101
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Xie S, Chai Y, Yuan Y, Bai L, Yuan R. A novel electrochemical aptasensor for highly sensitive detection of thrombin based on the autonomous assembly of hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme nanowires. Anal Chim Acta 2014; 832:51-7. [PMID: 24890694 DOI: 10.1016/j.aca.2014.04.065] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 04/28/2014] [Accepted: 04/30/2014] [Indexed: 11/26/2022]
Abstract
In this work, a new signal amplified strategy was constructed based on isothermal exponential amplification reaction (EXPAR) and hybridization chain reaction (HCR) generating the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme (HRP-mimicking DNAzyme) nanowires as signal output component for the sensitive detection of thrombin (TB). We employed EXPAR's ultra-high amplification efficiency to produce a large amount of two hairpin helper DNAs within a minutes. And then the resultant two hairpin helper DNAs could autonomously assemble the hemin/G-quadruplex HRP-mimicking DNAzymes nanowires as the redox-active reporter units on the electrode surface via hybridization chain reaction (HCR). The hemin/G-quadruplex structures simultaneously served as electron transfer medium and electrocatalyst to amplify the signal in the presence of H2O2. Specifically, only when the EXPAR reaction process has occurred, the HCR could be achieved and the hemin/G-quadruplex complexes could be formed on the surface of an electrode to give a detectable signal. The proposed strategy combines the amplification power of the EXPAR, HCR, and the inherent high sensitivity of the electrochemical detection. With such design, the proposed assay showed a good linear relationship within the range of 0.1 pM-50 nM with a detection limit of 33 fM (defined as S/N=3) for TB.
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Affiliation(s)
- Shunbi Xie
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Yali Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Lijuan Bai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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102
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Wong JKF, Yip SP, Lee TMH. Ultrasensitive and closed-tube colorimetric loop-mediated isothermal amplification assay using carboxyl-modified gold nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:1495-9. [PMID: 24623485 DOI: 10.1002/smll.201302348] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/06/2013] [Indexed: 05/07/2023]
Affiliation(s)
- Jacky K F Wong
- Interdisciplinary Division of Biomedical Engineering, The Hong Kong Polytechnic University Hung Hom, Kowloon, Hong Kong, China
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103
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He JL, Zhu SL, Wu P, Li PP, Li T, Cao Z. Enzymatic cascade based fluorescent DNAzyme machines for the ultrasensitive detection of Cu(II) ions. Biosens Bioelectron 2014; 60:112-7. [PMID: 24787125 DOI: 10.1016/j.bios.2014.03.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 03/20/2014] [Accepted: 03/31/2014] [Indexed: 10/25/2022]
Abstract
A novel enzymatic cascade based fluorescent DNAzyme machine has been developed for the amplified detection of copper (Cu(2+)) ions. This is the first attempt to carry out the combination of the self-cleaving DNAzyme and the polymerase/endonuclease reaction cycles involving cleaved substrate extension. In the presence of Cu(2+) ions, the enzyme strand carries out catalytic reactions to hydrolytic cleavage of the substrate strand. The cleaved DNAzyme substrates act as primers and trigger the Klenow Fragment polymerization. Nb.BbvCI endonuclease cuts the double-stranded niking site and thus opens a new site for a new replication. The replication regenerates the complete dsDNA to initiate another cycle of nicking, polymerization and displacement. Finally the fluorescence dye, SG, inserts into the DNA double helix to generate a distinguishable fluorescence enhancement. The Cu(2+) ions act as the activator for enzymatic cascade amplification generating multiple duplex structures in the nascent product. An increasing fluorescence is observed with increasing Cu(2+) ions concentration. A good nonlinear correlation (R=0.9997) was obtained between fluorescence intensity and the cubic logarithm of the Cu(2+) ions concentration over the range 0.50-200 nM. This nonlinear response phenomenon results in an efficient improvement of the sensitivity of our current proposed assay. The activation of such enzymatic cascades through analyte-DNAzyme interactions is not only valuable to activate the cooperation of enzyme networks, but also has a substantial impact on the development of amplified DNAzyme sensors.
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Affiliation(s)
- Jing-Lin He
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China.
| | - Shuang-Li Zhu
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Ping Wu
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Pan-Pan Li
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Ting Li
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Zhong Cao
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China.
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104
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Wu S, Liang P, Yu H, Xu X, Liu Y, Lou X, Xiao Y. Amplified single base-pair mismatch detection via aggregation of exonuclease-sheared gold nanoparticles. Anal Chem 2014; 86:3461-7. [PMID: 24611947 PMCID: PMC3982981 DOI: 10.1021/ac4040373] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Single
nucleotide polymorphism (SNP) detection is important for
early diagnosis, clinical prognostics, and disease prevention, and
a rapid and sensitive low-cost SNP detection assay would be valuable
for resource-limited clinical settings. We present a simple platform
that enables sensitive, naked-eye detection of SNPs with minimal reagent
and equipment requirements at room temperature within 15 min. SNP
detection is performed in a single tube with one set of DNA probe-modified
gold nanoparticles (AuNPs), a single exonuclease (Exo III), and the
target in question. Exo III’s apurinic endonucleolytic activity
differentially processes hybrid duplexes between the AuNP-bound probe
and DNA targets that are perfectly matched or contain a single-base
mismatch. For perfectly matched targets, Exo III’s exonuclease
activity facilitates a process of target recycling that rapidly shears
DNA probes from the particles, generating an AuNP aggregation-induced
color change, whereas no such change occurs for mismatched targets.
This color change is easily observed with as little as 2 nM of target,
100-fold lower than the target concentration required for reliable
naked eye observation with unmodified AuNPs in well-optimized reaction
conditions. We further demonstrate that this system can effectively
discriminate a range of different mismatches.
