA duplex, triggered by trans-cis isomerization of azobenzene in the DNA sequences by irradiation with light, induces mechanical motion of the DNA nanomachine. Moreover we have successfully developed azobenzene derivatives that improve its photoisomerizaition properties. Use of these derivatives and techniques have allowed us to design various DNA machines that demonstrate sophisticated motion in response to lights of different wavelengths without a drop in photoregulatory efficiency. In this Account, we emphasize the advantages of our methods including (1) ease of preparation, (2) comprehensive sequence design of azobenzene-tethered DNA, (3) efficient photoisomerization, and (4) reversible photocontrol of hybridization by irradiation with appropriate wavelengths of light. We believe that photon-fueled DNA nanomachines driven by azobenzene-derivative molecular photon-fueled engines will be soon science rather than "science fiction".
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Affiliation(s)
- Yukiko Kamiya
- Graduate
School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
- Ecotopia
Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma
- Graduate
School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
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