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San Juan A, Jaitpal S, Ng KW, Martinez C, Tripathy S, Phillips C, Coté GL, Mabbott S. Freeze-Driven Synthesis of DNA Hairpin-Conjugated Gold Nanoparticle Biosensors for Dual-Mode Detection. ACS APPLIED BIO MATERIALS 2024; 7:3005-3013. [PMID: 38629141 PMCID: PMC11110043 DOI: 10.1021/acsabm.4c00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 05/21/2024]
Abstract
Freeze-based immobilization of deoxyribonucleic acid (DNA) oligonucleotides on gold nanoparticles (AuNPs) is highly efficient for single-stranded oligonucleotides but typically does not accommodate structures such as snap-cooled DNA hairpins (Sc-HPs) and snap-cooled molecular beacons (Sc-MBs) frequently used for biorecognition applications. Recognizing this limitation, we have developed a modified, freeze-based technique specifically designed to enable the adsorption of such hairpin oligonucleotides onto AuNP surfaces while ensuring that they retain their biosensing capabilities. Successful hairpin oligonucleotide conjugation of varying lengths to a wide range of AuNP diameters was corroborated by dynamic light scattering, ζ-potential, and UV-vis spectrophotometry. Moreover, we conducted a thorough evaluation of this modified method, confirming the retention of the sensing functions of Sc-HPs and Sc-MBs. This advancement not only offers a more efficient route for DNA hairpin conjugation but also elucidates the underlying biorecognition functions, with implications for broader applications in molecular diagnostics.
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Affiliation(s)
- Angela
Michelle San Juan
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 77843-3120, United States
- Center
for Remote Health Technologies & Systems, Texas A&M Engineering Experiment Station, College Station, Texas 77845-3424, United States
| | - Siddhant Jaitpal
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 77843-3120, United States
| | - Ka Wai Ng
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 77843-3120, United States
| | - Cecilia Martinez
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 77843-3120, United States
| | - Sayantan Tripathy
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 77843-3120, United States
- Center
for Remote Health Technologies & Systems, Texas A&M Engineering Experiment Station, College Station, Texas 77845-3424, United States
| | - Christian Phillips
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 77843-3120, United States
| | - Gerard L Coté
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 77843-3120, United States
- Center
for Remote Health Technologies & Systems, Texas A&M Engineering Experiment Station, College Station, Texas 77845-3424, United States
| | - Samuel Mabbott
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 77843-3120, United States
- Center
for Remote Health Technologies & Systems, Texas A&M Engineering Experiment Station, College Station, Texas 77845-3424, United States
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2
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Zhu S, Chen J, Yu L, Li J, You S, Zheng Y, Zhuang W, Qiu B, Huang Y. Detection of fucosylated extracellular vesicles miR-4732-5p related to diagnosis of early lung adenocarcinoma by the electrochemical biosensor. Sci Rep 2024; 14:11217. [PMID: 38755208 PMCID: PMC11099009 DOI: 10.1038/s41598-024-61060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Our preliminary investigation has identified the potential of serum fucosylated extracellular vesicles (EVs) miR-4732-5p in the early diagnosis of lung adenocarcinoma (LUAD) by a fucose-captured strategy utilizing lentil lectin (LCA)-magnetic beads and subsequent screening of high throughput sequencing and validation of real-time quantitative polymerase chain reaction (RT-qPCR). Considering the relatively complicated procedure, expensive equipment, and stringent laboratory condition, we have constructed an electrochemical biosensor assay for the detection of miR-4732-5p. miR-4732-5p is extremely low in serum, down to the fM level, so it needs to be detected by highly sensitive electrochemical methods based on the Mg2+-dependent DNAzyme splitting nucleic acid lock (NAL) cycle and hybridization chain reaction (HCR) signal amplification. In this study, signal amplification is achieved through the dual amplification reactions using NAL cycle in combination with HCR. In addition, hybridized DNA strands bind to a large number of methylene blue (MB) molecules to enhance signaling. Based on the above strategy, we further enhance our signal amplification strategies to improve detection sensitivity and accuracy. The implementation of this assay proceeded as follows: initially, miR-4732-5p was combined with NAL, and then Mg2+-dependent DNAzyme splitted NAL to release auxiliary DNA (S1) strands, which were subsequently captured by the immobilized capture probe DNA (C1) strands on the electrode surface. Following this, abundant quantities of DNA1 (H1) and DNA2 (H2) tandems were generated by HCR, and S1 strands then hybridized with the H1 and H2 tandems through base complementary pairing. Finally, MB was bonded to the H1 and H2 tandems through π-π stacking interaction, leading to the generation of a signal current upon the detection of a potential capable of inducing a redox change of MB by the electrode. Furthermore, we evaluated the performance of our developed electrochemical biosensor assay. The results demonstrated that our assay is a reliable approach, characterized by its high sensitivity (with a detection limit of 2.6 × 10-17 M), excellent specificity, good accuracy, reproducibility, and stability. Additionally, it is cost-effective, requires simple operation, and is portable, making it suitable for the detection of serum fucosylated extracellular vesicles miR-4732-5p. Ultimately, this development has the potential to enhance the diagnostic efficiency for patients with early-stage LUAD.
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Affiliation(s)
- Shengting Zhu
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Blood Transfusion, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Jianlin Chen
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Lili Yu
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Jiawen Li
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology (Fuzhou University), Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou, 350108, China
| | - Shumin You
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology (Fuzhou University), Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou, 350108, China
| | - Yue Zheng
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Wanzhen Zhuang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology (Fuzhou University), Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou, 350108, China.
| | - Yi Huang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China.
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China.
- Central Laboratory, Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, 350001, China.
- Fujian Provincial Key Laboratory of Critical Care Medicine, Fujian Provincial Key Laboratory of Cardiovascular Disease, Fuzhou, 350001, China.
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3
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Fu Z, Huang J, Wei W, Wu Z, Shi X. A multimode biosensor based on prussian blue nanoparticles loaded with gold nanoclusters for the detection of aflatoxin B1. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 38690679 DOI: 10.1039/d3ay02330c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Herein, a novel fluorescent/colorimetric/photothermal biosensor is proposed for aflatoxin B1 (AFB1) detection in food based on Prussian blue nanoparticles (PBNPs) (∼50 nm), gold nanoclusters (AuNCs), and an aptamer (Apt) within three hours. Briefly, a multifunctional compound, namely PBNPs-PEI@AuNCs, was synthesized from PBNPs as the loading carrier, polyethyleneimine (PEI) as the cross-linking agent, and AuNCs directly combined on the surface of PBNPs. The AFB1 Apt was then modified on the PBNPs-PEI@AuNCs to form a PBNPs-PEI@AuNCs-Apt probe, whereby when AFB1 is present, AFB1 is specifically captured by the probe. Meanwhile, the MNPs@antibody was also introduced to capture AFB1, thereby forming a "sandwich" structure compound. After magnetic separation, high temperature was applied to this "sandwich" structure compound to induce the denaturation of the Apt. Then the fluorescent/colorimetric/photothermal signals were collected from the PBNPs-PEI@AuNCs@Apt to give information on its related condition. The detection limits of the biosensor were 0.64 × 10-14, 0.96 × 10-14, and 0.55 × 10-12 g mL-1 for the three signals, which were outputted independently and could be verified with each other to ensure the accuracy of the results. Moreover, the colorimetric and photothermal strategies with this probe do not require large-scale instruments, providing a promising choice for achieving the rapid field detection of AFB1.