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Affiliation(s)
- Shuo Wu
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW eighth Street, Miami, FL, 33199
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105
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CHEN WW, GUO YM, ZHENG WS, XIANYU YL, WANG Z, JIANG XY. Recent Progress of Colorimetric Assays Based on Gold Nanoparticles for Biomolecules. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/s1872-2040(13)60714-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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106
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Gao ZF, Ling Y, Lu L, Chen NY, Luo HQ, Li NB. Detection of single-nucleotide polymorphisms using an ON-OFF switching of regenerated biosensor based on a locked nucleic acid-integrated and toehold-mediated strand displacement reaction. Anal Chem 2014; 86:2543-8. [PMID: 24527790 DOI: 10.1021/ac500362z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although various strategies have been reported for single-nucleotide polymorphisms (SNPs) detection, development of a time-saving, specific, and regenerated electrochemical sensing platform still remains a realistic goal. In this study, an ON-OFF switching of a regenerated biosensor based on a locked nucleic acid (LNA)-integrated and toehold-mediated strand displacement reaction technique is constructed for detection of SNPs. The LNA-integrated and methylene blue-labeled capture probe with an external toehold is designed to switch on the sensing system. The mutant-type DNA probe completes complementary with the capture probe to trigger the strand displacement reaction, which switches off the sensing system. However, when the single-base mismatched wild-type DNA probe is presented, the strand displacement reaction cannot be achieved; therefore, the sensing system still keeps the ON state. This DNA sensor is stable over five reuses. We further testify that the LNA-integrated sequence has better recognition ability for SNPs detection compared to the DNA-integrated sequence. Moreover, this DNA senor exhibits a remarkable discrimination capability of SNPs among abundant wild-type targets and 6000-fold (m/m) excess of genomic DNA. In addition, it is selective enough in complex and contaminant-ridden samples, such as human urine, soil, saliva, and beer. Overall, these results demonstrate that this reliable DNA sensor is easy to be fabricated, simple to operate, and stable enough to be readily regenerated.
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Affiliation(s)
- Zhong Feng Gao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University , 2, Tiansheng Road, BeiBei District, Chongqing 400715, P.R. China
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107
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Mehdi khoshfetrat S, Mehrgardi MA. Electrochemical Genotyping of Single-Nucleotide Polymorphisms by using Monobase-Conjugated Modified Nanoparticles. ChemElectroChem 2014. [DOI: 10.1002/celc.201300221] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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108
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Yin J, Gan P, Zhou F, Wang J. Sensitive detection of transcription factors using near-infrared fluorescent solid-phase rolling circle amplification. Anal Chem 2014; 86:2572-9. [PMID: 24475783 DOI: 10.1021/ac403758p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This study describes a method for analyzing transcription factor (TF) activity, near-infrared fluorescent solid-phase rolling circle amplification (NIRF-sRCA). This method analyzes TF activity in four steps: (i) incubate DNA with protein sample and isolate TF-bound DNA, (ii) hybridize the TF-bound DNA and rolling circle to DNA microarray, (iii) amplify the TF-bound DNA with sRCA that contains biotin-labeled dUTP, and (iv) detect sRCA products by binding of NIRF-labeled streptavidin and NIRF imaging. This method was validated by proof-of-concept detection of purified TF protein and cell nuclear extract. Detection of purified TF protein demonstrated that NIRF-sRCA could quantitatively detect NF-κB p50 protein, and as little as 6.94 ng (∼140 fmol) of this protein was detected. Detection of nuclear extract revealed that NIRF-sRCA could specifically and quantitatively detect NF-κB p50 activity in HeLa cell nuclear extracts, and the activity of this TF in as little as 0.625 μg of nuclear extracts could be detected. Detection of nuclear extract also revealed that NIRF-sRCA could detect the relative activities of multiple TFs in HeLa cell nuclear extracts and the fold induction of multiple TFs in the TNFα-induced HeLa cell nuclear extracts. Therefore, this study provides a new tool for studying TFs.
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Affiliation(s)
- Junhuan Yin
- State Key Laboratory of Bioelectronics, Southeast University , Nanjing 210096, China
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109
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Deng R, Tang L, Tian Q, Wang Y, Lin L, Li J. Toehold-initiated Rolling Circle Amplification for Visualizing Individual MicroRNAs In Situ in Single Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309388] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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110
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Deng R, Tang L, Tian Q, Wang Y, Lin L, Li J. Toehold-initiated Rolling Circle Amplification for Visualizing Individual MicroRNAs In Situ in Single Cells. Angew Chem Int Ed Engl 2014; 53:2389-93. [DOI: 10.1002/anie.201309388] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/10/2013] [Indexed: 12/28/2022]
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111
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Ge J, Zhang LL, Liu SJ, Yu RQ, Chu X. A highly sensitive target-primed rolling circle amplification (TPRCA) method for fluorescent in situ hybridization detection of microRNA in tumor cells. Anal Chem 2014; 86:1808-15. [PMID: 24417222 DOI: 10.1021/ac403741y] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ability to detect spatial and temporal microRNA (miRNA) distribution at the single-cell level is essential for understanding the biological roles of miRNAs and miRNA-associated gene regulatory networks. We report for the first time the development of a target-primed RCA (TPRCA) strategy for highly sensitive and selective in situ visualization of miRNA expression patterns at the single-cell level. This strategy uses a circular DNA as the probe for in situ hybridization (ISH) with the target miRNA molecules, and the free 3' terminus of miRNA then initiates an in situ RCA reaction to generate a long tandem repeated sequence with thousands of complementary segments. After hybridization with fluorescent detection probes, target miRNA molecules can be visualized with ultrahigh sensitivity. Because the RCA reaction can only be initiated by the free 3' end of target miRNA, the developed strategy offers the advantage over existing ISH methods in eliminating the interference from precursor miRNA or mRNA. This strategy is demonstrated to show high sensitivity and selectivity for the detection of miR-222 expression levels in human hepatoma SMMC-7721 cells and hepatocyte L02 cells. Moreover, the developed TPRCA-based ISH strategy is successfully applied to multiplexed detection using two-color fluorescent probes for two miRNAs that are differentially expressed in the two cell lines. The results reveal that the developed strategy may have great potential for in situ miRNA expression analysis for basic research and clinical diagnostics.
