1
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Mi ZZ, Hu HC, Sun JJ, Wu SH. Heating promoted super sensitive electrochemical detection of p53 gene based on alkaline phosphatase and nicking endonuclease Nt.BstNBI-assisted target recycling amplification strategy at heated gold disk electrode. Anal Chim Acta 2023; 1275:341583. [PMID: 37524467 DOI: 10.1016/j.aca.2023.341583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 08/02/2023]
Abstract
An ultrasensitive electrochemical biosensor for detecting p53 gene was fabricated based on heated gold disk electrode coupling with endonuclease Nt.BstNBI-assisted target recycle amplification and alkaline phosphatase (ALP)-based electrocatalytic signal amplification. For biosensor assembling, biotinylated ssDNA capture probes were first immobilized on heated Au disk electrode (HAuDE), then combined with streptavidin-alkaline phosphatase (SA-ALP) by biotin-SA interaction. ALP could catalyze the hydrolysis of ascorbic acid 2-phosphate (AAP) to produce ascorbic acid (AA). While AA could induce the redox cycling to generate electrocatalytic oxidation current in the presence of ferrocene methanol (FcM). When capture probes hybridized with p53, Nt.BstNBI would recognize and cleave the duplexes and p53 was released for recycling. Meanwhile, the biotin group dropt from the electrode surface and subsequently SA-ALP could not adhere to the electrode. The signal difference before and after cleavage was proportional to the p53 gene concentration. Furthermore, with electrode temperature elevated, the Nt.BstNBI and ALP activities could be increased, greatly improving the sensitivity and efficiency for p53 detection. A detection limit of 9.5 × 10-17 M could be obtained (S/N = 3) with an electrode temperature of 40 °C, ca. four magnitudes lower than that at 25 °C.
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Affiliation(s)
- Zhen-Zhen Mi
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Hao-Cheng Hu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Jian-Jun Sun
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China
| | - Shao-Hua Wu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350108, China.
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2
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Tejedor JR, Martín G, Roberti A, Mangas C, Santamarina-Ojeda P, Fernández Pérez R, López V, González Urdinguio R, Alba-Linares JJ, Peñarroya A, Álvarez-Argüelles ME, Boga JA, Fernández Fernández A, Rojo-Alba S, Fernández Fraga M. Enhanced Detection of Viral RNA Species Using FokI-Assisted Digestion of DNA Duplexes and DNA/RNA Hybrids. Anal Chem 2022; 94:6760-6770. [PMID: 35467835 PMCID: PMC9063116 DOI: 10.1021/acs.analchem.2c00407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The accurate detection
of nucleic acids from certain biological
pathogens is critical for the diagnosis of human diseases. However,
amplified detection of RNA molecules from a complex sample by direct
detection of RNA/DNA hybrids remains a challenge. Here, we show that
type IIS endonuclease FokI is able to digest DNA duplexes and DNA/RNA
hybrids when assisted by a dumbbell-like fluorescent sensing oligonucleotide.
As proof of concept, we designed a battery of sensing oligonucleotides
against specific regions of the SARS-CoV-2 genome and interrogated
the role of FokI relaxation as a potential nicking enzyme for fluorescence
signal amplification. FokI-assisted digestion of SARS-CoV-2 probes
increases the detection signal of ssDNA and RNA molecules and decreases
the limit of detection more than 3.5-fold as compared to conventional
molecular beacon approaches. This cleavage reaction is highly specific
to its target molecules, and no detection of other highly related
B-coronaviruses was observed in the presence of complex RNA mixtures.
In addition, the FokI-assisted reaction has a high multiplexing potential,
as the combined detection of different viral RNAs, including different
SARS-CoV-2 variants, was achieved in the presence of multiple combinations
of fluorophores and sensing oligonucleotides. When combined with isothermal
rolling circle amplification technologies, FokI-assisted digestion
reduced the detection time of SARS-CoV-2 in COVID-19-positive human
samples with adequate sensitivity and specificity compared to conventional
reverse transcription polymerase chain reaction approaches, highlighting
the potential of FokI-assisted signal amplification as a valuable
sensing mechanism for the detection of human pathogens.