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Affiliation(s)
- Zhaodi Fu
- Testing Technology Company of Changsha Research Institute of Mining and Metallurgy Co., Ltd., Changsha 410012, China
| | - Juan Huang
- Laboratory of Micro & Nano Biosensing Technology in Food Safety, Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China.
| | - Wei Wei
- Testing Technology Company of Changsha Research Institute of Mining and Metallurgy Co., Ltd., Changsha 410012, China
| | - Zhihui Wu
- Laboratory of Micro & Nano Biosensing Technology in Food Safety, Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China.
| | - Xingbo Shi
- Laboratory of Micro & Nano Biosensing Technology in Food Safety, Hunan Provincial Key Laboratory of Food Science and Biotechnology, College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, China.
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4
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Li Y, Tang X, Deng R, Feng L, Xie S, Chen M, Zheng J, Chang K. Dumbbell Dual-Hairpin Triggered DNA Nanonet Assembly for Cascade-Amplified Sensing of Exosomal MicroRNA. ACS OMEGA 2024; 9:19723-19731. [PMID: 38708273 PMCID: PMC11064005 DOI: 10.1021/acsomega.4c02652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
Exosomal microRNAs (miRNAs) are valuable biomarkers closely associated with cancer progression. Therefore, sensitive and specific exosomal miRNA biosensing has been employed for cancer diagnosis, prognosis, and prediction. In this study, a miRNA-based DNA nanonet assembly strategy is proposed, enabling the biosensing of exosomal miRNAs through dumbbell dual-hairpin under isothermal enzyme-free conditions. This strategy dexterously designs a specific dumbbell dual-hairpin that can selectively recognize exosomal miRNA, inducing conformational changes to cascade-generated X-shaped DNA structures, facilitating the extension of the X-shaped DNA in three-dimensional space, ultimately forming a DNA nanonet assembly. On the basis of the target miRNA, our design enriches the fluorescence signal through the cascade assembly of DNA nanonet and realizes the secondary signal amplification. Using exosomal miR-141 as the target, the resultant fluorescence sensing demonstrates an impressive detection limit of 57.6 pM and could identify miRNA sequences with single-base variants with high specificity. Through the analysis of plasma and urine samples, this method effectively distinguishes between benign prostatic hyperplasia, prostate cancer, and metastatic prostate cancer. Serving as a novel noninvasive and accurate screening and diagnostic tool for prostate cancer, this dumbbell dual-hairpin triggered DNA nanonet assembly strategy is promising for clinical applications.
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Affiliation(s)
- Yongxing Li
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
- Department
of Urology, Urologic Surgery Center, Xinqiao Hospital, Third Military Medical University (Army Medical University), 183 Xinqiao, Shapingba
District, Chongqing 400037, P. R. China
- School
of Medicine, Chongqing University, Chongqing 400030, P. R. China
| | - Xiaoqi Tang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Ruijia Deng
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Liu Feng
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Shuang Xie
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Ming Chen
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
| | - Ji Zheng
- Department
of Urology, Urologic Surgery Center, Xinqiao Hospital, Third Military Medical University (Army Medical University), 183 Xinqiao, Shapingba
District, Chongqing 400037, P. R. China
- School
of Medicine, Chongqing University, Chongqing 400030, P. R. China
| | - Kai Chang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba
District, Chongqing 400038, P. R. China
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5
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Kim H, Noh H. Signal Amplification by Spatial Concentration for Immunoassay on Cellulose Media. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307556. [PMID: 38012537 DOI: 10.1002/smll.202307556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Immunoassay is one of the most common bioanalytical techniques from lab-based to point-of-care settings. Over time, various approaches have been developed to amplify signals for greater sensitivity. However, the need for effective, versatile, and simple signal amplification methods persists yet. This paper presents a novel signal amplification method for immunoassay that utilizes spatial concentration of a cellulose-based plate possessing sensor transducers, specifically gold nanoparticles. By modifying the dimensions of the plate, the density of nanoparticles increased, resulting in intensified color signals. The coating material, polydopamine, which is utilized to protect the gold nanoparticles. Chemical changes in nanocomposites are characterized using scanning electron microscopy, Raman spectroscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and scanning electron microscopy. The application of this method to colorimetric quantification demonstrated great consistency across various concentrations of nanoparticles, with better reliability at lower concentration ranges. A model immunoassay is designed to evaluate the analytical performance. As a result, this method successfully corrected a false-negative result with a lowered Kd of 0.509 pmol per zone. This method shows strong signal enhancement capability that can correct false-negative signals in the immunoassays, with potential benefits including versatility, simplicity, low cost, and the ability to operate multiple plates simultaneously.
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Affiliation(s)
- Hyeokjung Kim
- Department of Optometry, Seoul National University of Science and Technology, Seoul, 01811, South Korea
| | - Hyeran Noh
- Department of Optometry, Seoul National University of Science and Technology, Seoul, 01811, South Korea
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6
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Fattahi M, Rahdan F, Shaterabadi D, Zamani Sani M, Alizadeh M, Khatami SH, Taheri-Anganeh M, Movahedpour A, Ghasemi H. MicroRNA biosensors for the detection of liver cancer. Clin Chim Acta 2024; 554:117796. [PMID: 38272250 DOI: 10.1016/j.cca.2024.117796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
Liver cancer is one of the deadliest types worldwide and early diagnosis is highly important for successful treatment. Therefore, it is necessary to develop rapid, sensitive, simple, and inexpensive analytical tools for its detection. MicroRNAs (miRNA) represent unique biomarkers whose expression in biofluids is strongly associated with cancer in general and miR-21, -31, -122, -145, -146a, -200c, -221, -222, and -223 in liver cancer, specifically. Various biosensors for miRNA detection have been developed. These include electrochemical biosensors based on amperometric, potentiometric, conductometric and impedimetric technology. Furthermore, the use of advanced nanomaterials with enhanced chemical stability, conductivity and electrocatalytic activity have greatly increased the sensitivity and specificity of these devices. The present review focuses on recent advances in electrochemical biosensors for miRNA detection in liver cancer.
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Affiliation(s)
- Mehdi Fattahi
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam; School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
| | - Fereshteh Rahdan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Donya Shaterabadi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Zamani Sani
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Alizadeh
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
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7
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Wang X, Zheng D, Wang C, Xue D, Wang Q, Xia J. Harnessing intermolecular G-quadruplex-based spatial confinement effect for accelerated activation of CRISPR/Cas12a empowers ultra-sensitive detection of PML/RARA fusion genes. Anal Chim Acta 2024; 1287:342108. [PMID: 38182385 DOI: 10.1016/j.aca.2023.342108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/07/2024]
Abstract
Accurate detection and classification of the three isoforms of PML/RARA genomic fragments are crucial for predicting disease progression, stratifying risk, and administering precise drug therapies in acute promyelocytic leukemia (APL). In this study, we have developed a highly specific nucleic acid detection platform capable of quantifying the long isoform of the three main PML-RARA isoforms at a constant temperature. This platform integrates the strengths of the CRISPR/Cas12a nuclease-based method and the rolling circle amplification (RCA) technique. Notably, the RCA-assisted CRISPR/Cas12a trans-cleavage system incorporates a spatial confinement effect by utilizing intermolecular G-quadruplex structures. This innovative design effectively enhances the local concentration of CRISPR/Cas12a, thereby accelerating its cleaving efficiency towards reporter nucleic acids and enabling the detection of PML/RARA fusion gene expression through spectroscopy. The robust detection of PML/RARA fusion gene from human serum samples validates the reliability and potential of this platform in the screening, diagnosis, and prognosis of APL cases. Our findings present an approach that holds significant potential for the further development of the robust CRISPR/Cas sensor system, offering a rapid and adaptable paradigm for APL diagnosis.
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Affiliation(s)
- Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, 350000, PR China; NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian, 350000, PR China.
| | - Dan Zheng
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China
| | - Chengyi Wang
- Department of Hematology & Oncology, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, Fujian, 350011, PR China
| | - Danni Xue
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China
| | - Qi Wang
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China
| | - Juan Xia
- School of Chemistry and Materials Engineering, Fuyang Normal University, Fuyang, Anhui, 236037, PR China.