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Affiliation(s)
- Jia Ge
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University , Changsha 410082, P. R. China
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112
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Ali MM, Li F, Zhang Z, Zhang K, Kang DK, Ankrum JA, Le XC, Zhao W. Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. Chem Soc Rev 2014; 43:3324-41. [DOI: 10.1039/c3cs60439j] [Citation(s) in RCA: 650] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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113
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Xie S, Chai Y, Yuan Y, Bai L, Yuan R. Development of an electrochemical method for Ochratoxin A detection based on aptamer and loop-mediated isothermal amplification. Biosens Bioelectron 2013; 55:324-9. [PMID: 24412766 DOI: 10.1016/j.bios.2013.11.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/02/2013] [Accepted: 11/04/2013] [Indexed: 10/25/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an outstanding DNA amplification procedure, in which the reaction can accumulate 10(9) copies from less than 10 copies of input template within an hour. While the amplification reaction is extremely powerful, the quantitative detection of LAMP products is still analytically difficult. Besides, the type of targets that LAMP can detect is also less, which to some extent limited the application of LAMP. In this study, we are reporting for the first time an efficient and accurate detection system which employs the integration of LAMP, aptamer and the electrochemical method for the sensitive detection of Ochratoxin A (OTA). Aptamers were designed as the forward outer primer to trigger the LAMP reaction, and then the LAMP amplification products were combined with a redox active molecule methylene blue (MB) and analyzed by an electrode using differential pulse voltammograms (DPV). As the reaction progresses, the MB intercalated into double-stranded regions of LAMP amplicons reduces the free MB concentration. Hence, the peak current of reaction mixture decreased with the amplification because of the slow diffusion of MB-amplified DNA complex to the electrode surface. The peak height of the current was related to the input amount of the aptamers, providing a ready means to detection the concentration of OTA. With such design, the proposed assay showed a good linear relationship within the range of 0.001-50 nM with a detection limit of 0.3 pM (defined as S/N = 3) for OTA.
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Affiliation(s)
- Shunbi Xie
- Key Laboratory of Ministry of Education on Luminescence and Real-Time Analysis, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Ministry of Education on Luminescence and Real-Time Analysis, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Yali Yuan
- Key Laboratory of Ministry of Education on Luminescence and Real-Time Analysis, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Lijuan Bai
- Key Laboratory of Ministry of Education on Luminescence and Real-Time Analysis, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Ministry of Education on Luminescence and Real-Time Analysis, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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114
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Wang X, Lau C, Kai M, Lu J. Hybridization chain reaction-based instantaneous derivatization technology for chemiluminescence detection of specific DNA sequences. Analyst 2013; 138:2691-7. [PMID: 23515350 DOI: 10.1039/c3an36885h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We propose here a new amplifying strategy that uses hybridization chain reaction (HCR) to detect specific sequences of DNA, where stable DNA monomers assemble on the magnetic beads only upon exposure to a target DNA. Briefly, in the HCR process, two complementary stable species of hairpins coexist in solution until the introduction of initiator reporter strands triggers a cascade of hybridization events that yield nicked double helices analogous to alternating copolymers. Moreover, a "sandwich-type" detection strategy is employed in our design. Magnetic beads, which are functionalized with capture DNA, are reacted with the target, and sandwiched with the above nicked double helices. Then, chemiluminescence (CL) detection proceeds via an instantaneous derivatization reaction between a specific CL reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG), and the guanine nucleotides within the target DNA, reporter strands and DNA monomers for the generation of light. Our results clearly show that the amplification detection of specific sequences of DNA achieves a better performance (e.g. wide linear response range, low detection limit, and high specificity) as compared to the traditional sandwich type (capture/target/reporter) assays. Upon modification, the approach presented could be extended to detect other types of targets. We believe that this simple technique is promising for improving medical diagnosis and treatment.
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Affiliation(s)
- Xin Wang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
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115
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Enzymatic cleavage of type II restriction endonucleases on the 2'-O-methyl nucleotide and phosphorothioate substituted DNA. PLoS One 2013; 8:e79415. [PMID: 24260216 PMCID: PMC3829850 DOI: 10.1371/journal.pone.0079415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/21/2013] [Indexed: 11/19/2022] Open
Abstract
The effects of nucleotide analogue substitution on the cleavage efficiencies of type II restriction endonucleases have been investigated. Six restriction endonucleases (EcoRV, SpeI, XbaI, XhoI, PstI and SphI) were investigated respectively regarding their cleavage when substrates were substituted by 2′-O-methyl nucleotide (2′-OMeN) and phosphorothioate (PS). Substitutions were made in the recognition sequence and the two nucleotides flanking the recognition sequence for each endonuclease. The endonuclease cleavage efficiencies were determined using FRET-based assay. Results demonstrated a position-dependent inhibitory effect of substitution on the cleavage efficiency for all the six endonucleases. In general, the 2′-OMeN substitutions had greater impact than the PS substitutions on the enzymatic activities. Nucleotides of optimal substitutions for protection against RE cleavage were identified. Experimental results and conclusions in this study facilitate our insight into the DNA-protein interactions and the enzymatic cleavage mechanism, particularly for those whose detailed structure information is not available. In addition, the information could benefit the development of bioengineering and synthetic biology.
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116
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Wu W, Chen J, Fang Z, Ge C, Xiang Z, Ouyang C, Lie P, Xiao Z, Yu L, Wang L, Zeng L. A self-assembled deoxyribonucleic acid concatemer for sensitive detection of single nucleotide polymorphism. Anal Chim Acta 2013; 804:235-9. [PMID: 24267087 DOI: 10.1016/j.aca.2013.09.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/04/2013] [Accepted: 09/29/2013] [Indexed: 10/26/2022]
Abstract
Polymerase-free and label-free strategies for DNA detection have shown excellent sensitivity and specificity in various biological samples. Herein, we propose a method for single nucleotide polymorphism (SNP) detection by using self-assembled DNA concatemers. Capture probes, bound to magnetic beads, can joint mediator probes by T4 DNA ligase in the presence of target DNA that is complementary to the capture probe and mediator probe. The mediator probes trigger self-assembly of two auxiliary probes on magnetic beads to form DNA concatemers. Separated by a magnetic rack, the double-stranded concatemers on beads can recruit a great amount of SYBR Green I and eventually result in amplified fluorescent signals. In comparison with reported methods for SNP detection, the concatemer-based approach has significant advantages of low background, simplicity, and ultrasensitivity, making it as a convenient platform for clinical applications. As a proof of concept, BRAF(T1799A) oncogene mutation, a SNP involved in diverse human cancers, was used as a model target. The developed approach using a fluorescent intercalator can detect as low as 0.1 fM target BRAF(T1799A) DNA, which is better than those previously published methods for SNP detection. This method is robust and can be used directly to measure the BRAF(T1799A) DNA in complex human serum with excellent recovery (94-103%). It is expected that this assay principle can be directed toward other SNP genes by simply changing the mediator probe and auxiliary probes.