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Affiliation(s)
- Juan R Tejedor
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), El Entrego 33940, Spain.,Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,University Institute of Oncology (IUOPA), University of Oviedo, Oviedo 33006, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Gabriel Martín
- Central University Hospital of Asturias (HUCA), Oviedo 33011, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Annalisa Roberti
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), El Entrego 33940, Spain.,Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Cristina Mangas
- Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,University Institute of Oncology (IUOPA), University of Oviedo, Oviedo 33006, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Pablo Santamarina-Ojeda
- Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,University Institute of Oncology (IUOPA), University of Oviedo, Oviedo 33006, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Raúl Fernández Pérez
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), El Entrego 33940, Spain.,Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,University Institute of Oncology (IUOPA), University of Oviedo, Oviedo 33006, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Virginia López
- Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,University Institute of Oncology (IUOPA), University of Oviedo, Oviedo 33006, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Rocío González Urdinguio
- Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Juan J Alba-Linares
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), El Entrego 33940, Spain.,Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Alfonso Peñarroya
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), El Entrego 33940, Spain.,Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Marta E Álvarez-Argüelles
- Central University Hospital of Asturias (HUCA), Oviedo 33011, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - José A Boga
- Central University Hospital of Asturias (HUCA), Oviedo 33011, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Agustín Fernández Fernández
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), El Entrego 33940, Spain.,Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,University Institute of Oncology (IUOPA), University of Oviedo, Oviedo 33006, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Susana Rojo-Alba
- Central University Hospital of Asturias (HUCA), Oviedo 33011, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
| | - Mario Fernández Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), El Entrego 33940, Spain.,Foundation for Biomedical Research and Innovation in Asturias (FINBA), Oviedo 33011, Spain.,University Institute of Oncology (IUOPA), University of Oviedo, Oviedo 33006, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid 28029, Spain.,Health Research Institute of Asturias (ISPA), Oviedo 33011, Spain
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3
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Fu J, Li J, Chen J, Li Y, Liu J, Su X, Shi S. Ultra-specific nucleic acid testing by target-activated nucleases. Crit Rev Biotechnol 2021; 42:1061-1078. [PMID: 34706599 DOI: 10.1080/07388551.2021.1983757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Specific and sensitive detection of nucleic acids is essential to clinical diagnostics and biotechnological applications. Currently, amplification steps are necessary for most detection methods due to the low concentration of nucleic acid targets in real samples. Although amplification renders high sensitivity, poor specificity is prevalent because of the lack of highly accurate precise strategies, resulting in significant false positives and false negatives. Nucleases exhibit high catalytic activity for nucleic acid cleavage which is regulated in a programmable manner. This review focuses on the latest progress in nucleic acid testing methods based on the target-activated nucleases. It summarizes the property of enzymes such as CRISPR/Cas, Argonautes, and some gene-editing irrelevant nucleases, which have been leveraged to create highly specific and sensitive nucleic acid testing tools. We elaborate on recent advances in the field of nuclease-mediated DNA recognition techniques for nucleic acid detection, and discuss its future applications and challenges in molecular diagnostics.
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Affiliation(s)
- Jinyu Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jing Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yabei Li
- Department of Neurosurgery, People's Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jiajia Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xin Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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4
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Zhang C, Luo Z, Wu M, Ning W, Tian Z, Duan Y, Li Y. A highly sensitive fluorescence biosensor for detection of Staphylococcus aureus based on HCR-mediated three-way DNA junction nicking enzyme assisted signal amplification. Analyst 2021; 146:6528-6536. [PMID: 34569562 DOI: 10.1039/d1an01335a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sensitive and efficient monitoring of food-borne bacteria is of great importance for food safety control. Herein, a novel biosensor for highly sensitive detection of Staphylococcus aureus (S. aureus) was constructed by combining hybridization chain reaction (HCR) and nicking enzyme. Different from the upstream-downstream based circuit, the proposed biosensor integrated HCR circuit and three-way DNA junction nicking enzyme assisted signal amplification (3WJ-NEASA) into a virtuous circle of promotion. In the HCR-mediated 3WJ-NEASA sensing strategy, target DNA of S. aureus initiated the self-assembly between HCR hairpins (H1 and H2), which exposed the gap to capture molecular beacon (MB) and construct the 3WJ structure. Meanwhile, MB increased the stability of HCR nanowires and enhanced the efficiency of the HCR circuit, and thus more 3WJ-NEASA circuits were generated in HCR nanowires. Benefiting from the synergistic amplification coupling HCR and 3WJ-NEASA, this isothermal biosensor can detect as low as 6.7 pM of target DNA in one step within only 30 min. Furthermore, the HCR-mediated 3WJ-NEASA assay has been applied in the detection of S. aureus with a limit of detection (LOD) as low as 1.2 × 101 cfu mL-1, and has exhibited reliable practicability in spiked milk. It is the first time that a DNA biosensor combining HCR and 3WJ-NEASA for dual signal amplification was developed and has been adopted to the sensitive analysis of food-borne bacteria. Additionally, this strategy can serve as a universal platform for monitoring other analytes, and therefore possesses broad application prospects in food safety and environmental monitoring.