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8
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García JF, Reguera D, Valls A, Aviñó A, Dominguez A, Eritja R, Gargallo R. Detection of pyrimidine-rich DNA sequences based on the formation of parallel and antiparallel triplex DNA and fluorescent silver nanoclusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122752. [PMID: 37084680 DOI: 10.1016/j.saa.2023.122752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
In this work, the use of DNA-stabilized fluorescent silver nanoclusters for the detection of target pyrimidine-rich DNA sequences by formation of parallel and antiparallel triplex structures is studied by molecular fluorescence spectroscopy. In the case of parallel triplexes, the probe DNA fragments are Watson-Crick stabilized hairpins, and whereas in the case of antiparallel triplexes, the probe fragments are reverse-Hoogsteen clamps. In all cases, the formation of the triplex structures has been assessed by means of polyacrylamide gel electrophoresis, circular dichroism, and molecular fluorescence spectroscopies, as well as multivariate data analysis methods. The results have shown that it is possible the detection of pyrimidine-rich sequences with an acceptable selectivity by using the approach based on the formation of antiparallel triplex structures.
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Affiliation(s)
- Juan Fernando García
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - David Reguera
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - Andrea Valls
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Arnau Dominguez
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Raimundo Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain.
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9
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Wang J, Zhang X, Shi P, Cao B, Wang B. A DNA Finite-State Machine Based on the Programmable Allosteric Strategy of DNAzyme. Int J Mol Sci 2023; 24:ijms24043588. [PMID: 36834996 PMCID: PMC9963683 DOI: 10.3390/ijms24043588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 02/16/2023] Open
Abstract
Living organisms can produce corresponding functions by responding to external and internal stimuli, and this irritability plays a pivotal role in nature. Inspired by such natural temporal responses, the development and design of nanodevices with the ability to process time-related information could facilitate the development of molecular information processing systems. Here, we proposed a DNA finite-state machine that can dynamically respond to sequential stimuli signals. To build this state machine, a programmable allosteric strategy of DNAzyme was developed. This strategy performs the programmable control of DNAzyme conformation using a reconfigurable DNA hairpin. Based on this strategy, we first implemented a finite-state machine with two states. Through the modular design of the strategy, we further realized the finite-state machine with five states. The DNA finite-state machine endows molecular information systems with the ability of reversible logic control and order detection, which can be extended to more complex DNA computing and nanomachines to promote the development of dynamic nanotechnology.
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Affiliation(s)
- Jun Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
- Correspondence: ; Tel.: +86-0411-87402106
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10
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Recent advances in biosensors and sequencing technologies for the detection of mutations. Microchem J 2023. [DOI: 10.1016/j.microc.2022.108306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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DNA computational device-based smart biosensors. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2022.116911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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12
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Wang J, Davidson JL, Kaur S, Dextre AA, Ranjbaran M, Kamel MS, Athalye SM, Verma MS. Paper-Based Biosensors for the Detection of Nucleic Acids from Pathogens. BIOSENSORS 2022; 12:bios12121094. [PMID: 36551061 PMCID: PMC9776365 DOI: 10.3390/bios12121094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 05/17/2023]
Abstract
Paper-based biosensors are microfluidic analytical devices used for the detection of biochemical substances. The unique properties of paper-based biosensors, including low cost, portability, disposability, and ease of use, make them an excellent tool for point-of-care testing. Among all analyte detection methods, nucleic acid-based pathogen detection offers versatility due to the ease of nucleic acid synthesis. In a point-of-care testing context, the combination of nucleic acid detection and a paper-based platform allows for accurate detection. This review offers an overview of contemporary paper-based biosensors for detecting nucleic acids from pathogens. The methods and limitations of implementing an integrated portable paper-based platform are discussed. The review concludes with potential directions for future research in the development of paper-based biosensors.
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Affiliation(s)
- Jiangshan Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Josiah Levi Davidson
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Simerdeep Kaur
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Andres A. Dextre
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohsen Ranjbaran
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohamed S. Kamel
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Shreya Milind Athalye
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohit S. Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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13
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Xia J, Liu Z, Gao S, Wang Q, Xu J, Wu H. Intermolecular and Intramolecular Priming Co-directed Synergistic Multi-strand Displacement Amplification Empowers Ultrasensitive Determination of microRNAs. Anal Chem 2022; 94:16132-16141. [DOI: 10.1021/acs.analchem.2c03466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Juan Xia
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Chemistry and Materials Engineering, Fuyang Normal University, Anhui Fuyang 236037, P. R. China
| | - Zhaoqiang Liu
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Shulin Gao
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Qi Wang
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Anhui, Hefei 230601, P. R. China
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Anhui, Fuyang 236037, P. R. China
| | - Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China
| | - Hai Wu
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Chemistry and Materials Engineering, Fuyang Normal University, Anhui Fuyang 236037, P. R. China
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14
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Wang W, Gunasekaran S. MXene-Based Nucleic Acid Biosensors for Agricultural and Food Systems. BIOSENSORS 2022; 12:bios12110982. [PMID: 36354491 PMCID: PMC9688781 DOI: 10.3390/bios12110982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 05/04/2023]
Abstract
MXene is a two-dimensional (2D) nanomaterial that exhibits several superior properties suitable for fabricating biosensors. Likewise, the nucleic acid (NA) in oligomerization forms possesses highly specific biorecognition ability and other features amenable to biosensing. Hence the combined use of MXene and NA is becoming increasingly common in biosensor design and development. In this review, MXene- and NA-based biosensors are discussed in terms of their sensing mechanisms and fabrication details. MXenes are introduced from their definition and synthesis process to their characterization followed by their use in NA-mediated biosensor fabrication. The emphasis is placed on the detection of various targets relevant to agricultural and food systems, including microbial pathogens, chemical toxicants, heavy metals, organic pollutants, etc. Finally, current challenges and future perspectives are presented with an eye toward the development of advanced biosensors with improved detection performance.
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15
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Two-Dimensional Graphitic Carbon Nitride (g-C 3N 4) Nanosheets and Their Derivatives for Diagnosis and Detection Applications. J Funct Biomater 2022; 13:jfb13040204. [PMID: 36412845 PMCID: PMC9680252 DOI: 10.3390/jfb13040204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022] Open
Abstract
The early diagnosis of certain fatal diseases is vital for preventing severe consequences and contributes to a more effective treatment. Despite numerous conventional methods to realize this goal, employing nanobiosensors is a novel approach that provides a fast and precise detection. Recently, nanomaterials have been widely applied as biosensors with distinctive features. Graphite phase carbon nitride (g-C3N4) is a two-dimensional (2D) carbon-based nanostructure that has received attention in biosensing. Biocompatibility, biodegradability, semiconductivity, high photoluminescence yield, low-cost synthesis, easy production process, antimicrobial activity, and high stability are prominent properties that have rendered g-C3N4 a promising candidate to be used in electrochemical, optical, and other kinds of biosensors. This review presents the g-C3N4 unique features, synthesis methods, and g-C3N4-based nanomaterials. In addition, recent relevant studies on using g-C3N4 in biosensors in regard to improving treatment pathways are reviewed.