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Affiliation(s)
- Wei Wu
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
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117
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Ligase chain reaction amplification for sensitive electrochemiluminescent detection of single nucleotide polymorphisms. Anal Chim Acta 2013; 796:1-6. [DOI: 10.1016/j.aca.2013.07.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 07/22/2013] [Accepted: 07/25/2013] [Indexed: 11/18/2022]
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118
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Lin C, Zhang Y, Zhou X, Yao B, Fang Q. Naked-eye detection of nucleic acids through rolling circle amplification and magnetic particle mediated aggregation. Biosens Bioelectron 2013; 47:515-9. [DOI: 10.1016/j.bios.2013.03.056] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/28/2013] [Accepted: 03/17/2013] [Indexed: 12/30/2022]
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119
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An improved non-crosslinking gold nanoprobe-NASBA based on 16S rRNA for rapid discriminative bio-sensing of major salmonellosis pathogens. Biosens Bioelectron 2013; 47:231-6. [DOI: 10.1016/j.bios.2013.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/19/2013] [Accepted: 03/07/2013] [Indexed: 11/23/2022]
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120
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Chen Y, Wang Q, Xu J, Xiang Y, Yuan R, Chai Y. A new hybrid signal amplification strategy for ultrasensitive electrochemical detection of DNA based on enzyme-assisted target recycling and DNA supersandwich assemblies. Chem Commun (Camb) 2013; 49:2052-4. [PMID: 23386242 DOI: 10.1039/c3cc00034f] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly sensitive electrochemical sequence-specific DNA detection strategy is demonstrated by coupling N.BstNB I (a nicking endonuclease)-assisted target recycling amplification with DNA supersandwich assembly signal enhancement. The proposed method avoids any extra chemical labeling steps and offers high selectivity against single-base mismatch sequences and a low detection limit down to 0.36 fM.
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Affiliation(s)
- Ying Chen
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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121
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Guo L, Xu Y, Ferhan AR, Chen G, Kim DH. Oriented Gold Nanoparticle Aggregation for Colorimetric Sensors with Surprisingly High Analytical Figures of Merit. J Am Chem Soc 2013; 135:12338-45. [DOI: 10.1021/ja405371g] [Citation(s) in RCA: 272] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Longhua Guo
- Ministry of Education Key Laboratory
of Analysis and Detection Technology for Food Safety, Department of
Chemistry, Fuzhou University, Fuzhou, 350108,
China
| | - Yang Xu
- Ministry of Education Key Laboratory
of Analysis and Detection Technology for Food Safety, Department of
Chemistry, Fuzhou University, Fuzhou, 350108,
China
| | - Abdul Rahim Ferhan
- School of Chemical
and Biomedical
Engineering, Nanyang Technological University, 637457, Singapore
| | - Guonan Chen
- Ministry of Education Key Laboratory
of Analysis and Detection Technology for Food Safety, Department of
Chemistry, Fuzhou University, Fuzhou, 350108,
China
| | - Dong-Hwan Kim
- School of Chemical
and Biomedical
Engineering, Nanyang Technological University, 637457, Singapore
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122
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Wang D, Hu L, Zhou H, Abdel-Halim E, Zhu JJ. Molecular beacon structure mediated rolling circle amplification for ultrasensitive electrochemical detection of microRNA based on quantum dots tagging. Electrochem commun 2013. [DOI: 10.1016/j.elecom.2013.04.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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123
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Bead-based padlock rolling circle amplification for single DNA molecule counting. Anal Biochem 2013; 437:43-5. [DOI: 10.1016/j.ab.2013.02.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 02/20/2013] [Indexed: 11/21/2022]
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124
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Xing Y, Wang P, Zang Y, Ge Y, Jin Q, Zhao J, Xu X, Zhao G, Mao H. A colorimetric method for H1N1 DNA detection using rolling circle amplification. Analyst 2013; 138:3457-62. [PMID: 23653903 DOI: 10.1039/c3an00100h] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A highly sensitive and specific colorimetry-based rolling circle amplification (RCA) assay has been successfully developed as a method for the effective detection of H1N1 DNA. Specific oligonucleotide and reporter primer probes were designed together with a circular template, and the oligonucleotide probes were attached to the surfaces of magnetic beads (MBs) to form functional MB-DNA conjugates as capture probes for the target H1N1 DNA molecules. Together with the addition of DNA targets and reporter primer probes to the MB-DNA conjugates, sandwiched hybrids were formed. The initiation of RCA amplification using the circular template in the presence of phi29 polymerase allowed for the amplification of a large number of repeat sequences of the single-stranded (ss)-DNA product. This RCA product accumulated gold nanoparticles (AuNPs), resulting in a colorimetric change that could be viewed by the naked eye or detected using UV-vis spectroscopy. According to this method, H1N1 DNA could be detected at the 1 pmol L(-1) level. This platform exhibited design convenience, simplicity, and cost-effectiveness, and could be used to provide a new diagnostic assay for H1N1, and other infectious diseases.