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Affiliation(s)
- Chuyan Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
| | - Wei Ning
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
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5
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He Q, Ma S, Wang J, Chen K, Dong J, Zhou J, Chen D, Ning Y. Graphene Oxide-Based Fluorometric Determination of the eta Gene in Pseudomonas aeruginosa Using Nicking Enzyme-Mediated Cyclic Signal Amplification. ANAL LETT 2021. [DOI: 10.1080/00032719.2021.1980885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Qizhi He
- Academician Workstation, Changsha Medical University, Changsha, Hunan, People’s Republic of China
- School of Basic Medical Science, Changsha Medical University, Changsha, Hunan, People’s Republic of China
- Discipline of Basic Medical Application, Changsha Medical University, Changsha, Hunan, People’s Republic of China
| | - Shuheng Ma
- Academician Workstation, Changsha Medical University, Changsha, Hunan, People’s Republic of China
- Discipline of Basic Medical Application, Changsha Medical University, Changsha, Hunan, People’s Republic of China
| | - Jingya Wang
- Academician Workstation, Changsha Medical University, Changsha, Hunan, People’s Republic of China
| | - Keke Chen
- Academician Workstation, Changsha Medical University, Changsha, Hunan, People’s Republic of China
| | - Jun Dong
- Academician Workstation, Changsha Medical University, Changsha, Hunan, People’s Republic of China
- Discipline of Basic Medical Application, Changsha Medical University, Changsha, Hunan, People’s Republic of China
| | - Ji Zhou
- Academician Workstation, Changsha Medical University, Changsha, Hunan, People’s Republic of China
- School of Basic Medical Science, Changsha Medical University, Changsha, Hunan, People’s Republic of China
| | - Danna Chen
- Academician Workstation, Changsha Medical University, Changsha, Hunan, People’s Republic of China
- School of Basic Medical Science, Changsha Medical University, Changsha, Hunan, People’s Republic of China
| | - Yi Ning
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, People’s Republic of China
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6
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Zhang Y, Zhang Q, Weng X, Du Y, Zhou X. NEase-based amplification for detection of miRNA, multiple miRNAs and circRNA. Anal Chim Acta 2021; 1145:52-58. [DOI: 10.1016/j.aca.2020.12.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023]
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7
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Toehold-mediated strand displacement reaction formation of three-way junction DNA structure combined with nicking enzyme signal amplification for highly sensitive colorimetric detection of Salmonella Typhimurium. Anal Chim Acta 2020; 1139:138-145. [DOI: 10.1016/j.aca.2020.09.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/11/2020] [Indexed: 12/29/2022]
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8
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Liu S, Yu X, Wang J, Liu D, Wang L, Liu S. Exonuclease III-Powered Self-Propelled DNA Machine for Distinctly Amplified Detection of Nucleic Acid and Protein. Anal Chem 2020; 92:9764-9771. [DOI: 10.1021/acs.analchem.0c01197] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shuang Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Xiaoxiao Yu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Jialong Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Dengren Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Li Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Shufeng Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
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9
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Kim HY, Ahn JK, Lee CY, Park HG. A hairpin probe-mediated isothermal amplification method to detect target nucleic acid. Anal Chim Acta 2020; 1114:7-14. [DOI: 10.1016/j.aca.2020.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 03/11/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022]
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10
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Bodulev OL, Sakharov IY. Isothermal Nucleic Acid Amplification Techniques and Their Use in Bioanalysis. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:147-166. [PMID: 32093592 PMCID: PMC7223333 DOI: 10.1134/s0006297920020030] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022]
Abstract
Recently, there has been a rapid progress in the development of techniques for isothermal amplification of nucleic acids as an alternative to polymerase chain reaction (PCR). The advantage of these methods is that the nucleic acids amplification can be carried out at constant temperature, unlike PCR, which requires cyclic temperature changes. Moreover, isothermal amplification can be conducted directly in living cells. This review describes the principles of isothermal amplification techniques and demonstrates their high efficiency in designing new highly sensitive detection methods of nucleic acids and enzymes involved in their modifications. The data on successful application of isothermal amplification methods for the analysis of cells and biomolecules with the use of DNA/RNA aptamers are presented.
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Affiliation(s)
- O L Bodulev
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia
| | - I Yu Sakharov
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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11
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Abrosimova LA, Kisil OV, Romanova EA, Oretskaya TS, Kubareva EA. Nicking Endonucleases as Unique Tools for Biotechnology and Gene Engineering. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019050017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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13
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A Novel Design Combining Isothermal Exponential Amplification and Gold-Nanoparticles Visualization for Rapid Detection of miRNAs. Int J Mol Sci 2018; 19:ijms19113374. [PMID: 30373308 PMCID: PMC6275053 DOI: 10.3390/ijms19113374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/22/2018] [Accepted: 10/25/2018] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in a wide range of biological processes, and their aberrant expressions are associated with various diseases. The levels of miRNAs can be useful biomarkers for cellular events or disease diagnosis; thus, sensitive and selective detection of microRNAs is of great significance in understanding biological functions of miRNAs, early-phase diagnosis of cancers, and discovery of new targets for drugs. However, traditional approaches for the detection of miRNAs are usually laborious and time-consuming, with a low sensitivity. Here, we develop a simple, rapid, ultrasensitive colorimetric assay based on the combination of isothermal Exponential Amplification Reaction (EXPAR) and AuNP-labeled DNA probes for the detection of miRNAs (taking let-7a as a model analyte). In this assay, the presence of let-7a is converted to the reporter Y through EXPAR under isothermal conditions. The subsequent sandwich hybridization of the reporter Y with the AuNP-labeled DNA probes generates a red-to-purple color change. In other words, if the reporter Y is complementary to the AuNP-labeled DNA probes, the DNA-functionalized AuNPs will be aggregated, resulting in the change of solution color from red to purple/blue, while when the AuNP-labeled DNA probes are mismatched to the reporter Y, the solution remains red. This assay represents a simple, time-saving technique, and its results can be visually detected with the naked eye due to the colorimetric change. The method provides superior sensitivity, with a detection limit of 4.176 aM over a wide range from 1 nM to 1 aM under optimal conditions. The method also shows high selectivity for discriminating even single-nucleotide differences between let-7 miRNA family members. Notably, it is comparable to the most sensitive method reported to date, thus providing a promising alternative to standard approaches for the direct detection of let-7a miRNA. Importantly, through combination with specific templates, different miRNAs can be converted to the same reporter Y, which can hybridize with the same set of AuNP-labeled DNA probes to form sandwich hybrids. The color change of the solution can be observed in the presence of the target miRNA. This technique has potential as a routine method for assessing the levels of miRNAs, not only for let-7, but also for various miRNAs in the early phase of cancers. In addition, it can be a useful tool in biomedical research and clinical diagnosis, as well as diagnosis or surveillance programs in field conditions.