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16
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Handrea-Dragan IM, Botiz I, Tatar AS, Boca S. Patterning at the micro/nano-scale: Polymeric scaffolds for medical diagnostic and cell-surface interaction applications. Colloids Surf B Biointerfaces 2022; 218:112730. [DOI: 10.1016/j.colsurfb.2022.112730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 11/27/2022]
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17
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Chang Y, Lou J, Yang L, Liu M, Xia N, Liu L. Design and Application of Electrochemical Sensors with Metal-Organic Frameworks as the Electrode Materials or Signal Tags. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12183248. [PMID: 36145036 PMCID: PMC9506444 DOI: 10.3390/nano12183248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/01/2023]
Abstract
Metal-organic frameworks (MOFs) with fascinating chemical and physical properties have attracted immense interest from researchers regarding the construction of electrochemical sensors. In this work, we review the most recent advancements of MOF-based electrochemical sensors for the detection of electroactive small molecules and biological macromolecules (e.g., DNA, proteins, and enzymes). The types and functions of MOF-based nanomaterials in terms of the design of electrochemical sensors are also discussed. Furthermore, the limitations and challenges of MOF-based electrochemical sensing devices are explored. This work should be invaluable for the development of MOF-based advanced sensing platforms.
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Affiliation(s)
- Yong Chang
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
- School of Chemistry and Materials Engineering, Jiangnan University, Wuxi 214122, China
| | - Jiaxin Lou
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Luyao Yang
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Miaomiao Liu
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Ning Xia
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
| | - Lin Liu
- College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, China
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18
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Zhang X, Zhang Z, Yang C, Hu Z, Chen Y, Feng L. Cytidine-rich hydrogel as an electrochemical signal amplification strategy for microRNA detection. Analyst 2022; 147:2757-2763. [PMID: 35588251 DOI: 10.1039/d2an00667g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Signal amplification strategies increase the complexities of biosensors while improving the response signals. Herein, a novel electrochemical biosensor was developed based on a DNA hydrogel for sensitive analysis using microRNA-21 (miRNA-21) as a detection model. Poly C sequences combined with C-Ag(I)-C hydrogel formed a DNA hydrogel by the unique interaction between the cytosines and silver ions. Thus, with a three-way conjunction structure of DNA, this C-Ag(I)-C hydrogel was constructed as a novel biosensor for the detection of miRNAs. With the assistance of this hydrogel, numerous silver ions gathered around DNA strands, which would amplify the signal. Under these conditions, the silver ions produced distinct square wave voltammetry oxidation peak currents. This electrochemical biosensor we designed exhibited a great linear relationship for the logarithm of the concentration of miRNA-21 from 1 fM to 100 pM with a detection limit of 0.117 fM. Furthermore, our sensors were able to differentiate miRNA-21 from its homologous family with satisfactory responsiveness in the dilute bovine serum system.
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Affiliation(s)
- Xinying Zhang
- Department of Materials Genome Institute, and Department of Chemistry, College of Science, Shanghai University, 200444 Shanghai, China. .,Shanghai Engineering Research Center of Organ Repair, China
| | - Zhiwei Zhang
- Department of Materials Genome Institute, and Department of Chemistry, College of Science, Shanghai University, 200444 Shanghai, China. .,Shanghai Engineering Research Center of Organ Repair, China
| | - Chujing Yang
- Department of Materials Genome Institute, and Department of Chemistry, College of Science, Shanghai University, 200444 Shanghai, China. .,Shanghai Engineering Research Center of Organ Repair, China
| | - Ziheng Hu
- Department of Materials Genome Institute, and Department of Chemistry, College of Science, Shanghai University, 200444 Shanghai, China. .,Shanghai Engineering Research Center of Organ Repair, China.,Institute of Biological Information Processing, (IBI-3), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Yingying Chen
- Department of Materials Genome Institute, and Department of Chemistry, College of Science, Shanghai University, 200444 Shanghai, China. .,Shanghai Engineering Research Center of Organ Repair, China
| | - Lingyan Feng
- Department of Materials Genome Institute, and Department of Chemistry, College of Science, Shanghai University, 200444 Shanghai, China. .,Shanghai Engineering Research Center of Organ Repair, China
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19
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Tian T, Li Y, Lin Y. Prospects and challenges of dynamic DNA nanostructures in biomedical applications. Bone Res 2022; 10:40. [PMID: 35606345 PMCID: PMC9125017 DOI: 10.1038/s41413-022-00212-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/20/2022] [Indexed: 02/08/2023] Open
Abstract
The physicochemical nature of DNA allows the assembly of highly predictable structures via several fabrication strategies, which have been applied to make breakthroughs in various fields. Moreover, DNA nanostructures are regarded as materials with excellent editability and biocompatibility for biomedical applications. The ongoing maintenance and release of new DNA structure design tools ease the work and make large and arbitrary DNA structures feasible for different applications. However, the nature of DNA nanostructures endows them with several stimulus-responsive mechanisms capable of responding to biomolecules, such as nucleic acids and proteins, as well as biophysical environmental parameters, such as temperature and pH. Via these mechanisms, stimulus-responsive dynamic DNA nanostructures have been applied in several biomedical settings, including basic research, active drug delivery, biosensor development, and tissue engineering. These applications have shown the versatility of dynamic DNA nanostructures, with unignorable merits that exceed those of their traditional counterparts, such as polymers and metal particles. However, there are stability, yield, exogenous DNA, and ethical considerations regarding their clinical translation. In this review, we first introduce the recent efforts and discoveries in DNA nanotechnology, highlighting the uses of dynamic DNA nanostructures in biomedical applications. Then, several dynamic DNA nanostructures are presented, and their typical biomedical applications, including their use as DNA aptamers, ion concentration/pH-sensitive DNA molecules, DNA nanostructures capable of strand displacement reactions, and protein-based dynamic DNA nanostructures, are discussed. Finally, the challenges regarding the biomedical applications of dynamic DNA nanostructures are discussed.
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Affiliation(s)
- Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Yanjing Li
- Department of Prosthodontics, Tianjin Medical University School and Hospital of Stomatology, Tianjin, 300070, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China.
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20
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Chaperone Copolymer Assisted G-Quadruplex-Based Signal Amplification Assay for Highly Sensitive Detection of VEGF. BIOSENSORS 2022; 12:bios12050262. [PMID: 35624563 PMCID: PMC9138322 DOI: 10.3390/bios12050262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/10/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022]
Abstract
Vascular endothelial growth factor (VEGF) is a critical biomarker in the angiogenesis of several cancers. Nowadays, novel approaches to rapid, sensitive, and reliable VEGF detection are urgently required for early cancer diagnosis. Cationic comb-type copolymer, poly(L-lysine)-graft-dextran (PLL-g-Dex) accelerates DNA hybridization and chain exchange reaction while stabilizing the DNA assembly structure. In this work, we examined the chaperone activity of PLL-g-Dex to assist G-quadruplex-based fluorescent DNA biosensors for sensitive detection of VEGF. This convenient and effective strategy is based on chitosan hydrogel, c-myc, Thioflavin T (ThT), VEGF aptamer, and its partially complementary strand. The results show that chaperone copolymer PLL-g-Dex significantly promotes the accumulation of G-quadruplex and assembles into G-wires, allowing an effective signal amplification. Using this method, the detection limit of VEGF was as low as 23 pM, better than many previous works on aptamer-based VEGF detection. This chaperone copolymer-assisted signal amplification strategy has potential applications in the highly sensitive detection of target proteins, even including viruses.
