1
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Li B, Wang C. Endonuclease IV and T4 ligase enhanced detection of mutations in low abundance. Analyst 2024; 149:1050-1054. [PMID: 38231135 DOI: 10.1039/d3an02083e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
We propose a mutant detection approach based on endonuclease IV and DNA ligase in combination with qPCR. The enzymes functioned cooperatively to facilitate PCR for low abundance DNA detection. We demonstrate that our approach can distinguish mutations as low as 0.01%, indicating the potential application of this strategy in early cancer diagnosis.
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Affiliation(s)
- Bo Li
- Department of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010020, China.
| | - Chunyan Wang
- Department of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010020, China.
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2
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Wang LJ, Han Q, Hu JP, Wang HX, Liu M, Zhang CY. Structure-Switchable Hairpin-Powered Exponential Replications for Sensing Attomolar microRNA-Related Single Nucleotide Polymorphisms in Human Cancer Tissues with Zero Background. Anal Chem 2022; 94:15171-15175. [DOI: 10.1021/acs.analchem.2c04281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Li-juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Qian Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Jin-ping Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Hou-xiu Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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3
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Zhang Z, He T, Qi Y, Dai Y, Lao K, Gou X. Rapid and highly specific detection of site-specific 5-hydroxymethylcytosine based on peroxotungstate oxidation and mismatch ligation-based LAMP. RSC Adv 2022; 12:19885-19889. [PMID: 35865199 PMCID: PMC9261916 DOI: 10.1039/d2ra03310k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
We have developed a rapid and specific method for site-specific 5-hydroxymethylcytosine (5hmC) quantification at single-base resolution. This bisulfite-free method integrates the peroxotungstate oxidization with the mismatched probe-assisted ligation to guarantee the specificity. Moreover, the high-efficiency LAMP also makes the proposed method suitable for the detection of low-content samples. A facile and highly specific mismatch ligation-based amplification platform for quantification of site-specific 5hmC at single base resolution in low-content samples.![]()
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Affiliation(s)
- Zhenhao Zhang
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603.,School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710062 Shaanxi Province P. R. China
| | - Tong He
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603.,School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710062 Shaanxi Province P. R. China
| | - Yan Qi
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Yuxuan Dai
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Kejing Lao
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
| | - Xingchun Gou
- Shaanxi Key Laboratory of Brain Disorders, Shaanxi Provincial Key Laboratory of Infection and Immunity Diseases, Institute of Basic and Translational Medicine, Xi'an Medical University No. 1 Xin Wang Road Xi'an 710021 China +86 29 86177603
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4
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Sun W, Guo W, Liu Z, Qiao S, Wang Z, Wang J, Qu L, Shan L, Sun F, Xu S, Bai O, Liang C. Direct MYD88 L265P gene detection for diffuse large B-cell lymphoma (DLBCL) via a miniaturised CRISPR/dCas9-based sensing chip. LAB ON A CHIP 2022; 22:768-776. [PMID: 35073397 DOI: 10.1039/d1lc01055g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Traditional methods for single-nucleotide variants based on amplification and fluorescence signals require expensive reagents and cumbersome instruments, and they are time-consuming for each trial. Here, a porous anodised aluminium (PAA)-based sensing chip modified with deactivated Cas9 (dCas9) proteins and synthetic guide RNA (sgRNA) as the biorecognition receptor is developed, which can be used for the label-free sensing of the diffuse large B-cell lymphoma (DLBCL) MYD88L265P gene by integrating with electrochemical ionic current rectification (ICR) measurement. The sgRNA that can specifically identify and capture the MYD88L265P gene was screened, which has been proved to be workable to activate dCas9 for the target MYD88L265P. In the sensing process, the dCas9 proteins can capture the genome sequence, thus bringing negative charges over the PAA chip and correspondingly resulting in a variation in the ICR value due to the uneven transport of potassium anions through the ion channels of the PAA chip. The whole sensing can be finished within 40 min, and there is no need for gene amplification. The CRISPR/dCas9-based sensor demonstrates ultrasensitive detection performance in the concentration range of 50 to 200 ng μL-1 and it has been proved to be feasible for the genome sequence of patient tissues. This sensor shows the potential of targeting other mutations by designing the corresponding sgRNAs and expands the applications of CRISPR/dCas9 technology to the on-chip electrical detection of nucleic acids, which will be very valuable for rapid diagnosis of clinically mutated genes. This makes the hybrid CRISPR-PAA chip an ideal candidate for next-generation nucleic acid biosensors.