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14
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Park CR, Park SJ, Lee WG, Hwang BH. Biosensors Using Hybridization Chain Reaction - Design and Signal Amplification Strategies of Hybridization Chain Reaction. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0182-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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Detection of low-abundance point mutations by competitive strand assisted endonuclease IV signal amplification system. Curr Med Sci 2017; 37:803-806. [PMID: 29058299 DOI: 10.1007/s11596-017-1808-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 09/11/2017] [Indexed: 10/18/2022]
Abstract
Genetic mutations are important molecular biomarkers for cancer diagnosis and surveillance. Therefore, the development of methods for mutation detection characterized with straightforward, highly specific and sensitive to low-level mutations within various sequence contexts is extremely needed. Although some of the currently available methods have shown very encouraging results, their discrimination efficiency is still very low. Herein, we demonstrate a fluorescent probe coupled with blocker and property of melting temperature discrimination, which is able to identify the presence of known or unknown single-base variations at abundances down to 0.1% within 20 min. The discrimination factors between the perfect-match target and single-base mismatched target are determined to be 10.15-38.48. The method is sequence independent, which assures a wide range of application. The new method would be an ideal choice for high-throughput in vitro diagnosis and precise clinical treatment.
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16
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Li XY, Du YC, Zhang YP, Kong DM. Dual functional Phi29 DNA polymerase-triggered exponential rolling circle amplification for sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Sci Rep 2017; 7:6263. [PMID: 28740223 PMCID: PMC5524717 DOI: 10.1038/s41598-017-06594-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/14/2017] [Indexed: 12/31/2022] Open
Abstract
An exonucleolytic digestion-assisted exponential rolling circle amplification (RCA) strategy was developed for sensitive and sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Herein, Phi29 DNA polymerase plays two important roles as exonuclease and polymerase. Long-stranded genomic DNAs can be broken into small DNA fragments after ultrasonication. The fragments that contain target DNA, hybridize with a linear padlock probe to trigger the formation of a circular RCA template. The tails protruding from the 3'-end of the target DNA sequences are then digested by the 3' → 5' exonuclease activity of Phi29 DNA polymerase even if they fold into a double-stranded structure. The digested DNA fragments can then initiate subsequent RCA reaction. RCA products, which are designed to fold into G-quadruplex structures, exponentially accumulate when appropriate nicking endonuclease recognition sites are introduced rationally into the RCA template. This method is demonstrated to work well for real genomic DNA detection using human pathogen Cryptococcus neoformans as a model. In addition, this work has two other important discoveries: First, the presence of a 3'-tail can protect the RCA primer from degradation by Phi29 DNA polymerase. Second, 3' → 5' exonucleolytic activity of Phi29 DNA polymerase can work for both single- and double-stranded DNA.
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Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, P.R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - Yi-Chen Du
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - Yu-Peng Zhang
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, P.R. China.
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Nankai University, Tianjin, 300071, P.R. China.
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300071, P.R. China.
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17
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Hasanzadeh M, Shadjou N, de la Guardia M. Non-invasive diagnosis of oral cancer: The role of electro-analytical methods and nanomaterials. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.04.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Hong M, Wang M, Wang J, Xu X, Lin Z. Ultrasensitive and selective electrochemical biosensor for detection of mercury (II) ions by nicking endonuclease-assisted target recycling and hybridization chain reaction signal amplification. Biosens Bioelectron 2017; 94:19-23. [PMID: 28237902 DOI: 10.1016/j.bios.2017.02.031] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 01/17/2017] [Accepted: 02/21/2017] [Indexed: 11/29/2022]
Abstract
In this paper, a novel and signal-on electrochemical biosensor based on Hg2+- triggered nicking endonuclease-assisted target recycling and hybridization chain reaction (HCR) amplification tactics was developed for sensitive and selective detection of Hg2+. The hairpin-shaped capture probe A (PA) contained a specific sequence which was recognized by nicking endonuclease (NEase). In the presence of Hg2+, probe B (PB) hybridized with PA to form stand-up duplex DNA strands via the Hg2+ mediated thymine-Hg2+-thymine (T-Hg2+-T) structure, which automatically triggered NEase to selectively digest duplex region from the recognition sites, spontaneously dissociating PB and Hg2+ and leaving the remnant initiators. The released PB and Hg2+ could be reused to initiate the next cycle and more initiators were generated. The long nicked double helices were formed through HCR event, which was triggered by the initiators and two hairpin-shaped signal probes labeled with methylene blue, resulting in a significant signal increase. Under optimum conditions, the resultant biosensor showed the high sensitivity and selectivity for the detection of Hg2+ in a linear range from 10 pM to 50nM (R2=0.9990), and a detection limit as low as 1.6 pM (S/N=3). Moreover, the proposed biosensor was successfully applied in the detection of Hg2+ in environment water samples with satisfactory results.
