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Improving the sensitivity and selectivity of a DNA probe using graphene oxide-protected and T7 exonuclease-assisted signal amplification. Anal Bioanal Chem 2020; 412:3029-3035. [PMID: 32206848 DOI: 10.1007/s00216-020-02556-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/18/2019] [Accepted: 02/27/2020] [Indexed: 12/21/2022]
Abstract
The accurate analysis of single-nucleotide polymorphisms is of great significance for clinical detection and diagnosis. Based on the hybridization hindrance caused by graphene oxide (GO) and hairpin probe, we report a T7 Exo-assisted cyclic amplification technique to distinguish single-base mismatch for highly sensitive and selective detection of mutant-type DNA. When the mutant-type target is completely complementary to the probe, the T7 Exo hydrolyzes the probe and releases the fluorescent molecule from the GO surface, resulting in a fluorescence signal. Conversely, when the wild-type mismatch target is present, the weak hybridization prevents the release of FAM-labeled probe from the GO surface. Therefore, the FAM-labeled probe cannot be degraded efficiently by T7 Exo, and the fluorescence is still quenched by GO. The detection limit of the proposed method can be as low as 34 fM due to the cyclic signal amplification. The experimental results showed that the established method could be used to detect single-nucleotide polymorphisms accurately and sensitively at low cost.
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2
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Chung CH, Kim JH. One-step isothermal detection of multiple KRAS mutations by forming SNP specific hairpins on a gold nanoshell. Analyst 2019; 143:3544-3548. [PMID: 29687792 DOI: 10.1039/c8an00525g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed a one-step isothermal method for typing multiple KRAS mutations using a designed set of primers to form a hairpin on a gold nanoshell upon being ligated by a SNP specific DNA ligase after binding of targets. As a result, we could detect as low as 20 attomoles of KRAS mutations within 1 h.
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Affiliation(s)
- Chan Ho Chung
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea.
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3
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Kim JH. PCR free multiple ligase reactions and probe cleavages for the SNP detection of KRAS mutation with attomole sensitivity. Analyst 2016; 141:6381-6386. [DOI: 10.1039/c6an00909c] [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
A method to produce multiple ligated primers without PCR for a target DNA containing a single point mutation is presented.
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Affiliation(s)
- Joong Hyun Kim
- Medical Device Development Center
- Daegu-Gyeongbuk Medical Innovation Foundation
- Daegu
- 701-310 South Korea
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4
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Shen W, Tian Y, Ran T, Gao Z. Genotyping and quantification techniques for single-nucleotide polymorphisms. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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5
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Zhu X, Shen Y, Cao J, Yin L, Ban F, Shu Y, Li G. Detection of microRNA SNPs with ultrahigh specificity by using reduced graphene oxide-assisted rolling circle amplification. Chem Commun (Camb) 2015; 51:10002-5. [DOI: 10.1039/c5cc02039e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
By adopting reduced graphene oxide into a rolling cycle amplification system, we find that the specificity can be greatly improved, which would contribute to the accurate identification of miRNA SNPs.
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Affiliation(s)
- Xiaoli Zhu
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Yalan Shen
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Jiepei Cao
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Li Yin
- Department of Oncology
- the First Affiliated Hospital of Nanjing Medical University
- Nanjing 210029
- P. R. China
| | - Fangfang Ban
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Yongqian Shu
- Department of Oncology
- the First Affiliated Hospital of Nanjing Medical University
- Nanjing 210029
- P. R. China
| | - Genxi Li
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
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7
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Abstract
In this critical review, we present the recent advances in the design and fabrication of graphene/nucleic acid nanobiointerfaces, as well as the fundamental understanding of their interfacial properties and various nanobiotechnological applications.