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Affiliation(s)
- Weihan Sun
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, 130021 Changchun, China.
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Wei Guo
- Department of Hematology, The First Hospital of Jilin University, Jilin University, 71 Xinmin Street, 130021 Changchun, China.
| | - Zhiyi Liu
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Sennan Qiao
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Ziming Wang
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, 130021 Changchun, China.
| | - Jiayu Wang
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Lingxuan Qu
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Liang Shan
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, 130021 Changchun, China.
| | - Fei Sun
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, 130021 Changchun, China.
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Shuping Xu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2699 Qianjin Ave., 130012 Changchun, China.
| | - Ou Bai
- Department of Hematology, The First Hospital of Jilin University, Jilin University, 71 Xinmin Street, 130021 Changchun, China.
| | - Chongyang Liang
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, 130021 Changchun, China.
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
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5
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Tan G, Fei Z, Wei R, Wu X, Xiao P. Development of a Novel Bioluminescence Pyrophosphate Assay for the High-Sensitivity Detection of Hepatitis B Virus. Appl Biochem Biotechnol 2022; 194:725-736. [PMID: 34519921 DOI: 10.1007/s12010-021-03655-0] [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: 03/17/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
The transmission of bloodborne viruses through transfusion remains a major blood supply-related safety concern, with hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) being the most important pathogens in this context. Real-time bioluminescent pyrophosphate testing has been developed as a means of readily detecting bacterial cells within particular sample types without requiring the use of expensive or complex instrumentation. The sensitivity of this approach, however, is often limited such that it is not compatible with many potential applications. In this study, we sought to overcome the limitations of this pyrophosphate bioluminescent assay format by using 2-deoxyadenosine-5-(α-thio)-triphosphate (dATPαS) in place of dATP for PCR amplification, thereby dramatically reducing background signal levels. We leveraged this combination PCR and bioluminescent pyrophosphate assay approach to facilitate HBV detection. This assay yielded a limit of detection of 500 copies/mL, making it more sensitive than traditional bioluminescent assays, about 1000 times more sensitive than that of PCR product analysis by agarose gel electrophoresis, and roughly as sensitive as qPCR as a means of detecting viral DNA. We then used this assay to analyze 100 serum samples, with qPCR being used for result validation. The assay required 100 min to complete, and was able to detect as few as 500 copies/mL of viral DNA. Overall, our approach was rapid, sensitive, and simple, enabling users to readily detect HBV in a reliable and efficient manner.
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Affiliation(s)
- Guolei Tan
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Zhong Fu Lu 1#, Gulou District, Nanjing, 210003, China
| | - Zhongjie Fei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2#, Xuanwu District, Nanjing, 210096, China
| | - Rongbin Wei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2#, Xuanwu District, Nanjing, 210096, China
| | - Xuping Wu
- The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Zhong Fu Lu 1#, Gulou District, Nanjing, 210003, China.
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2#, Xuanwu District, Nanjing, 210096, China.
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6
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Zhang Z, Li L, Liu Q, Hu Y, Yuan W, Xiao X, Wu T. Sensitive
DNA
Mutation Detection at Physiological Temperature with Endonuclease
IV
by Inhibiting Its Side Activity. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zhen Zhang
- School of Pharmacy, Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei 430030 China
| | - Longjie Li
- School of Pharmacy, Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei 430030 China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Hangzhou Zhejiang 310024 China
| | - Qingxu Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei 430030 China
| | - Yuqiang Hu
- School of Pharmacy, Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei 430030 China
| | - Wenqian Yuan
- School of Pharmacy, Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei 430030 China
| | - Xianjin Xiao
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei 430030 China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei 430030 China
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7
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Landuzzi F, Viader-Godoy X, Cleri F, Pastor I, Ritort F. Detection of single DNA mismatches by force spectroscopy in short DNA hairpins. J Chem Phys 2020; 152:074204. [PMID: 32087630 DOI: 10.1063/1.5139284] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Identification of defective DNA structures is a difficult task, since small differences in base-pair bonding are hidden in the local structural variability of a generally random base-pair sequence. Defects, such as base mismatches, missing bases, crosslinks, and so on, occur in DNA with high frequency and must be efficiently identified and repaired to avoid dire consequences such as genetic mutations. Here, we focus on the detection of base mismatches, which is local deviations from the ideal Watson-Crick pairing rule, which may typically originate from DNA replication process, foreign chemical attack, or ionizing radiation. Experimental detection of a mismatch defect demands the ability to measure slight deviations in the free energy and molecular structure. We introduce different mismatches in short DNA hairpins (10 or 20 base pairs plus a 4-base loop) sandwiched between dsDNA handles to be used in single-molecule force spectroscopy with optical tweezers. We perform both hopping and force-pulling experiments to measure the excess free energies and deduce the characteristic kinetic signatures of the mismatch from the force-distance curves. All-atom molecular dynamics simulations lend support to the detailed interpretation of the experimental data. Such measurements, at the lowest sensitivity limits of this experimental technique, demonstrate the capability of identifying the presence of mismatches in a random complementary dsDNA sequence and provide lower bounds for the ability to distinguish different structural defects.