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Affiliation(s)
- Minqiang Hong
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Mengyan Wang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Jing Wang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Xueqin Xu
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China.
| | - Zhenyu Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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19
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Zhang FT, Cai LY, Zhou YL, Zhang XX. Immobilization-free DNA-based homogeneous electrochemical biosensors. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.08.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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20
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Label-free electrochemical detection of RNA based on “Y” junction structure and restriction endonuclease-aided target recycling strategy. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.05.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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21
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A novel ultrasensitive competition strategy for electrochemical and colorimetric cytosensing of acute leukemia cells. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Wei H, Zhao G, Hu T, Tang S, Jiang J, Hu B, Guan Y. Mapping the nicking efficiencies of nickase R.BbvCI for side-specific LNA-substituted substrates using rolling circle amplification. Sci Rep 2016; 6:32560. [PMID: 27582033 PMCID: PMC5007493 DOI: 10.1038/srep32560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/09/2016] [Indexed: 11/29/2022] Open
Abstract
We used a novel asymmetric cleavage analysis method based on rolling circle amplification (RCA) to determine the effects of LNA modification of substrate on the two subunits of R.BbvCI cleavage. We designed two sets of cleavage circular substrates by using two different ligation strategies and analyzed the single strand cleavage efficiency affected by different modification positions both from the cleaved strands and the uncleaved strands. Results showed that the effects of LNA on cleavage rates of modified strands and unmodified strands were both site-dependent. The Nb.BbvCI and Nt.BbvCI were affected by LNA modification in different way. Most of the modification positions showed strong inhibition of both of these two nickases cleavage. However, the modification in T3 position of bottom strand hardly affected both of the two nickases activities. The results suggested an intimated interaction between the two subunits of R.BbvCI, and the T3 position in bottom strand might be a less tight position which was hard to be disturbed.
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Affiliation(s)
- Hua Wei
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China.,Animal Science and Veterinary Medicine College, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Guojie Zhao
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Tianyu Hu
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Suming Tang
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Jiquan Jiang
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Bo Hu
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, #77 Puhe Road, Shenyang, Liaoning, 110122, China
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23
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Reverte M, Vasseur JJ, Smietana M. Nuclease stability of boron-modified nucleic acids: application to label-free mismatch detection. Org Biomol Chem 2016; 13:10604-8. [PMID: 26441029 DOI: 10.1039/c5ob01815c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
5'-End boronic acid-modified oligonucleotides were evaluated against various nucleases at single and double stranded levels. The results show that these modifications induce a high resistance to degradation by calf-spleen and snake venom phosphodiesterases. More importantly, this eventually led to the development of a new label-free enzyme-assisted fluorescence-based method for single mismatch detection.
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Affiliation(s)
- Maëva Reverte
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
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24
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Mishra S, Saadat D, Kwon O, Lee Y, Choi WS, Kim JH, Yeo WH. Recent advances in salivary cancer diagnostics enabled by biosensors and bioelectronics. Biosens Bioelectron 2016; 81:181-197. [PMID: 26946257 DOI: 10.1016/j.bios.2016.02.040] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/12/2016] [Accepted: 02/14/2016] [Indexed: 01/05/2023]
Abstract
There is a high demand for a non-invasive, rapid, and highly accurate tool for disease diagnostics. Recently, saliva based diagnostics for the detection of specific biomarkers has drawn significant attention since the sample extraction is simple, cost-effective, and precise. Compared to blood, saliva contains a similar variety of DNA, RNA, proteins, metabolites, and microbiota that can be compiled into a multiplex of cancer detection markers. The salivary diagnostic method holds great potential for early-stage cancer diagnostics without any complicated and expensive procedures. Here, we review various cancer biomarkers in saliva and compare the biomarkers efficacy with traditional diagnostics and state-of-the-art bioelectronics. We summarize biomarkers in four major groups: genomics, transcriptomics, proteomics, and metabolomics/microbiota. Representative bioelectronic systems for each group are summarized based on various stages of a cancer. Systematic study of oxidative stress establishes the relationship between macromolecules and cancer biomarkers in saliva. We also introduce the most recent examples of salivary diagnostic electronics based on nanotechnologies that can offer rapid, yet highly accurate detection of biomarkers. A concluding section highlights areas of opportunity in the further development and applications of these technologies.
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Affiliation(s)
- Saswat Mishra
- Department of Mechanical and Nuclear Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Darius Saadat
- School of Engineering and Computer Science, Washington State University, Vancouver, WA 98686, USA
| | - Ohjin Kwon
- Department of Mechanical and Nuclear Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Yongkuk Lee
- Department of Mechanical and Nuclear Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Woon-Seop Choi
- School of Display Engineering, Hoseo University, Asan, Republic of Korea
| | - Jong-Hoon Kim
- School of Engineering and Computer Science, Washington State University, Vancouver, WA 98686, USA.
| | - Woon-Hong Yeo
- Department of Mechanical and Nuclear Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA; Center for Rehabilitation Science and Engineering, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA.
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25
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Wang H, Wang Y, Liu S, Yu J, Guo Y, Xu Y, Huang J. Signal-on electrochemical detection of antibiotics based on exonuclease III-assisted autocatalytic DNA biosensing platform. RSC Adv 2016. [DOI: 10.1039/c6ra06061g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, a novel electrochemical DNA sensor based on exonuclease III (Exo III)-assisted autocatalytic DNA biosensing platform for ultrasensitive detection of antibiotics has been reported.
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Affiliation(s)
- Hongzhi Wang
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
| | - Yu Wang
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Su Liu
- College of Resources and Environment
- University of Jinan
- Jinan 250022
- P. R. China
| | - Jinghua Yu
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
| | - Yuna Guo
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
| | - Ying Xu
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Jiadong Huang
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
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26
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Linardy EM, Erskine SM, Lima NE, Lonergan T, Mokany E, Todd AV. EzyAmp signal amplification cascade enables isothermal detection of nucleic acid and protein targets. Biosens Bioelectron 2016; 75:59-66. [DOI: 10.1016/j.bios.2015.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/04/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022]
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27
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Miao X, Li Z, Ling L. Fluorescence recognition of double-stranded DNA based on the quenching of gold nanoparticles to a fluorophore labeled DNA probe. Analyst 2016; 141:5829-5834. [DOI: 10.1039/c6an01145d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work described an ultrasensitive fluorescent sensor for sequence-specific recognition of dsDNA based on the quenching of gold nanoparticles (AuNPs) to a fluorophore labeled DNA probe.