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Affiliation(s)
- Yasi Xing
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Science, Shanghai, 200050, China
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125
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Wang J, Qu X. Recent progress in nanosensors for sensitive detection of biomolecules. NANOSCALE 2013; 5:3589-3600. [PMID: 23529571 DOI: 10.1039/c3nr00084b] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Developing sensitive, rapid, and cost-effective methods for detection of biomolecules is important for both clinical and numerous non-clinical applications. During the last two decades, functional nanomaterials with unique physical and chemical properties have provided significant advantages for biological detection. In this feature article, we introduce recent progress in nanobiosensor development by exploiting the optical, electrical and catalytic properties of a range of nanomaterials, with a focus on gold nanoparticles, carbon nanotubes, graphene and carbon dots. In addition, the perspectives on future opportunities and unsolved challenges are also discussed.
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Affiliation(s)
- Jiasi Wang
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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126
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Design of label-free, homogeneous biosensing platform based on plasmonic coupling and surface-enhanced Raman scattering using unmodified gold nanoparticles. Biosens Bioelectron 2013; 43:308-14. [DOI: 10.1016/j.bios.2012.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 11/22/2012] [Accepted: 12/04/2012] [Indexed: 11/24/2022]
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127
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Zhou C, Mu Y, Yang MC, Wu QQ, Xu W, Zhang Y, Jin W, Song Q, Wu ZY, Jin QH. Gold nanoparticles based colorimetric detection of target DNA after loop-mediated isothermal amplification. Chem Res Chin Univ 2013. [DOI: 10.1007/s40242-013-2371-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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128
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Zhou L, Du F, Zhao Y, Yameen A, Chen H, Tang Z. DNAzyme based gap-LCR detection of single-nucleotide polymorphism. Biosens Bioelectron 2013; 45:141-7. [PMID: 23455054 DOI: 10.1016/j.bios.2013.01.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/24/2013] [Accepted: 01/30/2013] [Indexed: 11/18/2022]
Abstract
Fast and accurate detection of single-nucleotide polymorphism (SNP) is thought more and more important for understanding of human physiology and elucidating the molecular based diseases. A great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. However most of those methods developed to date incorporate complicated probe labeling and depend on advanced equipment. The DNAzyme based Gap-LCR detection method averts any chemical modification on probes and circumvents those problems by incorporating a short functional DNA sequence into one of LCR primers. Two kinds of exonuclease are utilized in our strategy to digest all the unreacted probes and release the DNAzymes embedded in the LCR product. The DNAzyme applied in our method is a versatile tool to report the result of SNP detection in colorimetric or fluorometric ways for different detection purposes.
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Affiliation(s)
- Li Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, PR China
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129
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Wang HB, Wang L, Huang KJ, Xu SP, Wang HQ, Wang LL, Liu YM. A highly sensitive and selective biosensing strategy for the detection of Pb2+ ions based on GR-5 DNAzyme functionalized AuNPs. NEW J CHEM 2013. [DOI: 10.1039/c3nj00328k] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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130
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Valentini P, Pompa PP. Gold nanoparticles for naked-eye DNA detection: smart designs for sensitive assays. RSC Adv 2013. [DOI: 10.1039/c3ra43729a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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131
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Wang P, Song Y, Zhao Y, Fan A. Hydroxylamine amplified gold nanoparticle-based aptameric system for the highly selective and sensitive detection of platelet-derived growth factor. Talanta 2012. [PMID: 23200404 DOI: 10.1016/j.talanta.2012.10.087] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This study developed a sensitive and selective aptamer-based chemiluminescent (CL) method for the determination of platelet-derived growth factor (PDGF)-BB using hydroxylamine enlarged gold nanoparticles (Au NPs). Rabbit anti-human PDGF-BB polyclonal antibody was covalently coupled on the 96-well plate that offers reactive N-oxysuccinimide ester (referred to as NOS group) surface. In the presence of target protein, the biotinylated aptamer was captured on the 96-well plate forming an antibody/PDGF-BB/biotinylated aptamer sandwiched complex, which was followed by the assembly of streptavidin coated Au NPs (streptavidin-gold). Au NPs assembled on the surface of 96-well plate reacted with HAuCl(4) and NH(2)OH, which enabled the catalytic deposition of gold metal onto the Au NPs surfaces. A huge number of Au(3+) ions were released from the hydroxylamine enlarged Au NPs after oxidative gold metal dissolution, which was determined by a simple and sensitive luminol CL reaction. The results showed that the detection limit of the assay is 60 pM of PDGF-BB (corresponding to 6 fmol in a 100 μL volume), which compares favorably with those of other PDGF-BB detection techniques. In addition, this aptameric CL biosensor demonstrated extraordinary specificity. And PDGF-BB has been determined in diluted serum indicating the applicability of this assay.
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Affiliation(s)
- Ping Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China
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132
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Zhu J, Chen L, Mao Y, Zhou H, Li R, Wang W. Multiplex allele-specific amplification from whole blood for detecting multiple polymorphisms simultaneously. Genet Test Mol Biomarkers 2012; 17:10-5. [PMID: 23072573 DOI: 10.1089/gtmb.2012.0261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Allele-specific amplification on the basis of polymerase chain reaction (PCR) has been widely used for single-nucleotide polymorphism (SNP) genotyping. However, the extraction of PCR-compatible genomic DNA from whole blood is usually required. This process is complicated and tedious, and is prone to cause cross-contamination between samples. To facilitate direct PCR amplification from whole blood without the extraction of genomic DNA, we optimized the pH value of PCR solution and the concentrations of magnesium ions and facilitator glycerol. Then, we developed multiplex allele-specific amplifications from whole blood and applied them to a case-control study. In this study, we successfully established triplex, five-plex, and eight-plex allele-specific amplifications from whole blood for determining the distribution of genotypes and alleles of 14 polymorphisms in 97 gastric cancer patients and 141 healthy controls. Statistical analysis results showed significant association of SNPs rs9344, rs1799931, and rs1800629 with the risk of gastric cancer. This method is accurate, time-saving, cost-effective, and easy-to-do, especially suitable for clinical prediction of disease susceptibility.