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Affiliation(s)
- F Landuzzi
- Department of Physics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Japan
| | - X Viader-Godoy
- Small Biosystems Lab., Univ. de Barcelona, Diagonal 647, 08028 Barcelona, Spain
| | - F Cleri
- I.E.M.N. (UMR Cnrs 8520), 59652 Villeneuve d'Ascq, France
| | - I Pastor
- Small Biosystems Lab., Univ. de Barcelona, Diagonal 647, 08028 Barcelona, Spain
| | - F Ritort
- Small Biosystems Lab., Univ. de Barcelona, Diagonal 647, 08028 Barcelona, Spain
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8
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Tang W, Zhong W, Tan Y, Wang GA, Li F, Liu Y. DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants. Top Curr Chem (Cham) 2020; 378:10. [PMID: 31894426 DOI: 10.1007/s41061-019-0274-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023]
Abstract
Single-nucleotide variants (SNVs) that are strongly associated with many genetic diseases and tumors are important both biologically and clinically. Detection of SNVs holds great potential for disease diagnosis and prognosis. Recent advances in DNA nanotechnology have offered numerous principles and strategies amenable to the detection and quantification of SNVs with high sensitivity, specificity, and programmability. In this review, we will focus our discussion on emerging techniques making use of DNA strand displacement, a basic building block in dynamic DNA nanotechnology. Based on their operation principles, we classify current SNV detection methods into three main categories, including strategies using toehold-mediated strand displacement reactions, toehold-exchange reactions, and enzyme-mediated strand displacement reactions. These detection methods discriminate SNVs from their wild-type counterparts through subtle differences in thermodynamics, kinetics, or response to enzymatic manipulation. The remarkable programmability of dynamic DNA nanotechnology also allows the predictable design and flexible operation of diverse strand displacement probes and/or primers. Here, we offer a systematic survey of current strategies, with an emphasis on the molecular mechanisms and their applicability to in vitro diagnostics.
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Affiliation(s)
- Weiyang Tang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yun Tan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Guan A Wang
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada
| | - Feng Li
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada. .,College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China. .,Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Wuhan University, Wuhan, China.
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9
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Chen M, Li H, Zhou D, Peng W, Lian G, Gao W, Gong X, Chang J. Reusable Bioluminescent Sensor for Ultrasensitive MicroRNA Detection Based on a Target-Introducing "Fuel-Loading" Mechanism. ACS APPLIED MATERIALS & INTERFACES 2019; 11:38586-38594. [PMID: 31559822 DOI: 10.1021/acsami.9b16480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
As a kind of important potential biomarkers, the expression level of some microRNAs (miRNAs) is closely related to cancer development and progression. Herein, a reusable ultra-sensitive "fuel-loadings" bioluminescent sensor was constructed to detect the trace miRNA based on the cascading signal amplification, which combined the target-introducing "fuel-loading" mechanism and cyclic bioluminescence assay. In this sensor, magnetic beads labeled with hairpin DNA probes (hDNA) could specifically hybridize with the target miRNA and isolate these targets from samples. Then, the target-introducing "fuel loading" mechanism worked because the poly(A) polymerase can catalyze the template-independent sequential addition of adenosine monophosphate (AMP) to the 3' ends of the miRNA targets to produce long poly(A) tails. The long poly(A) tails provided lots of 5'AMPs (cleaved by Exonuclease T), which further as fuels were converted into adenosine-triphosphate (ATP) to generate an enhanced bioluminescent signal by cyclic AMP pyrophosphorylation-ATP dephosphorylation. The "fuel-loadings" bioluminescent sensor realized a high sensitivity with a limit-of-detection of about 22.6 aM for miRNA 21. Moreover, this "fuel-loadings" bioluminescent sensor not only achieved regenerable and reusable measurement in the same microwell to decrease the analysis costs, but also could directly detect miRNA 21 in the serum without complicated extraction procedures. It showed excellent coherence with quantitative reverse transcription polymerase chain reaction for miRNA 21 detection of cancer patients' samples, indicating clinical translation potential for miRNA detection.