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Affiliation(s)
- Xiangmin Miao
- School of Life Science
- Jiangsu Normal University
- Xuzhou 221116
- PR China
| | - Zongbing Li
- School of Life Science
- Jiangsu Normal University
- Xuzhou 221116
- PR China
| | - Liansheng Ling
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- PR China
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28
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Lv Y, Cui L, Peng R, Zhao Z, Qiu L, Chen H, Jin C, Zhang XB, Tan W. Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids. Anal Chem 2015; 87:11714-20. [PMID: 26505212 PMCID: PMC4898272 DOI: 10.1021/acs.analchem.5b02654] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Here, we propose an efficient strategy
for enzyme- and hairpin-free
nucleic acid detection called an entropy beacon (abbreviated as Ebeacon).
Different from previously reported DNA hybridization/displacement-based
strategies, Ebeacon is driven forward by increases in the entropy
of the system, instead of free energy released from new base-pair
formation. Ebeacon shows high sensitivity, with a detection limit
of 5 pM target DNA in buffer and 50 pM in cellular homogenate. Ebeacon
also benefits from the hairpin-free amplification strategy and zero-background,
excellent thermostability from 20 °C to 50 °C, as well as
good resistance to complex environments. In particular, based on the
huge difference between the breathing rate of a single base pair and
two adjacent base pairs, Ebeacon also shows high selectivity toward
base mutations, such as substitution, insertion, and deletion and,
therefore, is an efficient nucleic acid detection method, comparable
to most reported enzyme-free strategies.
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Affiliation(s)
- Yifan Lv
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Liang Cui
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Zilong Zhao
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Liping Qiu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida , Gainesville, Florida 32611-7200, United States
| | - Huapei Chen
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Cheng Jin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida , Gainesville, Florida 32611-7200, United States
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29
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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30
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Yan M, Bai W, Zhu C, Huang Y, Yan J, Chen A. Design of nuclease-based target recycling signal amplification in aptasensors. Biosens Bioelectron 2015; 77:613-23. [PMID: 26485175 DOI: 10.1016/j.bios.2015.10.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/21/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
Compared with conventional antibody-based immunoassay methods, aptasensors based on nucleic acid aptamer have made at least two significant breakthroughs. One is that aptamers are more easily used for developing various simple and rapid homogeneous detection methods by "sample in signal out" without multi-step washing. The other is that aptamers are more easily employed for developing highly sensitive detection methods by using various nucleic acid-based signal amplification approaches. As many substances playing regulatory roles in physiology or pathology exist at an extremely low concentration and many chemical contaminants occur in trace amounts in food or environment, aptasensors for signal amplification contribute greatly to detection of such targets. Among the signal amplification approaches in highly sensitive aptasensors, the nuclease-based target recycling signal amplification has recently become a research focus because it shows easy design, simple operation, and rapid reaction and can be easily developed for homogenous assay. In this review, we summarized recent advances in the development of various nuclease-based target recycling signal amplification with the aim to provide a general guide for the design of aptamer-based ultrasensitive biosensing assays.
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Affiliation(s)
- Mengmeng Yan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
| | - Wenhui Bai
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
| | - Chao Zhu
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
| | - Yafei Huang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China; College of Food Science and Technology, Hainan University, Haikou 570228, China
| | - Jiao Yan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China; College of Food Science and Technology, Hainan University, Haikou 570228, China
| | - Ailiang Chen
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture, Beijing 100081, China.
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31
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Tan Y, Wei X, Zhao M, Qiu B, Guo L, Lin Z, Yang HH. Ultraselective Homogeneous Electrochemical Biosensor for DNA Species Related to Oral Cancer Based on Nicking Endonuclease Assisted Target Recycling Amplification. Anal Chem 2015; 87:9204-8. [DOI: 10.1021/acs.analchem.5b01470] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yue Tan
- Ministry
of Education Key
Laboratory of Analysis and Detection for Food Safety, Fujian Provincial
Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Xiaofeng Wei
- Ministry
of Education Key
Laboratory of Analysis and Detection for Food Safety, Fujian Provincial
Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Mengmeng Zhao
- Ministry
of Education Key
Laboratory of Analysis and Detection for Food Safety, Fujian Provincial
Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Bin Qiu
- Ministry
of Education Key
Laboratory of Analysis and Detection for Food Safety, Fujian Provincial
Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Longhua Guo
- Ministry
of Education Key
Laboratory of Analysis and Detection for Food Safety, Fujian Provincial
Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zhenyu Lin
- Ministry
of Education Key
Laboratory of Analysis and Detection for Food Safety, Fujian Provincial
Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Huang-Hao Yang
- Ministry
of Education Key
Laboratory of Analysis and Detection for Food Safety, Fujian Provincial
Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
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32
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Gerasimova YV, Kolpashchikov DM. Enzyme-assisted target recycling (EATR) for nucleic acid detection. Chem Soc Rev 2015; 43:6405-38. [PMID: 24901032 DOI: 10.1039/c4cs00083h] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fast, reliable and sensitive methods for nucleic acid detection are of growing practical interest with respect to molecular diagnostics of cancer, infectious and genetic diseases. Currently, PCR-based and other target amplification strategies are most extensively used in practice. At the same time, such assays have limitations that can be overcome by alternative approaches. There is a recent explosion in the design of methods that amplify the signal produced by a nucleic acid target, without changing its copy number. This review aims at systematization and critical analysis of the enzyme-assisted target recycling (EATR) signal amplification technique. The approach uses nucleases to recognize and cleave the probe-target complex. Cleavage reactions produce a detectable signal. The advantages of such techniques are potentially low sensitivity to contamination and lack of the requirement of a thermal cycler. Nucleases used for EATR include sequence-dependent restriction or nicking endonucleases or sequence independent exonuclease III, lambda exonuclease, RNase H, RNase HII, AP endonuclease, duplex-specific nuclease, DNase I, or T7 exonuclease. EATR-based assays are potentially useful for point-of-care diagnostics, single nucleotide polymorphisms genotyping and microRNA analysis. Specificity, limit of detection and the potential impact of EATR strategies on molecular diagnostics are discussed.