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Affiliation(s)
- Jianjie Zhu
- Department of Pharmaceutical Analysis, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
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133
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Chen X, Hong CY, Lin YH, Chen JH, Chen GN, Yang HH. Enzyme-Free and Label-Free Ultrasensitive Electrochemical Detection of Human Immunodeficiency Virus DNA in Biological Samples Based on Long-Range Self-Assembled DNA Nanostructures. Anal Chem 2012; 84:8277-83. [DOI: 10.1021/ac3017828] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Xian Chen
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Cheng-Yi Hong
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Ya-Hui Lin
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Jing-Hua Chen
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350004, China
| | - Guo-Nan Chen
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
| | - Huang-Hao Yang
- The Key Lab of Analysis and Detection
Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory
of Analysis and Detection Technology for Food Safety, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350108, China
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134
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Xie X, Xu W, Liu X. Improving colorimetric assays through protein enzyme-assisted gold nanoparticle amplification. Acc Chem Res 2012; 45:1511-20. [PMID: 22786666 DOI: 10.1021/ar300044j] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The discovery of the DNA-mediated assembly of gold nanoparticles was a great moment in the history of science; this understanding and chemical control enabled the rational design of functional nanomaterials as novel probes in biodetection. In contrast with conventional probes such as organic dyes, gold nanoparticles exhibit high photostability and unique size-dependent optical properties. Because of their high extinction coefficients and strong distance dependent optical properties, these nanoparticles have emerged over the past decade as a promising platform for rapid, highly sensitive colorimetric assays that allow for the visual detection of low concentrations of metal ions, small molecules, and biomacromolecules. These discoveries have deepened our knowledge of biological phenomena and facilitated the development of many new diagnostic and therapeutic tools. Despite these many advances and continued research efforts, current nanoparticle-based colorimetric detection systems still suffer from several drawbacks, such as limited sensitivity and selectivity. This Account describes the recent development of colorimetric assays based on protein enzyme-assisted gold nanoparticle amplification. The benefits of such detection systems include significantly improved detection sensitivity and selectivity. First, we discuss the general design of enzyme-modified nanoparticle systems in colorimetric assays. We show that a quantitative understanding of the unique properties of different enzymes is paramount for effective biological assays. We then examine the assays for nucleic acid detection based on different types of enzymes, including endonucleases, ligases, and polymerases. For each of these assays, we identify the underlying principles that contribute to the enhanced detection capability of nanoparticle systems and illustrate them with selected examples. Furthermore, we demonstrate that the combination of gold nanoparticles and specific enzymes can probe enzyme dynamics and function with high specificity, offering substantial advantages in both sensitivity and specificity over conventional detection methods. The screening of nuclease, methyltransferase, protease, and kinase activities can be colorimetrically performed in a straightforward manner. Finally, we discuss examples of colorimetric assays for metal ions and small molecules that constitute important advances toward visual monitoring of enzyme catalytic functions and gene expression. Although these enzyme-assisted assay methods hold great promise for myriad applications in biomedicine and bioimaging, the application of the described techniques in vivo faces formidable challenges. In addition, researchers do not fully understand the interactions of gold nanoparticles with enzyme molecules. This understanding will require the development of new techniques to probe enzyme substrate dynamics at the particle interface with higher spatial resolution and chemical specificity.
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Affiliation(s)
- Xiaoji Xie
- Department of Chemistry, National University of Singapore, Singapore, and Institute of Material Research and Engineering, Singapore
| | - Wei Xu
- Department of Chemistry, National University of Singapore, Singapore, and Institute of Material Research and Engineering, Singapore
| | - Xiaogang Liu
- Department of Chemistry, National University of Singapore, Singapore, and Institute of Material Research and Engineering, Singapore
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135
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Dong H, Wang C, Xiong Y, Lu H, Ju H, Zhang X. Highly sensitive and selective chemiluminescent imaging for DNA detection by ligation-mediated rolling circle amplified synthesis of DNAzyme. Biosens Bioelectron 2012; 41:348-53. [PMID: 22981413 DOI: 10.1016/j.bios.2012.08.050] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 08/10/2012] [Accepted: 08/23/2012] [Indexed: 11/26/2022]
Abstract
A highly sensitive DNA biosensing method down to sub-femtomolar level with excellent selectivity was proposed by designing an amplified synthesis of horseradish peroxidase mimicking DNAzyme and introducing the amplified DNAzyme to chemiluminescent (CL) imaging. The amplified synthesis was achieved by combining a target DNA related ligase reaction with rolling circle amplification (RCA), which produced thousands of repeated sequences to bind hemin and form a mass of horseradish peroxidase-mimicing DNAzyme units. The amplification strategy greatly enhanced the CL emission of the luminol-H(2)O(2) system. The genotyping method displayed highly specific biochemistry in allele discrimination. The novel CL imaging strategy based on ligation-mediated RCA synthesis of DNAzyme showed high fidelity in discriminating single-base mismatch and efficiently facilitated signal amplification for sensitive target DNA detection. It could detect DNA ranging from 1×10(-15) M to 1×10(-11) M with a detection limit of 0.26 fM. The proposed approach provided a robust, cost-efficient, highly sensitive and specific platform for genetic target analysis in bioanalysis and clinic biomedical application.
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Affiliation(s)
- Haifeng Dong
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210093, PR China
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136
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Electrochemical detection of individual single nucleotide polymorphisms using monobase-modified apoferritin-encapsulated nanoparticles. Biosens Bioelectron 2012; 37:11-8. [DOI: 10.1016/j.bios.2012.04.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/18/2012] [Accepted: 04/10/2012] [Indexed: 11/24/2022]
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137
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Ji H, Yan F, Lei J, Ju H. Ultrasensitive Electrochemical Detection of Nucleic Acids by Template Enhanced Hybridization Followed with Rolling Circle Amplification. Anal Chem 2012; 84:7166-71. [DOI: 10.1021/ac3015356] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hanxu Ji
- State Key Laboratory of Analytical
Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210093, P.R. China
| | - Feng Yan
- Jiangsu Institute of Cancer Prevention and Cure, Nanjing 210009, P.R.