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Affiliation(s)
- Minghui Chen
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin), Tianjin 300072, China
| | - Hengxuan Li
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin), Tianjin 300072, China
| | - Dianming Zhou
- Department of Toxicology, Tianjin Center for Disease Control and Prevention, Tianjin 300011, China
| | - Weipan Peng
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin), Tianjin 300072, China
| | - Guowei Lian
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin), Tianjin 300072, China
| | - Weichen Gao
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin), Tianjin 300072, China
| | - Xiaoqun Gong
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin), Tianjin 300072, China
| | - Jin Chang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology (Tianjin), Tianjin 300072, China
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10
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Mirzapoor A, Turner APF, Tiwari A, Ranjbar B. Electrochemical detection of DNA mismatches using a branch-shaped hierarchical SWNT-DNA nano-hybrid bioelectrode. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 104:109886. [PMID: 31500014 DOI: 10.1016/j.msec.2019.109886] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/26/2022]
Abstract
Common approaches for DNA mutation detection are high cost and have difficult or complex procedure. We propose a fast quantitative method for recognition of DNA mutation based on SWNT/DNA self-assembled nanostructure. Covalent SWNT/DNA hybrid nanostructures are widely used in the fabrication of electrochemical biosensors. Interfacing carbon nanotubes with DNA in particular, is used as a detection method for the analysis of genetic disorders or the detection of mismatches in DNA hybridisation. We have designed a self-assembled, branch-shaped hybrid nanostructure by hybridisation of two sticky oligos that are attached to the ends of SWNTs via a linker oligo. These hybrid nanostructures showed a good conductivity that was greater than free SWNTs. Impedance spectroscopy studies illustrated that the conductivity of these hybrid nanostructures depended on the conformation and structure of the hybridised DNA. We demonstrated that the strategy of using SWNT/DNA self-assembled hybrid nanostructure fabrication yields sensitive and selective tools to discriminate mismatches in DNA. Cyclic voltammetry (CV) and impedance spectroscopy clearly revealed that the conductivity of the branch-shaped and hierarchical hybridised SWNT/DNA nanostructure is higher when matched, than when mismatched in a 1 and 1' hybridised SWNT/DNA nanostructure. Rapid biosensing of match and mismatch nanostructure based on carbon printed electrode showed similar results which can be used for rapid and fast detection of DNA mismatch.
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Affiliation(s)
- Aboulfazl Mirzapoor
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Anthony P F Turner
- Biosensors and Bioelectronics Centre, Department of Physics, Chemistry and Biology (IFM), Linköping University, 58183 Linköping, Sweden
| | - Ashutosh Tiwari
- Institute of Advanced Materials, VBRI, Teknikringen 4A, Mjärdevi Science Park, 583 30 Linköping, Sweden; Innovation Centre, Vinoba Bhave Research Institute (VBRI), New Delhi 110019, India
| | - Bijan Ranjbar
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran; Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
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11
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Wu F, Lin Q, Wang L, Zou Y, Chen M, Xia Y, Lan J, Chen J. A DNA electrochemical biosensor based on triplex DNA-templated Ag/Pt nanoclusters for the detection of single-nucleotide variant. Talanta 2019; 207:120257. [PMID: 31594620 DOI: 10.1016/j.talanta.2019.120257] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 01/24/2023]
Abstract
A label-free electrochemical biosensor based on the triplex DNA-templated Ag/Pt bimetallic nanoclusters (triplex-Ag/PtNCs) and locked nucleic acid (LNA) modified X-shaped DNA probe was developed for the detection of single-nucleotide variant (SNV) related to β-thalassemia. Firstly, using triplex DNA as template, a site-specific and homogeneous Ag/PtNCs was prepared, which can effectively catalyze the 3,3,5,5-tetramethylbenzidine-H2O2 system and thus be employed as a signal reporter in the field of electrochemical biosensor. Secondly, the LNA modified X-shaped probes were assembled on gold electrode surface, which can only be dissociated in the presence of target, leading to the hybridization with triplex-Ag/PtNCs and significant increase of current signal. In this way, the detection limit for SNV of β-thalassemia was 0.8 fM with variant allele frequency (VAF) as low as 0.0001%.