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Affiliation(s)
- Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
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33
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Zheng J, Yang R, Shi M, Wu C, Fang X, Li Y, Li J, Tan W. Rationally designed molecular beacons for bioanalytical and biomedical applications. Chem Soc Rev 2015; 44:3036-55. [PMID: 25777303 PMCID: PMC4431697 DOI: 10.1039/c5cs00020c] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then be described. In particular, we emphasize recent progress in constructing MB-based biosensors in homogeneous solution or on solid surfaces. We expect that such rationally designed and functionalized MBs will open up new and exciting avenues for biological and medical research and applications.
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Affiliation(s)
- Jing Zheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
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34
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Sensitive and specific colorimetric DNA detection by invasive reaction coupled with nicking endonuclease-assisted nanoparticles amplification. Biosens Bioelectron 2015; 66:50-4. [DOI: 10.1016/j.bios.2014.10.077] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/19/2014] [Accepted: 10/31/2014] [Indexed: 11/18/2022]
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35
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Yan L, Zhou J, Zheng Y, Gamson AS, Roembke BT, Nakayama S, Sintim HO. Isothermal amplified detection of DNA and RNA. MOLECULAR BIOSYSTEMS 2014; 10:970-1003. [PMID: 24643211 DOI: 10.1039/c3mb70304e] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.
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Affiliation(s)
- Lei Yan
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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36
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Lu L, Shiu-Hin Chan D, Kwong DWJ, He HZ, Leung CH, Ma DL. Detection of nicking endonuclease activity using a G-quadruplex-selective luminescent switch-on probe. Chem Sci 2014. [DOI: 10.1039/c4sc02032d] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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37
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Xu G, Wang G, He X, Zhu Y, Chen L, Zhang X. An ultrasensitive electrochemical method for detection of Ag(+) based on cyclic amplification of exonuclease III activity on cytosine-Ag(+)-cytosine. Analyst 2014; 138:6900-6. [PMID: 24071747 DOI: 10.1039/c3an01320k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ag(+) is known to bind very strongly with cytosine-cytosine (C-C) mismatches in DNA duplexes to form C-Ag(+)-C base pairs. Exonuclease III (Exo III) can catalyze the stepwise removal of mononucleotides of duplex DNA. In this work, we study Exo III activity on DNA hybrids containing C-Ag(+)-C base pairs. Our experiments show that Ag(+) ions could intentionally trigger the activity of Exo III towards a designed cytosine-rich DNA oligonucleotide (C-rich probe) by the conformational change of the probe. Our sensing strategy uses this conformation-dependent activity of Exo III, which is controlled through the cyclical shuffling of Ag(+) ions between the solid DNA hybrid and the solution phase. This interesting conversion has led to the development of an ultrasensitive detection platform for Ag(+) ions with a detection limit of 0.03 nM and a total assay time possible within minutes. This simple detection strategy could also be used for the detection of other metal ions which exhibit specific interactions with natural or synthetic bases.
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Affiliation(s)
- Gang Xu
- College of Chemistry and Materials Science, Anhui Key Laboratory of Functional Molecular Solids, Anhui Key Laboratory of Chem-Biosensing, Anhui Normal University, Wuhu, 241000, P R China.
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38
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Duan R, Zuo X, Wang S, Quan X, Chen D, Chen Z, Jiang L, Fan C, Xia F. Quadratic isothermal amplification for the detection of microRNA. Nat Protoc 2014; 9:597-607. [DOI: 10.1038/nprot.2014.036] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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39
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Zou B, Song Q, Wang J, Liu Y, Zhou G. Invasive reaction assisted strand-displacement signal amplification for sensitive DNA detection. Chem Commun (Camb) 2014; 50:13722-4. [PMID: 25249213 DOI: 10.1039/c4cc06079b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An extension-block base in a molecular beacon enables beacon-assisted strand-displacement amplification to couple with invasive reaction efficiently by flap extension.