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Affiliation(s)
- Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation
- Department of Optical Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Ying Wang
- Department of Chemistry
- Shanghai Key Laboratory of Chemical Assessment and Sustainability
- UNEP-Tongji Institute of Environment for Sustainable Development
- Tongji University
- Shanghai
| | - Jinghong Li
- Department of Chemistry
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Tsinghua University
- Beijing 100084
- China
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8
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Zou Z, Qing Z, He X, Wang K, He D, Shi H, Yang X, Qing T, Yang X. Ligation-rolling circle amplification combined with γ-cyclodextrin mediated stemless molecular beacon for sensitive and specific genotyping of single-nucleotide polymorphism. Talanta 2014; 125:306-12. [PMID: 24840448 DOI: 10.1016/j.talanta.2014.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/26/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
A novel approach for highly sensitive and selective genotyping of single-nucleotide polymorphism (SNP) has been developed based on ligation-rolling circle amplification (L-RCA) and stemless molecular beacon. In this approach, two tailored DNA probes were involved. The stemless molecular beacon, formed through the inclusion interactions of γ-cyclodextrin (γ-CD) and bis-pyrene labeled DNA fragment, was served as signal probe. In the absence of mutant target, the two pyrene molecules were bound in the γ-CD cavity to form an excimer and showed a strong fluorescence at 475 nm. It was here named γ-CD-P-MB. The padlock DNA probe was designed as recognition probe. Upon the recognition of a point mutation DNA targets, the padlock probe was ligated to generate a circular template. An RCA amplification was then initiated using the circular template in the presence of Phi29 polymerase and dNTPs. The L-RCA products, containing repetitive sequence units, subsequently hybridized with the γ-CD-P-MB. This made pyrene molecules away from γ-CD cavity and caused a decrease of excimer fluorescence. As a proof-of-concept, SNP typing of β-thalassemia gene at position -28 was investigated using this approach. The detection limit of mutated target was determined to be 40 fM. In addition, DNA ligase offered high fidelity in distinguishing the mismatched bases at the ligation site, resulting in positive detection of mutant target even when the ratio of the wildtype to the mutant is 999:1. Given these attractive characteristics, the developed approach might provide a great genotyping platform for pathogenic diagnosis and genetic analysis.
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Affiliation(s)
- Zhen Zou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Zhihe Qing
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China.
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China.
| | - Dinggeng He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Xue Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Taiping Qing
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
| | - Xiaoxiao Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Changsha 410082, PR China; College of Biology, Hunan University, Changsha 410082, PR China; Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, PR China
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Graphene materials-based energy acceptor systems and sensors. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2014. [DOI: 10.1016/j.jphotochemrev.2013.10.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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10
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Li F, Yu Y, Li Q, Zhou M, Cui H. A Homogeneous Signal-On Strategy for the Detection of rpoB Genes of Mycobacterium tuberculosis Based on Electrochemiluminescent Graphene Oxide and Ferrocene Quenching. Anal Chem 2014; 86:1608-13. [DOI: 10.1021/ac403281g] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Fang Li
- CAS
Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, P. R. China
| | - Yuqi Yu
- CAS
Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, P. R. China
| | - Qi Li
- CAS
Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, P. R. China
| | - Ming Zhou
- Division
of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, 398 Ruoshui Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, P. R. China
| | - Hua Cui
- CAS
Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, P. R. China
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Kumar A, Khandelwal M. Amino acid mediated functionalization and reduction of graphene oxide – synthesis and the formation mechanism of nitrogen-doped graphene. NEW J CHEM 2014. [DOI: 10.1039/c4nj00308j] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Amino acid mediated reduction of GO through the nucleophilic attack yields N doped graphene in both acidic and basic media.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Roorkee
- , India
| | - Mahima Khandelwal
- Department of Chemistry
- Indian Institute of Technology Roorkee
- , India
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12
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Jung YK, Lee T, Shin E, Kim BS. Highly tunable aptasensing microarrays with graphene oxide multilayers. Sci Rep 2013; 3:3367. [PMID: 24284474 PMCID: PMC3842537 DOI: 10.1038/srep03367] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 11/13/2013] [Indexed: 11/09/2022] Open
Abstract
A highly tunable layer-by-layer (LbL)-assembled graphene oxide (GO) array has been devised for high-throughput multiplex protein sensing. In this array, the fluorescence of different target-bound aptamers labeled with dye is efficiently quenched by GO through fluorescence resonance energy transfer (FRET), and simultaneous multiplex target detection is performed by recovering the quenched fluorescence caused by specific binding between an aptamer and a protein. Thin GO films consisting of 10 bilayers displayed a high quenching ability, yielding over 85% fluorescence quenching with the addition of a 2 μM dye-labeled aptamer. The limit for human thrombin detection in the 6- and 10-bilayered GO array is estimated to be 0.1 and 0.001 nM, respectively, indicating highly tunable nature of LbL assembled GO multilayers in controlling the sensitivity of graphene-based FRET aptasensor. Furthermore, the GO chip could be reused up to four times simply by cleaning it with distilled water.