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Affiliation(s)
- Fang Wu
- Department of Basic Chemistry, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Qian Lin
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Liangliang Wang
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Yulian Zou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Mei Chen
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Yaokun Xia
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Jianming Lan
- Department of Basic Chemistry, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Jinghua Chen
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China.
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12
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Abstract
Advances in nucleic acid sequencing and genotyping technologies have facilitated the discovery of an increasing number of single-nucleotide variations (SNVs) associated with disease onset, progression, and response to therapy. The reliable detection of such disease-specific SNVs can ensure timely and effective therapeutic action, enabling precision medicine. This has driven extensive efforts in recent years to develop novel methods for the fast and cost-effective analysis of targeted SNVs. In this Review, we highlight the most recent and significant advances made toward the development of such methodologies.
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Affiliation(s)
- Alireza Abi
- Department of Chemistry, Faculty of Sciences, Shiraz University, Shiraz 7194684795, Iran
| | - Afsaneh Safavi
- Department of Chemistry, Faculty of Sciences, Shiraz University, Shiraz 7194684795, Iran
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13
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Fu Y, Duan X, Huang J, Huang L, Zhang L, Cheng W, Ding S, Min X. Detection of KRAS mutation via ligation-initiated LAMP reaction. Sci Rep 2019; 9:5955. [PMID: 30976068 PMCID: PMC6459849 DOI: 10.1038/s41598-019-42542-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
KRAS mutations are abnormalities widely found in genomic DNA and circulating tumor DNA (ctDNA) of various types of cancers. Thus, highly sensitive detection of KRAS mutations in genomic DNA is of great significance in disease diagnosis and personalized medicine. Here, we developed a ligation-initiated loop-mediated isothermal amplification (LAMP) assaying method for ultrasensitive detection of KRAS mutation. In the presence of mutant KRAS DNA (mutDNA), the dumbbell-shaped structure (DSS) is formed by the specific ligation of two substrates (SLS1 and SLS2), which act as a template to initiate the following LAMP amplification. Making use of the outstanding specificity of ligation reaction and superior amplification of LAMP, 10 aM mutDNA can be accurately determined. In addition, as low as 0.1% mutDNA can be detected in the presence of a large excess of wild-type KRAS DNA (wtDNA), indicating the high sensitivity and specificity of the method. Furthermore, this strategy has been successfully applied for detection of a KRAS mutation from tissue samples of colorectal cancer patients. Thus, the developed ligation-initiated LAMP fluorescence assaying strategy presents a promising prospect for ultrasensitive detection of mutations.
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Affiliation(s)
- Yixin Fu
- Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, P.R. China.,School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China
| | - Xiaolei Duan
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China.,Key Laboratory of Clinical Laboratory Diagnostics (Ministry of education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Jian Huang
- Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, P.R. China.,School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China
| | - Lizhen Huang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Lutan Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Xun Min
- Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, P.R. China. .,School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China.
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14
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Aligner mediated cleavage of nucleic acids for site-specific detection of single base mismatch. Talanta 2019; 201:358-363. [PMID: 31122435 DOI: 10.1016/j.talanta.2019.03.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/25/2019] [Accepted: 03/30/2019] [Indexed: 01/03/2023]
Abstract
Single base mismatch can always connect with various gene-related diseases, whose determination has aroused widespread interest. So far, various methods have been developed to determine the common base mismatch. However most of them are complex, time-consuming. Herein, we report a novel method, which only need one conventional endonuclease (NEase) and achieve site-specific cleavage in a programmable way, to detect single base mismatch, termed aligner-mediated cleavage-based single base mismatch discrimination (AMCMD). The DNA aligner (DA) is in a stem-loop structure, consistent with an incomplete recognition site of NEase on its stem and a 5'-side arm complementary to the target sequence (TS). Once TS contains matched base and hybridizes with DA, the complete recognition site of NEase is formed, and the TS will be cleavaged with fast speed, while converse is not. Based on it, the method can clearly distinguish mismatched and complementary bases. Without sample pre-processing, we were able to obtain and verify all the test result in about 30 min through the polyacrylamide gel electrophoresis analysis. This endows the proposed method with a simpler advantage. Then we combined AMCMD and EXPAR to create a new method for single base mismatch discrimination, the short sequence obtained by AMCMD as a target to trigger EXPAR, with a detection limit at 1pM level. Another process with human serum underlines that AMCMD is compatible with the complex biological sample, thus it has the potentials for practical applications.