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21
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Wang C, Liu Y, Chen R, Wang X, Wang Y, Wei J, Zhang K, Zhang C. Electrochemical biosensing of circulating microRNA-21 in cerebrospinal fluid of medulloblastoma patients through target-induced redox signal amplification. Mikrochim Acta 2022; 189:105. [DOI: 10.1007/s00604-022-05210-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/30/2022] [Indexed: 12/21/2022]
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22
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Baghbaderani SS, Mokarian P, Moazzam P. A Review on Electrochemical Sensing of Cancer Biomarkers Based on
Nanomaterial - Modified Systems. CURR ANAL CHEM 2022. [DOI: 10.2174/1573411016999200917161657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Diagnosis of cancer in the early stages can help treat efficiently and reduce cancerrelated
death. Cancer biomarkers can respond to the presence of cancer in body fluids before the
appearance of any other symptoms of cancer. The integration of nanomaterials into biosensors as
electrochemical platforms offer rapid, sensitive detection for cancer biomarkers. The use of surface-
modified electrodes by carbon nanomaterials and metal nanoparticles enhances the performance
of electrochemical analysis in biosensing systems through the increase of bioreceptors loading
capacity on the surface. In this review, novel approaches based on nanomaterial-modified systems
in the point of care diagnostics are highlighted.
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Affiliation(s)
- Sorour Salehi Baghbaderani
- Department of Nanotechnology Engineering, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan 81746-73441,Iran
| | - Parastou Mokarian
- Department of Biology, Faculty of Sciences, Central Tehran Branch, Islamic Azad University, Tehran 14676-86831,Iran
| | - Parisa Moazzam
- School of Chemistry, University of New South Wales, Sydney, 2052,Australia
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23
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Hu Q, Luo Y, Cao X, Chen Z, Huang Y, Niu L. Bioinspired Electro-RAFT Polymerization for Electrochemical Sensing of Nucleic Acids. ACS APPLIED MATERIALS & INTERFACES 2021; 13:54794-54800. [PMID: 34751560 DOI: 10.1021/acsami.1c17564] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sensing of ultralow-abundance nucleic acids (NAs) is integral to medical diagnostics and pathogen screening. We present herein an electrochemical method for the highly selective and amplified sensing of NAs, using a peptide nucleic acid (PNA) recognition probe and a bioinspired electro-RAFT polymerization (BERP)-based amplification strategy. The presented method is based on the recognition of target NAs by end-tethered PNA probes, the labeling of thiocarbonylthio reversible addition-fragmentation chain transfer (RAFT) agents, and the BERP-assisted growth of ferrocenyl polymers. The dynamic growth of polymers is electrochemically regulated by the reduction of 1-methylnicotinamide (MNA) organic cations, the redox center of nicotinamide adenine dinucleotide (NAD+, coenzyme I). Specifically, electroreduction of the MNA cations causes the fragmentation of thiocarbonylthio RAFT agents into radical species, triggering the polymerization of ferrocenyl monomers, thereby recruiting plenty of ferrocene electroactive tags for amplified sensing. It is obvious that the BERP-based strategy is inexpensive and simple in operation. Benefiting from the high specificity of the PNA recognition probe and the amplified signal by the BERP-based strategy, this method is highly selective and the detection limit is as low as 0.58 fM (S/N = 3). Besides, it is applicable to the sensing of NAs in serum samples, thus showing great promise in the selective and amplified sensing of NAs.
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Affiliation(s)
- Qiong Hu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Yilin Luo
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Xiaojing Cao
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Zhuohua Chen
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Yanyu Huang
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Li Niu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
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24
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Shen L, Wang P, Ke Y. DNA Nanotechnology-Based Biosensors and Therapeutics. Adv Healthc Mater 2021; 10:e2002205. [PMID: 34085411 DOI: 10.1002/adhm.202002205] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Indexed: 12/19/2022]
Abstract
Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson-Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.
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Affiliation(s)
- Luyao Shen
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Pengfei Wang
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
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25
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Detection of lipase activity in rice bran with AuNPs colorimetric sensor. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2021. [DOI: 10.1007/s11694-021-00916-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Abolhasan R, Khalilzadeh B, Yousefi H, Samemaleki S, Chakari-Khiavi F, Ghorbani F, Pourakbari R, Kamrani A, Khataee A, Rad TS, Rashidi MR, Yousefi M, AghebatiMaleki L. Ultrasensitive and label free electrochemical immunosensor for detection of ROR1 as an oncofetal biomarker using gold nanoparticles assisted LDH/rGO nanocomposite. Sci Rep 2021; 11:14921. [PMID: 34290319 PMCID: PMC8295321 DOI: 10.1038/s41598-021-94380-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/30/2021] [Indexed: 11/09/2022] Open
Abstract
In the present article, we developed a highly sensitive label-free electrochemical immunosensor based on NiFe-layered double hydroxides (LDH)/reduced graphene oxide (rGO)/gold nanoparticles modified glassy carbon electrode for the determination of receptor tyrosine kinase-like orphan receptor (ROR)-1. In this electrochemical immunoassay platform, NiFe-LDH/rGO was used due to great electron mobility, high specific surface area and flexible structures, while Au nanoparticles were prepared and coated on the modified electrodes to improve the detection sensitivity and ROR1 antibody immobilizing (ROR1Ab). The modification procedure was approved by using cyclic voltammetry and differential pulse voltammetry based on the response of peak current to the step by step modifications. Under optimum conditions, the experimental results showed that the immunosensor revealed a sensitive response to ROR1 in the range of 0.01-1 pg mL-1, and with a lower limit of quantification of 10 attogram/mL (10 ag mL-1). Furthermore, the designed immunosensor was applied for the analysis of ROR1 in several serum samples of chronic lymphocytic leukemia suffering patients with acceptable results, and it also exhibited good selectivity, reproducibility and stability.
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Affiliation(s)
- Rozita Abolhasan
- Stem Cell Research Center (SCRC), Tabriz University of Medical Sciences, 51664-14766, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Balal Khalilzadeh
- Stem Cell Research Center (SCRC), Tabriz University of Medical Sciences, 51664-14766, Tabriz, Iran. .,Biosensor Sciences and Technologies Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
| | - Hadi Yousefi
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran
| | - Sahar Samemaleki
- Student Research Committee, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Forough Chakari-Khiavi
- Pharmaceutical Chemistry, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Ghorbani
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ramin Pourakbari
- Stem Cell Research Center (SCRC), Tabriz University of Medical Sciences, 51664-14766, Tabriz, Iran
| | - Amin Kamrani
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Khataee
- Research Laboratory of Advanced Water and Wastewater Treatment Processes, Department of Applied Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran.,Department of Environmental Engineering, Gebze Technical University, 41400, Gebze, Turkey.,Department of Materrial Science and Physical Chemistry of Materials, South Ural State University, 454080, Chelyabinsk, Russian Federation
| | - Tannaz Sadeghi Rad
- Research Laboratory of Advanced Water and Wastewater Treatment Processes, Department of Applied Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Mohammad Reza Rashidi
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leili AghebatiMaleki
- Stem Cell Research Center (SCRC), Tabriz University of Medical Sciences, 51664-14766, Tabriz, Iran. .,Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran. .,Immunology Research Center, Tabriz University of Medical Sciences, PO Box 6446-14155, Tabriz, Iran.
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27
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A Dual-Sensor-Based Screening System for In Vitro Selection of TDP1 Inhibitors. SENSORS 2021; 21:s21144832. [PMID: 34300575 PMCID: PMC8309759 DOI: 10.3390/s21144832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
DNA sensors can be used as robust tools for high-throughput drug screening of small molecules with the potential to inhibit specific enzymes. As enzymes work in complex biological pathways, it is important to screen for both desired and undesired inhibitory effects. We here report a screening system utilizing specific sensors for tyrosyl-DNA phosphodiesterase 1 (TDP1) and topoisomerase 1 (TOP1) activity to screen in vitro for drugs inhibiting TDP1 without affecting TOP1. As the main function of TDP1 is repair of TOP1 cleavage-induced DNA damage, inhibition of TOP1 cleavage could thus reduce the biological effect of the TDP1 drugs. We identified three new drug candidates of the 1,5-naphthyridine and 1,2,3,4-tetrahydroquinolinylphosphine sulfide families. All three TDP1 inhibitors had no effect on TOP1 activity and acted synergistically with the TOP1 poison SN-38 to increase the amount of TOP1 cleavage-induced DNA damage. Further, they promoted cell death even with low dose SN-38, thereby establishing two new classes of TDP1 inhibitors with clinical potential. Thus, we here report a dual-sensor screening approach for in vitro selection of TDP1 drugs and three new TDP1 drug candidates that act synergistically with TOP1 poisons.