China
| | - Jianping Lei
- State Key Laboratory of Analytical
Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210093, P.R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical
Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210093, P.R. China
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138
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Hun X, Liu F, Mei Z, Ma L, Wang Z, Luo X. Signal amplified strategy based on target-induced strand release coupling cleavage of nicking endonuclease for the ultrasensitive detection of ochratoxin A. Biosens Bioelectron 2012; 39:145-51. [PMID: 22938841 DOI: 10.1016/j.bios.2012.07.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/29/2012] [Accepted: 07/07/2012] [Indexed: 11/19/2022]
Abstract
In this work, a new signal amplified strategy based on target-induced strand release coupling cleavage of nicking endonuclease for the ultrasensitive detection of ochratoxin A (OTA) is reported. OTA aptamer (DNA1) and OTA aptamer complementary (DNA2) were immobilized onto a magnetic bead (MB). In the presence of OTA, DNA2 was dissociated and released from the MB. The released DNA2 then hybridized with DNA3, which was linked at the 5' terminus of the amplification template and can extend along the template in the presence of Phi 29 DNA polymerase. The formed double-stranded DNA was cleaved by nicking endonuclease Nb.BbvCI and produced a short single-stranded DNA. The cleaved DNA strand generated a new site by Phi 29 DNA polymerase and the process of extension and cleavage was cyclical. Thus, a amount of the short single-stranded DNA were produced. Using DNA and ABEI labeled carboxylic silica nanoparticles chemiluminescence (CL) probe, the short single-stranded DNA could be sensitively detected. The CL intensity (ΔI) versus the concentration of OTA was linear in the range from 1.0×10(-12) to 5.0×10(-8)g mL(-1). The detection limit was 3.0×10(-13)g mL(-1), and the RSD was 3.4% at 1.0×10(-10)g mL(-1) (n=7). The developed method has been applied to detect OTA in naturally contaminated wheat samples. Due to its simplicity, sensitivity and no need of specific recognition of aptamer for cleavage, this CL bioassay offers a promising approach for the detection of OTA and other biomolecules.
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Affiliation(s)
- Xu Hun
- Shandong Provincial Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
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139
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Xu W, Xie X, Li D, Yang Z, Li T, Liu X. Ultrasensitive colorimetric DNA detection using a combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA). SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:1846-50. [PMID: 22461378 DOI: 10.1002/smll.201200263] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Indexed: 05/18/2023]
Abstract
A combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA) is used for the rapid, colorimetric detection of DNA. The integration of rolling circle amplification into the NEANA approach allows for detection of oligonucleotides with arbitrary sequences at ultralow concentrations.
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Affiliation(s)
- Wei Xu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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140
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Chang CC, Chen CC, Wei SC, Lu HH, Liang YH, Lin CW. Diagnostic devices for isothermal nucleic acid amplification. SENSORS (BASEL, SWITZERLAND) 2012; 12:8319-37. [PMID: 22969402 PMCID: PMC3436031 DOI: 10.3390/s120608319] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 05/29/2012] [Accepted: 06/07/2012] [Indexed: 11/23/2022]
Abstract
Since the development of the polymerase chain reaction (PCR) technique, genomic information has been retrievable from lesser amounts of DNA than previously possible. PCR-based amplifications require high-precision instruments to perform temperature cycling reactions; further, they are cumbersome for routine clinical use. However, the use of isothermal approaches can eliminate many complications associated with thermocycling. The application of diagnostic devices for isothermal DNA amplification has recently been studied extensively. In this paper, we describe the basic concepts of several isothermal amplification approaches and review recent progress in diagnostic device development.
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Affiliation(s)
- Chia-Chen Chang
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10617, Taiwan.
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141
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Tang L, Liu Y, Ali MM, Kang DK, Zhao W, Li J. Colorimetric and ultrasensitive bioassay based on a dual-amplification system using aptamer and DNAzyme. Anal Chem 2012; 84:4711-7. [PMID: 22533853 DOI: 10.1021/ac203274k] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Rapid detection of ultralow amount of biomarkers in a biologically complex mixture remains a major challenge. Herein, we report a novel aptamer-based protein detection assay that integrates two signal amplification processes, namely, polymerase-mediated rolling-circle amplification (RCA) and DNA enzyme-catalyzed colorimetric reaction. The target biomarker is captured in a sandwich assay by primary aptamer-functionalized microbeads (MBs) and a secondary aptamer that is connected to a RCA primer/circular template complex. RCA reaction, which amplifies the single biomarker binding events by a factor of hundreds to thousands (the first amplification) produces a long DNA molecule containing multiple DNAzyme units. The peroxidase-like DNAzyme catalyzes the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (the second amplification), which generates a blue-green colorimetric signal. This new biosensing platform permits the ultrasensitive, label-free, colorimetric detection of biomarker in real time. Using platelet-derived growth factor B-chain (PDGF-BB) as a model system, we demonstrated that our assay can detect a protein marker specifically in a serum-containing medium, at a concentration as low as 0.2 pg/mL in ∼2 h, which rivals traditional assays such as ELISA. We anticipate this simple methodology for biomarker detection can find utility in point-of-care applications.
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Affiliation(s)
- Longhua Tang
- Department of Chemistry, Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing, China 100084
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142
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Cheng Y, Du Q, Wang L, Jia H, Li Z. Fluorescently Cationic Conjugated Polymer as an Indicator of Ligase Chain Reaction for Sensitive and Homogeneous Detection of Single Nucleotide Polymorphism. Anal Chem 2012; 84:3739-44. [DOI: 10.1021/ac300314c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yongqiang Cheng
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Qing Du
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Liyong Wang
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Hailian Jia
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Zhengping Li
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
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143
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Dong H, Zhu Z, Ju H, Yan F. Triplex signal amplification for electrochemical DNA biosensing by coupling probe-gold nanoparticles–graphene modified electrode with enzyme functionalized carbon sphere as tracer. Biosens Bioelectron 2012; 33:228-32. [DOI: 10.1016/j.bios.2012.01.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/09/2011] [Accepted: 01/06/2012] [Indexed: 12/11/2022]
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144
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Detection of single-nucleotide polymorphisms with novel leaky surface acoustic wave biosensors, DNA ligation and enzymatic signal amplification. Biosens Bioelectron 2012; 33:274-8. [DOI: 10.1016/j.bios.2011.12.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 12/27/2022]
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145
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Noble metal nanoparticles for biosensing applications. SENSORS 2012; 12:1657-87. [PMID: 22438731 PMCID: PMC3304133 DOI: 10.3390/s120201657] [Citation(s) in RCA: 318] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/29/2012] [Accepted: 02/02/2012] [Indexed: 12/24/2022]
Abstract
In the last decade the use of nanomaterials has been having a great impact in biosensing. In particular, the unique properties of noble metal nanoparticles have allowed for the development of new biosensing platforms with enhanced capabilities in the specific detection of bioanalytes. Noble metal nanoparticles show unique physicochemical properties (such as ease of functionalization via simple chemistry and high surface-to-volume ratios) that allied with their unique spectral and optical properties have prompted the development of a plethora of biosensing platforms. Additionally, they also provide an additional or enhanced layer of application for commonly used techniques, such as fluorescence, infrared and Raman spectroscopy. Herein we review the use of noble metal nanoparticles for biosensing strategies—from synthesis and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics laboratory.