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15
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Ren Y, Li Y, Duan X, Wang H, Wang H, Li Z. One-Step Quantitative Single Nucleotide Polymorphism (SNP) Diagnosis By Modified Loop-Mediated Isothermal Amplification (mLAMP). ChemistrySelect 2019. [DOI: 10.1002/slct.201802693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yiqian Ren
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Yanru Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Xinrui Duan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Honghong Wang
- School of Chemistry and Biological Engineering; University of Science&Technology Beijing; Beijing 100083, P.R. China
| | - Hui Wang
- School of Chemistry and Biological Engineering; University of Science&Technology Beijing; Beijing 100083, P.R. China
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
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16
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Zhong W, Tang W, Fan J, Zhang J, Zhou X, Liu Y. A domain-based DNA circuit for smart single-nucleotide variant identification. Chem Commun (Camb) 2018; 54:1311-1314. [PMID: 29177325 DOI: 10.1039/c7cc07733e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
According to the differential information of four homologous oligonucleotides, two domain-based encoders have been constructed with the molecular information as the input. Based on the one-to-one correspondence between the input and output, SNVs can be identified and their sites can be located at the domain level.
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Affiliation(s)
- Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, P. R. China.
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17
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Xu Q, Zhang Y, Xiang D, Li CC, Zhang CY. A universal DNAzyme-based bioluminescent sensor for label-free detection of biomolecules. Anal Chim Acta 2018; 1043:81-88. [PMID: 30392672 DOI: 10.1016/j.aca.2018.08.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 12/28/2022]
Abstract
We demonstrate for the first time the development of a universal DNAzyme-based bioluminescent sensor for label-free detection of various biomolecules including DNAzyme and DNA. The presence of DNAzyme may induce the cyclic cleavage of riboadenosine (rA)-containing substrates, and the subsequent digestion of the cleaved substrates by exonuclease III (Exo III) releases abundant AMPs to initiate cyclic AMP pyrophosphorylation-ATP depyrophosphorylation for the generation of an enhanced bioluminescence signal. This sensor can real-time monitor the DNAzyme activity with a detection limit of 3.16 × 10-12 M. Moreover, the DNAzyme may be divided into two subunits for sensitive detection of target DNA. In the presence of target DNA, the two separated subunits may assemble into an active DNAzyme which can catalyze the cyclic cleavage of substrates and initiate the digestion of cleaved substrates by Exo III for the generation of an enhanced bioluminescence signal. This sensor can sensitively detect target DNA with a detection limit of 3.31 × 10-12 M. Importantly, this bioluminescent sensor can achieve a zero-background signal, and its output signal originates from the release of AMP for the generation of self-illuminating light emission without the requirement of either the external labels or the reporting reagents.
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Affiliation(s)
- Qinfeng Xu
- College of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Dongxue Xiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
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18
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Dou B, Li J, Jiang B, Yuan R, Xiang Y. Electrochemical screening of single nucleotide polymorphisms with significantly enhanced discrimination factor by an amplified ratiometric sensor. Anal Chim Acta 2018; 1038:166-172. [PMID: 30278899 DOI: 10.1016/j.aca.2018.07.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 06/14/2018] [Accepted: 07/10/2018] [Indexed: 01/12/2023]
Abstract
The detection of single nucleotide polymorphisms (SNPs) is of great clinical significance to the diagnosis of various genetic diseases and cancers. In this work, the development of an ultrasensitive ratiometric electrochemical sensor for screening SNP with a significantly enhanced discrimination factor is reported. The ferrocene (Fc) and methylene blue (MB) dual-tagged triple helix complex (THC) probes are self-assembled on the gold electrode to construct the sensing interface. The addition of the mutant p53 gene causes the disassembly of the THC probes with the release of the Fc-tagged sequence and the folding of the MB-labeled sequence into a hairpin structure, causing the change in the current response ratio of MB to Fc for monitoring the mutant p53 gene. Such ratio is dramatically enhanced by the toehold-mediated displacement reaction-assisted target recycling amplification with the presence of an assistance hairpin sequence. With the significant signal amplification and the advantageous specificity of the THC probes, sub-femtomolar detection limit and a highly enhanced SNP discrimination factor for the mutant p53 gene can be obtained. Besides, the proof-of-demonstration application of the sensor for diluted real samples has been verified, offering such sensor new opportunities for monitoring various genetic related diseases.