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28
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Jin F, Xu D. A fluorescent microarray platform based on catalytic hairpin assembly for MicroRNAs detection. Anal Chim Acta 2021; 1173:338666. [PMID: 34172148 DOI: 10.1016/j.aca.2021.338666] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/09/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
Abstract
The DNA microarray has distinctive advantages of high-throughput and less complicated operations, but tends to have a relatively low sensitivity. Catalytic hairpin assembly (CHA) is one of the most promising enzyme-free, isothermal DNA circuit for high efficient signal amplification. Here, a microarray-based catalytic hairpin assembly (mi-CHA) biosensing method has been developed to detect various miRNAs in a single test simultaneously. The target miRNA can trigger conformational transformations of hairpin-structured DNA probes on the chip surface and lead to the specific signal amplification. A significant advantage of this approach is that each duplex produced by the solid-phase CHA will be immobilized on the certain location of the chip and release fluorescent signal via the universal domain, eliminating the requirement of different fluorophores. This method has manifested a high detection sensitivity of human cancer-associated miRNAs (miR-21 and miR-155) down to 1.33 fM and promised a high specificity to distinguish single-base mismatches. Furthermore, the practicability of this method was demonstrated by analyzing target miRNAs in human serum and cancer cells. The experimental results suggest that the proposed method has high-throughput analytical potential and could be applied to many other clinical diagnosis.
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Affiliation(s)
- Furui Jin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, PR China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, PR China.
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Sun Y, Shi L, Mi L, Guo R, Li T. Recent progress of SERS optical nanosensors for miRNA analysis. J Mater Chem B 2021; 8:5178-5183. [PMID: 32432312 DOI: 10.1039/d0tb00280a] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review focuses on emerging applications of surface-enhanced Raman spectroscopy (SERS) optical nanosensors for miRNA analysis, in which the key enhancement factors of the SERS signal, i.e. SERS-active substrates, SERS nanoprobes and nano-assembly strategy, are emphasized. This article includes many nanomaterials for miRNA analysis by the SERS technique. We summarize these reported nanomaterials mainly according to their function in the miRNA assay biosensor. We also briefly summarize the research progress of these nanomaterials in SERS detection of intracellular miRNA. Finally, we discussed the prospect and limitations of SERS nanosensors for analyzing miRNA.
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Affiliation(s)
- Yudie Sun
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China. and School of Chemistry and Chemical Engineering, Anhui University of Technology, Ma'anshan, Anhui 243032, China
| | - Lin Shi
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China.
| | - Lan Mi
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China.
| | - Ruiyan Guo
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China.
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China.
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Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing. Talanta 2021; 226:122146. [PMID: 33676697 DOI: 10.1016/j.talanta.2021.122146] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 01/19/2023]
Abstract
Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.
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Ke Y, Huang S, Ghalandari B, Li S, Warden AR, Dang J, Kang L, Zhang Y, Wang Y, Sun Y, Wang J, Cui D, Zhi X, Ding X. Hairpin-Spacer crRNA-Enhanced CRISPR/Cas13a System Promotes the Specificity of Single Nucleotide Polymorphism (SNP) Identification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003611. [PMID: 33747742 PMCID: PMC7967054 DOI: 10.1002/advs.202003611] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/05/2020] [Indexed: 06/12/2023]
Abstract
The Cas13a system has great potential in RNA interference and molecular diagnostic fields. However, lacking guidelines for crRNA design hinders practical applications of the Cas13a system in RNA editing and single nucleotide polymorphism identification. This study posits that crRNAs with hairpin spacers improve the specificity of CRISPR/Cas13a system (termed hs-CRISPR). Gibbs free energy analysis suggests that the hairpin-spacer crRNAs (hs-crRNAs) suppress Cas13a's affinity to off-target RNA. A hepatitis B virus DNA genotyping platform is established to further validate the high-specificity of hs-CRISPR/Cas13a system. Compared to ordinary crRNA, hs-crRNAs increase the specificity by threefold without sacrificing the sensitivity of the CRISPR/Cas13a system. Furthermore, the mechanism of the Cas13a/hs-crRNA/target RNA composition is elucidated with theoretical simulations. This work builds on the fundamental understanding of Cas13a activation and offers significant improvements for the rational design of crRNA for the CRISPR/Cas13a system.
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Affiliation(s)
- Yuqing Ke
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Shiyi Huang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Behafarid Ghalandari
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Sijie Li
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Antony R. Warden
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Jingqi Dang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Lin Kang
- State Key Laboratory of Pathogen and BiosecurityInstitute of Microbiology and EpidemiologyBeijing100071China
| | - Yu Zhang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Yunqing Wang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Yiqing Sun
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Jinglin Wang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Daxiang Cui
- Shanghai Engineering Centre for Intelligent Diagnosis and Treatment InstrumentSchool of Electronic Information and Electrical EngineeringShanghai Jiao Tong UniversityShanghai200240China
| | - Xiao Zhi
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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Suhito IR, Koo KM, Kim TH. Recent Advances in Electrochemical Sensors for the Detection of Biomolecules and Whole Cells. Biomedicines 2020; 9:15. [PMID: 33375330 PMCID: PMC7824644 DOI: 10.3390/biomedicines9010015] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023] Open
Abstract
Electrochemical sensors are considered an auspicious tool to detect biomolecules (e.g., DNA, proteins, and lipids), which are valuable sources for the early diagnosis of diseases and disorders. Advances in electrochemical sensing platforms have enabled the development of a new type of biosensor, enabling label-free, non-destructive detection of viability, function, and the genetic signature of whole cells. Numerous studies have attempted to enhance both the sensitivity and selectivity of electrochemical sensors, which are the most critical parameters for assessing sensor performance. Various nanomaterials, including metal nanoparticles, carbon nanotubes, graphene and its derivatives, and metal oxide nanoparticles, have been used to improve the electrical conductivity and electrocatalytic properties of working electrodes, increasing sensor sensitivity. Further modifications have been implemented to advance sensor platform selectivity and biocompatibility using biomaterials such as antibodies, aptamers, extracellular matrix (ECM) proteins, and peptide composites. This paper summarizes recent electrochemical sensors designed to detect target biomolecules and animal cells (cancer cells and stem cells). We hope that this review will inspire researchers to increase their efforts to accelerate biosensor progress-enabling a prosperous future in regenerative medicine and the biomedical industry.
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Affiliation(s)
- Intan Rosalina Suhito
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (I.R.S.); (K.-M.K.)
| | - Kyeong-Mo Koo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (I.R.S.); (K.-M.K.)
| | - Tae-Hyung Kim
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (I.R.S.); (K.-M.K.)
