101
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Zhu X, Zhao J, Wu Y, Shen Z, Li G. Fabrication of a highly sensitive aptasensor for potassium with a nicking endonuclease-assisted signal amplification strategy. Anal Chem 2011; 83:4085-9. [PMID: 21545113 DOI: 10.1021/ac200058r] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A novel strategy to fabricate an aptasensor for potassium with high sensitivity and selectivity by using nicking endonuclease is proposed in this work. A nicking endonuclease (Nt.CviPII), which may recognize specific nucleotide sequences in double-stranded DNA formed by a potassium-binding aptamer and a linker DNA but cleave only the linker strand, may transfer and amplify the quantitative information of the potassium detection to that of the linker DNA through elaborate strand-scission cycles. Since the technique for gene assay is much more mature, the linker DNA can thereby be detected by a number of available methods. Here, taking advantage of a simple and fast gold nanoparticles-based sensing technique, we are able to assay the linker and consequently potassium ion simply by UV-vis spectroanalysis and even with the naked eye. Results show that a 2 μL sample containing 0.1 mM of potassium is enough to induce distinct color appearance of the nanoparticles, and the potassium ion can be easily distinguished from many other ions. The strategy proposed in this work shows some unique advantages over some traditional methods and may be further developed for the detection of some other chemicals in the future.
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Affiliation(s)
- Xiaoli Zhu
- Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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102
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Nakayama S, Wang J, Sintim HO. DNA-based peroxidation catalyst--what is the exact role of topology on catalysis and is there a special binding site for catalysis? Chemistry 2011; 17:5691-8. [PMID: 21469226 DOI: 10.1002/chem.201002349] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 01/19/2011] [Indexed: 12/11/2022]
Abstract
In the last decade, there has been growing interests in studies aimed at delineating the strategies used by various nucleic acid enzymes to facilitate catalysis. Insights gained from such studies would enable the design of better DNA/RNA catalysts for various applications such as biosensing. DNA and RNA catalysts have been shown to be able to catalyze myriads of reactions, including peroxidation reactions, which are catalyzed by G-quadruplexes. In this report, we provide data that clarifies how G-quadruplex peroxidases achieve catalysis. Firstly, we show that by covalently linking a hemin cofactor to DNAzymes, anti-parallel G-quadruplexes, which have been previously shown to be catalytically inefficient, can be "resurrected" to become good peroxidation catalysts. We also reveal that the relative rates of peroxidation by DNAzyme peroxidases depend on the nature of the organic reductant, arguing for a special binding site in the peroxidase-mimicking DNAzymes for catalysis.
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Affiliation(s)
- Shizuka Nakayama
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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103
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Ali MM, Aguirre SD, Lazim H, Li Y. Fluorogenic DNAzyme Probes as Bacterial Indicators. Angew Chem Int Ed Engl 2011; 50:3751-4. [DOI: 10.1002/anie.201100477] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Indexed: 12/19/2022]
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104
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Ali MM, Aguirre SD, Lazim H, Li Y. Fluorogenic DNAzyme Probes as Bacterial Indicators. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100477] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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105
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Silverman SK. DNA as a versatile chemical component for catalysis, encoding, and stereocontrol. Angew Chem Int Ed Engl 2011; 49:7180-201. [PMID: 20669202 DOI: 10.1002/anie.200906345] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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106
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Ali MM, Kanda P, Aguirre SD, Li Y. Modulation of DNA-modified gold-nanoparticle stability in salt with concatemeric single-stranded DNAs for colorimetric bioassay development. Chemistry 2011; 17:2052-6. [PMID: 21294175 DOI: 10.1002/chem.201002677] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Indexed: 01/08/2023]
Affiliation(s)
- M Monsur Ali
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Canada
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107
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Stougaard M, Juul S, Andersen FF, Knudsen BR. Strategies for highly sensitive biomarker detection by Rolling Circle Amplification of signals from nucleic acid composed sensors. Integr Biol (Camb) 2011; 3:982-92. [DOI: 10.1039/c1ib00049g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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108
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Bi S, Li L, Zhang S. Triggered polycatenated DNA scaffolds for DNA sensors and aptasensors by a combination of rolling circle amplification and DNAzyme amplification. Anal Chem 2010; 82:9447-54. [PMID: 20954711 DOI: 10.1021/ac1021198] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The concept of triggered polycatenated DNA scaffolds has been elegantly introduced into ultrasensitive biosensing applications by a combination of rolling circle amplification (RCA) and DNAzyme amplification. As compared to traditional methods in which one target could only initiate the formation of one circular template for RCA reaction, in the present study two species of linear single-stranded DNA (ssDNA) monomers are self-assembled into mechanically interlocked polycatenated nanostructures on capture probe-tagged magnetic nanoparticles (MNPs) only upon the introduction of one base mutant DNA sequence as initiator for single-nucleotide polymorphisms (SNPs) analysis. The resultant topologically polycatenated DNA ladder is further available for RCA process by using the serially ligated circular DNA as template for the synthesis of hemin/G-quadruplex HRP-mimicking DNAzyme chains, which act as biocatalytic labels for the luminol-H(2)O(2) chemiluminescence (CL) system. Notably, the problem of high background induced by excess hemin itself is circumvented by immobilizing the biotinylated RCA products on streptavidin-modified MNPs via biotin-streptavidin interaction. Similarly, a universal strategy is contrived by substitutedly employing aptamer as initiator for the construction of polycatenated DNA scaffolds to accomplish ultrasensitive detection of proteins based on structure-switching of aptamer upon target binding, which is demonstrated by using thrombin as a model analyte in this study. Overall, with two successive amplification steps and one magnetic separation procedure, this flexible biosensing system exhibits not only high sensitivity and specificity with the detection limits of SNPs and thrombin as low as 71 aM and 6.6 pM, respectively, but also excellent performance in real human serum assay with no PCR preamplification for SNPs assay. Given the unique and attractive characteristics, this study illustrates the potential of DNA nanotechnology in bioanalytical applications for both fundamental and practical research.