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Affiliation(s)
- Baoting Dou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jin Li
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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19
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Aggeli D, Karas VO, Sinnott-Armstrong NA, Varghese V, Shafer RW, Greenleaf WJ, Sherlock G. Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery. Nucleic Acids Res 2018; 46:e42. [PMID: 29361139 PMCID: PMC5909455 DOI: 10.1093/nar/gky022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/15/2017] [Accepted: 01/16/2018] [Indexed: 01/15/2023] Open
Abstract
Much of the within species genetic variation is in the form of single nucleotide polymorphisms (SNPs), typically detected by whole genome sequencing (WGS) or microarray-based technologies. However, WGS produces mostly uninformative reads that perfectly match the reference, while microarrays require genome-specific reagents. We have developed Diff-seq, a sequencing-based mismatch detection assay for SNP discovery without the requirement for specialized nucleic-acid reagents. Diff-seq leverages the Surveyor endonuclease to cleave mismatched DNA molecules that are generated after cross-annealing of a complex pool of DNA fragments. Sequencing libraries enriched for Surveyor-cleaved molecules result in increased coverage at the variant sites. Diff-seq detected all mismatches present in an initial test substrate, with specific enrichment dependent on the identity and context of the variation. Application to viral sequences resulted in increased observation of variant alleles in a biologically relevant context. Diff-Seq has the potential to increase the sensitivity and efficiency of high-throughput sequencing in the detection of variation.
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Affiliation(s)
- Dimitra Aggeli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vlad O Karas
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Vici Varghese
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert W Shafer
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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20
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Hu S, Li N, Liu F. Combining cooperativity with sequestration: a novel strategy for discrimination of single nucleotide variants. Chem Commun (Camb) 2018. [PMID: 29528359 DOI: 10.1039/c8cc00838h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a novel strategy for the discrimination of single nucleotide variants (SNVs) by combining cooperativity with sequestration, which displays remarkably high specificity (discrimination factors ranging from 67 to 618 with a median of 194) against 12 model SNVs and can be easily integrated with PCR amplification to detect KRAS G12D mutation.
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Affiliation(s)
- Shichao Hu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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21
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Ma F, Liu H, Li CC, Zhang CY. A simple and isothermal ligase-based amplification approach based on a ligation-activated cleavage reaction. Chem Commun (Camb) 2018; 54:12638-12641. [DOI: 10.1039/c8cc07843b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We develop a simple and isothermal ligase-based cyclic amplification approach for the sensitive detection of polynucleotide kinase, DNA, proteins and ATP.
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Affiliation(s)
- Fei Ma
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Huan Liu
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chen-chen Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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22
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Wang Y, Gao J, Meng X, Wang Z. DNA microarray-based resonance light scattering assay for multiplexed detection of DNA mutation in papillary thyroid cancer. Analyst 2018; 143:914-919. [PMID: 29362729 DOI: 10.1039/c7an01773a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A DNA microarray-based resonance light scattering assay has been developed for multiplexed detection of papillary thyroid carcinoma (PTC) related genic mutation.
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Affiliation(s)
- Yaoqi Wang
- Department of Thyroid Surgery
- the First Hospital of Jilin University
- Changchun 130021
- P. R. China
| | - Jiaxue Gao
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
| | - Xianying Meng
- Department of Thyroid Surgery
- the First Hospital of Jilin University
- Changchun 130021
- P. R. China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun 130022
- P. R. China
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23
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Zhang Y, Li QN, Li CC, Zhang CY. Label-free and high-throughput bioluminescence detection of uracil-DNA glycosylase in cancer cells through tricyclic cascade signal amplification. Chem Commun (Camb) 2018; 54:6991-6994. [DOI: 10.1039/c8cc03769h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We develop a label-free and high-throughput bioluminescence method for the sensitive detection of uracil DNA glycosylase through tricyclic cascade signal amplification.