- Integrative Research Center for Two-Dimensional Functional Materials, Institute of Interdisciplinary Convergence Research, Chung Ang University, Seoul 06974, Korea
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Liu S, Lai C, Liu X, Li B, Zhang C, Qin L, Huang D, Yi H, Zhang M, Li L, Wang W, Zhou X, Chen L. Metal-organic frameworks and their derivatives as signal amplification elements for electrochemical sensing. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213520] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Wang Y, Hu Y, He Q, Yan J, Xiong H, Wen N, Cai S, Peng D, Liu Y, Liu Z. Metal-organic frameworks for virus detection. Biosens Bioelectron 2020; 169:112604. [PMID: 32980805 PMCID: PMC7489328 DOI: 10.1016/j.bios.2020.112604] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/16/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023]
Abstract
Virus severely endangers human life and health, and the detection of viruses is essential for the prevention and treatment of associated diseases. Metal-organic framework (MOF), a novel hybrid porous material which is bridged by the metal clusters and organic linkers, has become a promising biosensor platform for virus detection due to its outstanding properties including high surface area, adjustable pore size, easy modification, etc. However, the MOF-based sensing platforms for virus detection are rarely summarized. This review systematically divided the detection platforms into nucleic acid and immunological (antigen and antibody) detection, and the underlying sensing mechanisms were interpreted. The nucleic acid sensing was discussed based on the properties of MOF (such as metal ion, functional group, geometry structure, size, porosity, stability, etc.), revealing the relationship between the sensing performance and properties of MOF. Moreover, antibodies sensing based on the fluorescence detection and antigens sensing based on molecular imprinting or electrochemical immunoassay were highlighted. Furthermore, the remaining challenges and future development of MOF for virus detection were further discussed and proposed. This review will provide valuable references for the construction of sophisticated sensing platform for the detection of viruses, especially the 2019 coronavirus.
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Affiliation(s)
- Ying Wang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Yaqin Hu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Qunye He
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Jianhua Yan
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Hongjie Xiong
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Nachuan Wen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Shundong Cai
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Dongming Peng
- Department of Medicinal Chemistry, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, Hunan Province, PR China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China.
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China.
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35
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Wang LL, Chen WQ, Wang YR, Zeng LP, Chen TT, Chen GY, Chen JH. Numerous long single-stranded DNAs produced by dual amplification reactions for electrochemical detection of exosomal microRNAs. Biosens Bioelectron 2020; 169:112555. [DOI: 10.1016/j.bios.2020.112555] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 02/09/2023]
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36
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Liu C, Liu Y, Zhu E, Zhang Q, Wei X, Wang B. Cross-Inhibitor: a time-sensitive molecular circuit based on DNA strand displacement. Nucleic Acids Res 2020; 48:10691-10701. [PMID: 33045746 PMCID: PMC7641751 DOI: 10.1093/nar/gkaa835] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 01/19/2023] Open
Abstract
Designing biochemical systems that can be effectively used in diverse fields, including diagnostics, molecular computing and nanomachines, has long been recognized as an important goal of molecular programming and DNA nanotechnology. A key issue in the development of such practical devices on the nanoscale lies in the development of biochemical components with information-processing capacity. In this article, we propose a molecular device that utilizes DNA strand displacement networks and allows interactive inhibition between two input signals; thus, it is termed a cross-inhibitor. More specifically, the device supplies each input signal with a processor such that the processing of one input signal will interdict the signal of the other. Biochemical experiments are conducted to analyze the interdiction performance with regard to effectiveness, stability and controllability. To illustrate its feasibility, a biochemical framework grounded in this mechanism is presented to determine the winner of a tic-tac-toe game. Our results highlight the potential for DNA strand displacement cascades to act as signal controllers and event triggers to endow molecular systems with the capability of controlling and detecting events and signals.
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Affiliation(s)
- Chanjuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Enqiang Zhu
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou 510006, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
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Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Recent advances in computational methods for biosensor design. Biotechnol Bioeng 2020; 118:555-578. [PMID: 33135778 DOI: 10.1002/bit.27618] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Accepted: 10/29/2020] [Indexed: 01/20/2023]
Abstract
Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.
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Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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Zhang Q, Hao T, Hu D, Guo Z, Wang S, Hu Y. RNA aptamer-driven ECL biosensing for tracing histone acetylation based on nano-prism substrate and cascade DNA amplification strategy. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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39
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Lu X, Ye Y, Zhang Y, Sun X. Current research progress of mammalian cell-based biosensors on the detection of foodborne pathogens and toxins. Crit Rev Food Sci Nutr 2020; 61:3819-3835. [PMID: 32885986 DOI: 10.1080/10408398.2020.1809341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Foodborne diseases caused by pathogens and toxins are a serious threat to food safety and human health; thus, they are major concern to society. Existing conventional foodborne pathogen or toxin detection methods, including microbiological assay, nucleic acid-based assays, immunological assays, and instrumental analytical method, are time-consuming, labor-intensive and expensive. Because of the fast response and high sensitivity, cell-based biosensors are promising novel tools for food safety risk assessment and monitoring. This review focuses on the properties of mammalian cell-based biosensors and applications in the detection of foodborne pathogens (bacteria and viruses) and toxins (bacterial toxins, mycotoxins and marine toxins). We discuss mammalian cell adhesion and how it is involved in the establishment of 3D cell culture models for mammalian cell-based biosensors, as well as evaluate their limitations for commercialization and further development prospects.
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Affiliation(s)
- Xin Lu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, PR China
| | - Yongli Ye
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, PR China
| | - Yinzhi Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, PR China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, PR China
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40
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Kim DM, Yoo SM. DNA-modifying enzyme reaction-based biosensors for disease diagnostics: recent biotechnological advances and future perspectives. Crit Rev Biotechnol 2020; 40:787-803. [DOI: 10.1080/07388551.2020.1764485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Dong Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
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Tamayo AIB, Rizo LSL, de Armas MB, Ferreira AAP, Manzani D, Yamanaka H, Guas AME. Biotin self-assembled monolayer for impedimetric genosensor for direct detection of HIV-1. Microchem J 2020. [DOI: 10.1016/j.microc.2019.104462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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42
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Shrivastava S, Trung TQ, Lee NE. Recent progress, challenges, and prospects of fully integrated mobile and wearable point-of-care testing systems for self-testing. Chem Soc Rev 2020; 49:1812-1866. [PMID: 32100760 DOI: 10.1039/c9cs00319c] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The rapid growth of research in the areas of chemical and biochemical sensors, lab-on-a-chip, mobile technology, and wearable electronics offers an unprecedented opportunity in the development of mobile and wearable point-of-care testing (POCT) systems for self-testing. Successful implementation of such POCT technologies leads to minimal user intervention during operation to reduce user errors; user-friendly, easy-to-use and simple detection platforms; high diagnostic sensitivity and specificity; immediate clinical assessment; and low manufacturing and consumables costs. In this review, we discuss recent developments in the field of highly integrated mobile and wearable POCT systems. In particular, aspects of sample handling platforms, recognition elements and sensing methods, and new materials for signal transducers and powering devices for integration into mobile or wearable POCT systems will be highlighted. We also summarize current challenges and future prospects for providing personal healthcare with sample-in result-out mobile and wearable POCT.
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Affiliation(s)
- Sajal Shrivastava
- School of Advanced Materials Science & Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Korea.
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43
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Ghorbani F, Abbaszadeh H, Mehdizadeh A, Ebrahimi-Warkiani M, Rashidi MR, Yousefi M. Biosensors and nanobiosensors for rapid detection of autoimmune diseases: a review. Mikrochim Acta 2019; 186:838. [DOI: 10.1007/s00604-019-3844-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/17/2019] [Indexed: 12/15/2022]
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Azadmehr F, Zarei K. An imprinted polymeric matrix containing DNA for electrochemical sensing of 2,4-dichlorophenoxyacetic acid. Mikrochim Acta 2019; 186:814. [PMID: 31745651 DOI: 10.1007/s00604-019-3980-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/25/2019] [Indexed: 10/25/2022]
Abstract
The authors describe an electrochemical method for the determination of herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). It is based on the use of a molecularly imprinted polymer (MIP) and of dsDNA as a bio-specific substance. The modified electrode was prepared by electropolymerization of ortho-phenylenediamine (oPD) in the presence of DNA and of 2,4-D (the template). The imprinted MIP was placed on a pencil graphite electrode (PGE) modified with chitosan and multiwalled carbon nanotubes (MWCNTs). The template was removed with 0.4 M NaOH. The interaction of DNA with 2,4-D leads to its adsorption on the electrode, and this increases the sensitivity and selectivity of the method. After rebinding 2,4-D, the decrease in the peak current of oxidation of iron(II) acting as an electrochemical redox probe was measured by differential pulse voltammetry (DPV). The current, typically measured at around 0.5 V, increases linearly in the 0.01 to 10 pM 2,4-D concentration range, and the detection limit is 4.0 fM. The method is highly selective for 2,4-D. The modified electrode was applied to quantify 2,4-D in spiked environmental water and soil samples and gave absolute recoveries varying from 91.5 to 109.0%. Graphical abstractSchematic representation of the fabrication of an electrochemical sensor for determination of 2,4-dichlorophenoxyacetic acid (2,4-D). Initially, the electrode was modified with chitosan and MWCNTs and then a composite was formed on it consisting of ortho-phenylenediamine (oPD), DNA and 2,4-D.