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Affiliation(s)
- Sai Bi
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China
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109
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Hu J, Zhang CY. Sensitive Detection of Nucleic Acids with Rolling Circle Amplification and Surface-Enhanced Raman Scattering Spectroscopy. Anal Chem 2010; 82:8991-7. [DOI: 10.1021/ac1019599] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Juan Hu
- Institute of Biomedical Engineering and Health Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chun-yang Zhang
- Institute of Biomedical Engineering and Health Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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110
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Peng X, Li H, Seidman M. A Template-Mediated Click-Click Reaction: PNA-DNA, PNA-PNA (or Peptide) Ligation, and Single Nucleotide Discrimination. European J Org Chem 2010; 2010:4194-4197. [PMID: 23504541 PMCID: PMC3597112 DOI: 10.1002/ejoc.201000615] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Indexed: 01/29/2023]
Abstract
A highly efficient chemical ligation was developed for quantitative conjugation of PNA with DNA (PNA or peptide) using the copper-catalyzed azide-alkyne cycloaddition reaction. While PNAs with an alkyne at the C-terminus and an azide at the N-terminus have been used, an efficient click-click reaction occurs. The PNA click ligation is sequence-specific and capable of single nucleotide discrimination.
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Affiliation(s)
- Xiaohua Peng
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St., Milwaukee, 53211, U.S.A
| | - Hong Li
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, Maryland 21224
| | - Michael Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, Maryland 21224
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111
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Silverman SK. DNA - eine vielseitige chemische Verbindung für die Katalyse, zur Kodierung und zur Stereokontrolle. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906345] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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112
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Cheng W, Yan F, Ding L, Ju H, Yin Y. Cascade signal amplification strategy for subattomolar protein detection by rolling circle amplification and quantum dots tagging. Anal Chem 2010; 82:3337-42. [PMID: 20345087 DOI: 10.1021/ac100144g] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A cascade signal amplification strategy was proposed for detection of protein target at ultralow concentration by combining the rolling circle amplification (RCA) technique with oligonucleotide functionalized quantum dots (QDs), multiplex binding of the biotin-strepavidin system, and anodic stripping voltammetric detection. The RCA product containing tandem-repeat sequences could serve as excellent template for periodic assembly of QDs, which presented per protein recognition event to numerous quantum dot tags for electrochemical readout. Both the RCA and the multiplex binding system showed remarkable amplification efficiency, very little nonspecific adsorption, and low background signal. Using human vascular endothelial growth factor as a model protein, the designed strategy could quantitatively detect protein down to 16 molecules in a 100 microL sample with a linear calibration range from 1 aM to 1 pM and was amenable to quantification of protein target in complex biological matrixes. The proposed cascade signal amplification strategy would become a powerful tool for proteomics research and clinical diagnostics.
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Affiliation(s)
- Wei Cheng
- Key Laboratory of Laboratory Medical Diagnostics (Ministry of Education of China), Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
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113
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Colorimetric detection of DNA, small molecules, proteins, and ions using unmodified gold nanoparticles and conjugated polyelectrolytes. Proc Natl Acad Sci U S A 2010; 107:10837-41. [PMID: 20534499 DOI: 10.1073/pnas.1005632107] [Citation(s) in RCA: 379] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We have demonstrated a novel sensing strategy employing single-stranded probe DNA, unmodified gold nanoparticles, and a positively charged, water-soluble conjugated polyelectrolyte to detect a broad range of targets including nucleic acid (DNA) sequences, proteins, small molecules, and inorganic ions. This nearly "universal" biosensor approach is based on the observation that, while the conjugated polyelectrolyte specifically inhibits the ability of single-stranded DNA to prevent the aggregation of gold-nanoparticles, no such inhibition is observed with double-stranded or otherwise "folded" DNA structures. Colorimetric assays employing this mechanism for the detection of hybridization are sensitive and convenient--picomolar concentrations of target DNA are readily detected with the naked eye, and the sensor works even when challenged with complex sample matrices such as blood serum. Likewise, by employing the binding-induced folding or association of aptamers we have generalized the approach to the specific and convenient detection of proteins, small molecules, and inorganic ions. Finally, this new biosensor approach is quite straightforward and can be completed in minutes without significant equipment or training overhead.
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114
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Zheng J, Li J, Gao X, Jin J, Wang K, Tan W, Yang R. Modulating Molecular Level Space Proximity: A Simple and Efficient Strategy to Design Structured DNA Probes. Anal Chem 2010; 82:3914-21. [DOI: 10.1021/ac1004713] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jishan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaoxia Gao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jianyu Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Weihong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ronghua Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China, and Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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115
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Lee JB, Campolongo MJ, Kahn JS, Roh YH, Hartman MR, Luo D. DNA-based nanostructures for molecular sensing. NANOSCALE 2010; 2:188-197. [PMID: 20644794 DOI: 10.1039/b9nr00142e] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Nanotechnology has opened up new avenues towards ultra-sensitive, highly selective detection of biological molecules and toxic agents, as well as for therapeutic targeting and screening. Though the goals may seem singular, there is no universal method to identify or detect a molecular target. Each system is application-specific and must not only identify the target, but also transduce this interaction into a meaningful signal rapidly, reliably, and inexpensively. This review focuses on the current capabilities and future directions of DNA-based nanostructures in sensing and detection.
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Affiliation(s)
- Jong Bum Lee
- Department of Biological & Environmental Engineering, Cornell University, 226 Riley Robb, Ithaca, New York 14853, USA
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