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Affiliation(s)
- Yun Kyung Jung
- Interdisciplinary School of Green Energy, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Eonyang-eup, Ulju-gun, Ulsan 689-798, Republic of Korea
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Xu H, Yang Q, Li F, Tang L, Gao S, Jiang B, Zhao X, Wang L, Fan C. A graphene-based platform for fluorescent detection of SNPs. Analyst 2013; 138:2678-82. [PMID: 23507980 DOI: 10.1039/c3an36740a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel fluorescent single nucleotide polymorphism (SNP) assay was developed by using Graphene Oxide (GO), which provides a fast, sensitive and simple method for SNP detection. The strategy was based on the single base extension reaction and different absorption capacity of fluorescein labeled dGTP (dGTP-Fl) and double-stranded DNA (dsDNA) to GO. dGTP-Fl is incorporated into the probe by extension reaction for the mutant target but not for the wild target, which leads to recovered fluorescence for the mutant target because of weak interaction between dsDNA and GO and weak fluorescence for the wild target because of the quenched fluorescence of dGTP-Fl by GO. The method shows a linear range for the mutant-type target from 3 nM to 50 nM and 3 nM is the detection limit. It was noted that as low as 10% mutant-type target could be detected in the presence of the wild-type target, in which the concentration is 9 times higher than that of the mutant-type target.
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Affiliation(s)
- Hui Xu
- School of Chemistry and Material Sciences, Ludong University, Yantai 264025, China.
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14
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Wang X, Zou M, Huang H, Ren Y, Li L, Yang X, Li N. Gold nanoparticle enhanced fluorescence anisotropy for the assay of single nucleotide polymorphisms (SNPs) based on toehold-mediated strand-displacement reaction. Biosens Bioelectron 2013; 41:569-75. [DOI: 10.1016/j.bios.2012.09.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 09/15/2012] [Indexed: 10/27/2022]
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15
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Asari M, Oka K, Omura T, Maseda C, Tasaki Y, Shiono H, Matsubara K, Matsuda M, Shimizu K. Universal fluorescent labeling of amplification products using locked nucleic acids. Electrophoresis 2013; 34:448-55. [PMID: 23161600 DOI: 10.1002/elps.201200215] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 09/16/2012] [Accepted: 09/25/2012] [Indexed: 12/15/2022]
Abstract
Amplification/hybridization-based genetic analyses using primers containing locked nucleic acids (LNAs) present many benefits. Here, we developed a novel design for universal fluorescent PCR using LNAs. Universal fluorescent PCR generates intermediate nonlabeled fragments and final fluorescent fragments in a two-step amplification process that uses locus-specific primers with universal tails and universal fluorescent primers. In this study, a few standard nucleotides were replaced with LNAs only in the fluorescent universal primers. The sequence of the fluorescent universal primer significantly affected the amplification efficiency. For primers with three LNAs, the fluorescent primers with stable M13(-47) sequences provided the most efficient signal (approximately tenfold higher than the primers with M13(-21) sequences at lower Tm values). Moreover, AT-rich LNA substitutions in the fluorescent primers produced much lower amplification efficiencies than GC-rich substitutions. GC-rich LNAs produced greater differences in Tm values among primers, and resulted in the preferential production of fluorescently labeled amplicons. The specificity and sensitivity of LNA-containing fluorescent primers were assessed by genotyping eight STRs in Japanese individuals, and full STR profiles could be generated using as little as 0.25 ng of genomic DNA. The method permitted clear discrimination of alleles and represents sensitive STR genotyping at a reduced cost.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa, Japan
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Yao J, Sun Y, Yang M, Duan Y. Chemistry, physics and biology of graphene-based nanomaterials: new horizons for sensing, imaging and medicine. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm31632c] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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18
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Abstract
Progress and development in biosensor development will inevitably focus upon the technology of the nanomaterials that offer promise to solve the biocompatibility and biofouling problems. The biosensors using smart nanomaterials have applications for rapid, specific, sensitive, inexpensive, in-field, on-line and/or real-time detection of pesticides, antibiotics, pathogens, toxins, proteins, microbes, plants, animals, foods, soil, air, and water. Thus, biosensors are excellent analytical tools for pollution monitoring, by which implementation of legislative provisions to safeguard our biosphere could be made effectively plausible. The current trends and challenges with nanomaterials for various applications will have focus biosensor development and miniaturization. All these growing areas will have a remarkable influence on the development of new ultrasensitive biosensing devices to resolve the severe pollution problems in the future that not only challenges the human health but also affects adversely other various comforts to living entities. This review paper summarizes recent progress in the development of biosensors by integrating functional biomolecules with different types of nanomaterials, including metallic nanoparticles, semiconductor nanoparticles, magnetic nanoparticles, inorganic/organic hybrid, dendrimers, and carbon nanotubes/graphene.
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Affiliation(s)
- Ravindra P. Singh
- Nanotechnology Application Centre, University of Allahabad, Allahabad 211 002, India
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