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Affiliation(s)
- Fatemeh Azadmehr
- School of Chemistry, Damghan University, Damghan, 36716-41167, Iran
| | - Kobra Zarei
- School of Chemistry, Damghan University, Damghan, 36716-41167, Iran.
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Mohajeri N, Imani M, Akbarzadeh A, Sadighi A, Zarghami N. An update on advances in new developing DNA conjugation diagnostics and ultra-resolution imaging technologies: Possible applications in medical and biotechnological utilities. Biosens Bioelectron 2019; 144:111633. [DOI: 10.1016/j.bios.2019.111633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
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46
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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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Deshpande S, Yang Y, Chilkoti A, Zauscher S. Enzymatic synthesis and modification of high molecular weight DNA using terminal deoxynucleotidyl transferase. Methods Enzymol 2019; 627:163-188. [PMID: 31630739 PMCID: PMC7241426 DOI: 10.1016/bs.mie.2019.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The recognition that nucleic acids can be used as polymeric materials led to the blossoming of the field of DNA nanotechnology, with a broad range of applications in biotechnology, biosensors, diagnostics, and drug delivery. These applications require efficient methods to synthesize and chemically modify high molecular weight DNA. Here, we discuss terminal deoxynucleotidyl transferase (TdT)-catalyzed enzymatic polymerization (TcEP) as an alternative to conventional enzymatic and solid-phase DNA synthesis. We describe biochemical requirements for TcEP and provide step-by-step protocols to carry out TcEP in solution and from surfaces.
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Affiliation(s)
- Sonal Deshpande
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Yunqi Yang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, United States; Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States.
| | - Stefan Zauscher
- Department of Biomedical Engineering, Duke University, Durham, NC, United States; Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, United States.
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Ghorbani F, Abbaszadeh H, Dolatabadi JEN, Aghebati-Maleki L, Yousefi M. Application of various optical and electrochemical aptasensors for detection of human prostate specific antigen: A review. Biosens Bioelectron 2019; 142:111484. [PMID: 31284103 DOI: 10.1016/j.bios.2019.111484] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 12/17/2022]
Abstract
Early stage detection of prostate cancer, one of the main causes of mortality among men, is of great importance for better treatment of the patients. Prostate specific antigen (PSA) is a glycoprotein which has been considered as the most potential serological biomarker for the detection of prostate cancer. Among the various techniques employed for PSA detection, aptamer-based biosensors (aptasensors) have achieved notable attention because of their unique features and great potentials as diagnostic tools. A variety of strategies such as integration of nanomaterials (NMs) into the structure of aptasensors have also been applied for enhancing the sensitivity of PSA detection. This article reviews recent advances in various optical and electrochemical aptasensors used for PSA detection.
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Affiliation(s)
- Farzaneh Ghorbani
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Abbaszadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Leili Aghebati-Maleki
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Faculty of Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mehdi Yousefi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Faculty of Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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Saylan Y, Erdem Ö, Ünal S, Denizli A. An Alternative Medical Diagnosis Method: Biosensors for Virus Detection. BIOSENSORS 2019; 9:E65. [PMID: 31117262 PMCID: PMC6627152 DOI: 10.3390/bios9020065] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/15/2019] [Accepted: 05/18/2019] [Indexed: 12/14/2022]
Abstract
Infectious diseases still pose an omnipresent threat to global and public health, especially in many countries and rural areas of cities. Underlying reasons of such serious maladies can be summarized as the paucity of appropriate analysis methods and subsequent treatment strategies due to the limited access of centralized and equipped health care facilities for diagnosis. Biosensors hold great impact to turn our current analytical methods into diagnostic strategies by restructuring their sensing module for the detection of biomolecules, especially nano-sized objects such as protein biomarkers and viruses. Unquestionably, current sensing platforms require continuous updates to address growing challenges in the diagnosis of viruses as viruses change quickly and spread largely from person-to-person, indicating the urgency of early diagnosis. Some of the challenges can be classified in biological barriers (specificity, low number of targets, and biological matrices) and technological limitations (detection limit, linear dynamic range, stability, and reliability), as well as economical aspects that limit their implementation into resource-scarce settings. In this review, the principle and types of biosensors and their applications in the diagnosis of distinct infectious diseases were comprehensively explained. The deployment of current biosensors into resource-scarce settings is further discussed for virus detection by elaborating the pros and cons of existing methods as a conclusion and future perspective.
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Affiliation(s)
- Yeşeren Saylan
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey.
| | - Özgecan Erdem
- Department of Biology, Hacettepe University, Ankara 06800, Turkey.
| | - Serhat Ünal
- Department of Infectious Disease and Clinical Microbiology, Hacettepe University, Ankara 06230, Turkey.
| | - Adil Denizli
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey.
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Tang Z, Yin ZX, Sun X, Cui JZ, Yang J, Wang RS. Dynamically NAND gate system on DNA origami template. Comput Biol Med 2019; 109:112-120. [PMID: 31054386 DOI: 10.1016/j.compbiomed.2019.04.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/21/2019] [Accepted: 04/21/2019] [Indexed: 12/22/2022]
Abstract
Molecular logic gates play an important role in many fields and DNA-based logic gates are the basis of DNA computers. A dynamically NAND gate system on the DNA origami template is established in this paper. Naturally, the system is stable in solution without any reaction. Different logical values are mapped into different DNA input strands. When logical values are entered into the system, the corresponding DNA input strands undergo a directed hybridization chain reaction (HCR) at corresponding positions on the DNA origami template. The operation results are identified by disassembly between the nanogold particles (AuNPs) and DNA origami template. The nanogold particles remain on the DNA origami template, indicating that the result is true; The nanogold particles are dynamically separated from the DNA origami template, indicating that the result is false. The simulation of the system through Visual DSD shows that the reaction strictly followed the designed direction, and no error products are generated during the reaction. These simulation results show that the system has the advantages of feasibility, stability and intelligence.
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Affiliation(s)
- Zhen Tang
- School of Mathematics and Big Data, AnHui University of Science&Technology, Huainan, 232001, AnHui, China
| | - Zhi-Xiang Yin
- School of Mathematics and Big Data, AnHui University of Science&Technology, Huainan, 232001, AnHui, China.
| | - Xia Sun
- School of Mathematics and Big Data, AnHui University of Science&Technology, Huainan, 232001, AnHui, China
| | - Jian-Zhong Cui
- School of Electronic and Information Engineering, AnHui University of Science&Technology, Huainan, 232001, AnHui, China
| | - Jing Yang
- School of Mathematics and Big Data, AnHui University of Science&Technology, Huainan, 232001, AnHui, China
| | - Ri-Sheng Wang
- School of Mathematics and Big Data, AnHui University of Science&Technology, Huainan, 232001, AnHui, China
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