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Affiliation(s)
- Yan Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Qing-nan Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chen-chen Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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24
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Li L, Xiao X, Ge J, Han M, Zhou X, Wang L, Su X, Yu C. Discrimination Cascade Enabled Selective Detection of Single-Nucleotide Mutation. ACS Sens 2017; 2:419-425. [PMID: 28723215 DOI: 10.1021/acssensors.7b00005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Owing to the significance of single nucleotide mutation (SNM) for personalized medicine, the detection of SNM with high accuracy has recently attracted considerable interest. Here, we present a kinetic method for selective detection of SNM based on a discrimination cascade constructed by combining the toehold strand displacement (TSD) and endonuclease IV (Endo IV) catalyzed hydrolysis. The single-nucleotide specificity of the two DNA reactions allows highly selective detection of all types of single nucleotide changes (including single-nucleotide insertion and deletion), achieving a high discrimination factor with a median of 491 which is comparable with recently reported methods. For the first time, the enzyme assisted nucleic acid assay was characterized by single molecule analysis on total internal reflection fluorescence microscope (TIRFM) suggesting that the two steps do not work independently and the rate of TSD can be tuned by Endo IV facilitated conformation selection. The effective discrimination of the point mutation of BRAF gene in cancer and normal cell line suggests that this method can be a prominent post-PCR genotyping assay.
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Affiliation(s)
- Lidan Li
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xianjin Xiao
- Family
Planning Research Institute/Center of Reproductive Medicine, Tongji
Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jingyang Ge
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Manli Han
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xu Zhou
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lei Wang
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xin Su
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Changyuan Yu
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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25
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Hu S, Tang W, Zhao Y, Li N, Liu F. Ultra-specific discrimination of single-nucleotide mutations using sequestration-assisted molecular beacons. Chem Sci 2017; 8:1021-1026. [PMID: 28451240 PMCID: PMC5356502 DOI: 10.1039/c6sc03048c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/17/2016] [Indexed: 12/31/2022] Open
Abstract
Reliably distinguishing single-nucleotide mutations (SNMs) at low abundance is of great significance in clinical diagnosis. However, the specificity of most current SNM discrimination methods based on the Watson-Crick hybridization is seriously limited by the cross-reactivity of the probe with closely related unintended sequences. Herein, we propose a sequestration-assisted molecular beacon (MB) strategy for highly specific SNM discrimination. The new SNM discrimination system consists of a target-specific MB and a series of hairpin sequestering agents (SEQs). The rationally designed hairpin SEQs can effectively sequester the corresponding unintended sequences and thus dramatically improve the hybridization specificity of the MB in recognizing SNMs. The developed SNM discrimination method shows remarkably high specificity (discrimination factors ranging from 12 to 1144 with a median of 117) against 20 model SNMs, and can work rapidly and robustly over a wide range of conditions. Notably, our SNM discrimination method can be easily combined with PCR amplification for the detection of KRAS G12D (c.35G>A) and G12V (c.35G>T) mutations at abundance as low as 0.5%. This work expands the rule set of designing hybridization-based SNM discrimination strategies and shows promising potential application in clinical diagnosis.
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Affiliation(s)
- Shichao Hu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Wei Tang
- Institute of Materials , China Academy of Engineering Physics , Mianyang , 621700 , China
| | - Yan Zhao
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Na Li
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
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26
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Xu X, Wang L, Wu Y, Jiang W. Uracil removal-inhibited ligase reaction in combination with catalytic hairpin assembly for the sensitive and specific detection of uracil-DNA glycosylase activity. Analyst 2017; 142:4655-4660. [DOI: 10.1039/c7an01666b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Uracil removal-inhibited ligase reaction in combination with a catalytic hairpin assembly sensing strategy is demonstrated for UDG activity detection.
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Affiliation(s)
- Xiaowen Xu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P.R. China
| | - Lei Wang
- School of Pharmaceutical Sciences
- Shandong University
- 250012 Jinan
- P.R. China
| | - Yushu Wu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P.R. China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P.R. China
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