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146
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Xiang Y, Lu Y. Using commercially available personal glucose meters for portable quantification of DNA. Anal Chem 2012; 84:1975-80. [PMID: 22235863 DOI: 10.1021/ac203014s] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA detection is commonly used in molecular biology, pathogen analysis, genetic disorder diagnosis, and forensic tests. While traditional methods for DNA detection such as polymerase chain reaction (PCR) and DNA microarrays have been well developed, they require sophisticated equipment and operations, and thus it is still challenging to develop a portable and quantitative DNA detection method for the public use at home or in the field. Although many other techniques and devices have been reported to make the DNA detection simple and portable, very few of them are currently accessible to the public for quantitative DNA detection because of either the requirement of laboratory-based instrument or lack of quantitative detection. Herein we report application of personal glucose meters (PGMs), which are widely available, low cost, and simple to use, for quantitative detection of DNA, including a hepatitis B virus DNA fragment. The quantification is based on target-dependent binding of cDNA-invertase conjugate with the analyte DNA, thereby transforming the concentration of DNA in the sample into glucose through invertase-catalyzed hydrolysis of sucrose. Instead of amplifying DNA strands through PCR, which is vulnerable to contaminations commonly encountered for home and field usage, we demonstrate here signal amplifications based on enzymatic turnovers, making it possible to detect 40 pM DNA using PGM that can detect glucose only at the mM level. The method also shows excellent selectivity toward single nucleotide mismatches.
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Affiliation(s)
- Yu Xiang
- Department of Chemistry and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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147
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Zhou X, Su Q, Xing D. An electrochemiluminescent assay for high sensitive detection of mercury (II) based on isothermal rolling circular amplification. Anal Chim Acta 2012; 713:45-9. [DOI: 10.1016/j.aca.2011.11.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 10/26/2011] [Accepted: 11/02/2011] [Indexed: 11/26/2022]
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148
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Wong JKF, Yip SP, Lee TMH. Silica-modified oligonucleotide-gold nanoparticle conjugate enables closed-tube colorimetric polymerase chain reaction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:214-9. [PMID: 22095584 DOI: 10.1002/smll.201101925] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Indexed: 05/11/2023]
Abstract
A facile silica coating significantly enhances the thermal stability and polymerase chain reaction (PCR) compatibility of oligonucleotide-gold nanoparticle conjugates, thus enabling colorimetric detection of PCR results in a closed-tube format. This method is specific, sensitive, and generally applicable. Its simplicity, visual readout, and carryover contamination-free features hold promise for point-of-care or on-site DNA testing.
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Affiliation(s)
- Jacky K F Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
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149
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Wang Y, Zhan R, Li T, Pu KY, Wang Y, Tan YC, Liu B. Fluorescence and visual detection of single nucleotide polymorphism using cationic conjugated polyelectrolyte. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:889-895. [PMID: 22047010 DOI: 10.1021/la203714e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We report a simple assay for visual detection of single nucleotide polymorphisms (SNPs) with good sensitivity and selectivity. The selectivity is determined by Escherichia coli (E. coli) DNA ligase mediated circular formation upon recognition of the point mutation on DNA targets. Rolling cycle amplification (RCA) of the perfect-matched DNA target is then initiated using the in situ formed circular template in the presence of Phi29 enzyme. Due to amplification of the DNA target, the RCA product has a tandem-repeated sequence, which is significantly longer than that for the SNP strand. Direct addition of a cationic conjugated polymer of poly[9,9'-bis(6'-(N,N,N-trimethylammonium)hexyl)fluorene-co-9,9'-bis(2-(2-(2-(N,N,N-trimethylammonium)ethoxyl)-ethoxy)-ethyl)fluorene tetrabromide] containing 20 mol% 2,1,3-benzothiadiazole (PFBT(20)) into the RCA solution leads to blue-whitish fluorescent color for SNP strand and yellowish fluorescent color for amplified DNA, due to PFBT(20)/DNA complexation induced intrachain/interchain energy transfer. To further improve the contrast for visual detection, FAM-labeled peptide nucleic acid (PNA) was hybridized to each amplified sequence, which is followed by the addition of poly{2,7-[9,9-bis(6'-N,N,N-trimethylammoniumhexyl)]fluorene-co-2,5-difluoro-1,4-phenylene dibromide} (PFP). The PNA/DNA hybridization brings PFP and FAM-PNA into close proximity for energy transfer, and the solution fluorescent color appears green in the presence of target DNA with a detection limit of 1 nM, which is significantly improved as compared to that for most reported visual SNP assay.
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Affiliation(s)
- Yifan Wang
- Department of Chemical and Biomolecular Engineering, 4 Engineering Drive 4, National University of Singapore, Singapore 117567, Singapore
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150
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Wang C, Jia XM, Jiang C, Zhuang GN, Yan Q, Xiao SJ. DNA microarray fabricated on poly(acrylic acid) brushes-coated porous silicon by in situ rolling circle amplification. Analyst 2012; 137:4539-45. [DOI: 10.1039/c2an35417a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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