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Affiliation(s)
- Bingjie Zou
- Department of Pharmacology
- Jinling Hospital, Medical School of Nanjing University
- Nanjing, China
| | - Qinxin Song
- Department of Pharmacology
- Jinling Hospital, Medical School of Nanjing University
- Nanjing, China
- School of Life Science and Technology
- China Pharmaceutical University
| | - Jianping Wang
- Department of Pharmacology
- Jinling Hospital, Medical School of Nanjing University
- Nanjing, China
- School of Life Science and Technology
- China Pharmaceutical University
| | - Yunlong Liu
- Department of Pharmacology
- Jinling Hospital, Medical School of Nanjing University
- Nanjing, China
| | - Guohua Zhou
- Department of Pharmacology
- Jinling Hospital, Medical School of Nanjing University
- Nanjing, China
- State Key Laboratory of Analytical Chemistry for Life Science
- Nanjing University
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40
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Wang G, Xu G, Zhu Y, Zhang X. A “turn-on” carbon nanotube–Ag nanoclusters fluorescent sensor for sensitive and selective detection of Hg2+with cyclic amplification of exonuclease III activity. Chem Commun (Camb) 2014; 50:747-50. [DOI: 10.1039/c3cc46716c] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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41
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Ma C, Han D, Shi C. A new isothermal nucleic acid detection strategy mediated by a double-nicked beacon. Chem Commun (Camb) 2014; 50:3799-801. [DOI: 10.1039/c3cc49841g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Highly sensitive fluorescence assay of DNA methyltransferase activity via methylation-sensitive cleavage coupled with nicking enzyme-assisted signalamplification. Biosens Bioelectron 2013. [DOI: 10.1016/j.bios.2012.10.022] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Duan R, Zuo X, Wang S, Quan X, Chen D, Chen Z, Jiang L, Fan C, Xia F. Lab in a Tube: Ultrasensitive Detection of MicroRNAs at the Single-Cell Level and in Breast Cancer Patients Using Quadratic Isothermal Amplification. J Am Chem Soc 2013; 135:4604-7. [DOI: 10.1021/ja311313b] [Citation(s) in RCA: 298] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ruixue Duan
- School of
Chemistry and Chemical
Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaolei Zuo
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shutao Wang
- Beijing National Laboratory for
Molecular Sciences (BNLMS), Key Laboratory of Organic Solids, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiyun Quan
- The Pathology Department of Zhuzhou No. 1 Hospital, Hunan 412000, China
| | - Dongliang Chen
- The Pathology Department of Zhuzhou No. 1 Hospital, Hunan 412000, China
| | - Zhifei Chen
- School of
Chemistry and Chemical
Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lei Jiang
- Beijing National Laboratory for
Molecular Sciences (BNLMS), Key Laboratory of Organic Solids, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Chunhai Fan
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Fan Xia
- School of
Chemistry and Chemical
Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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44
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Liu S, Wang C, Zhang C, Wang Y, Tang B. Label-Free and Ultrasensitive Electrochemical Detection of Nucleic Acids Based on Autocatalytic and Exonuclease III-Assisted Target Recycling Strategy. Anal Chem 2013; 85:2282-8. [DOI: 10.1021/ac303225p] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Shufeng Liu
- College of Chemistry, Chemical Engineering
and Materials Science, Engineering Research Center of Pesticide and
Medicine Intermediate Clean Production, Ministry of Education, Key
Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China
- College of Chemistry and Molecular
Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chunfeng Wang
- College of Chemistry and Molecular
Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chengxin Zhang
- College of Chemistry and Molecular
Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Ying Wang
- College of Chemistry and Molecular
Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Bo Tang
- College of Chemistry, Chemical Engineering
and Materials Science, Engineering Research Center of Pesticide and
Medicine Intermediate Clean Production, Ministry of Education, Key
Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China
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45
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Abstract
Although many approaches based on template replication were developed and applied in DNA detection, cross-contamination from amplicons is always a vexing problem. Thus, signal amplification is preferable for DNA detection due to its low risk of cross-contamination from amplicons. Here, we proposed a cascade enzymatic signal amplification (termed as CESA) by coupling Afu flap endonuclease with nicking endonuclease, including three steps: invasive signal amplification, flap ligation, and nicking endonuclease signal amplification. Because of the advantages of low risk of contamination, no sequence requirement of target DNA, and the universal reaction conditions for any target detection, CESA has a great potential in clinical diagnosis.
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Affiliation(s)
- Bingjie Zou
- Department of Pharmacology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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46
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Gao F, Lei J, Ju H. Assistant DNA recycling with nicking endonuclease and molecular beacon for signal amplification using a target-complementary arched structure. Chem Commun (Camb) 2013; 49:4006-8. [DOI: 10.1039/c3cc40723c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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47
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Zhu Z, Lei J, Liu L, Ju H. Label-free electrochemical DNA sensing with a one-target-multitriggered hybridization chain reaction strategy. Analyst 2013; 138:5995-6000. [DOI: 10.1039/c3an01212c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Sub-femtomolar electrochemical detection of DNA using surface circular strand-replacement polymerization and gold nanoparticle catalyzed silver deposition for signal amplification. Biosens Bioelectron 2013; 39:199-203. [DOI: 10.1016/j.bios.2012.07.035] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/19/2012] [Accepted: 07/20/2012] [Indexed: 11/19/2022]
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49
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Liu S, Zhang C, Ming J, Wang C, Liu T, Li F. Amplified detection of DNA by an analyte-induced Y-shaped junction probe assembly followed with a nicking endonuclease-mediated autocatalytic recycling process. Chem Commun (Camb) 2013; 49:7947-9. [DOI: 10.1039/c3cc45211e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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50
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Zhang H, Li F, Dever B, Li XF, Le XC. DNA-mediated homogeneous binding assays for nucleic acids and proteins. Chem Rev 2012; 113:2812-41. [PMID: 23231477 DOI: 10.1021/cr300340p] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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