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Ngo LT, Wang WK, Tseng YT, Chang TC, Kuo PL, Chau LK, Huang TT. MutS protein-based fiber optic particle plasmon resonance biosensor for detecting single nucleotide polymorphisms. Anal Bioanal Chem 2021; 413:3329-3337. [PMID: 33712917 DOI: 10.1007/s00216-021-03271-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/08/2021] [Accepted: 03/04/2021] [Indexed: 01/29/2023]
Abstract
A new biosensing method is presented to detect gene mutation by integrating the MutS protein from bacteria with a fiber optic particle plasmon resonance (FOPPR) sensing system. In this method, the MutS protein is conjugated with gold nanoparticles (AuNPs) deposited on an optical fiber core surface. The target double-stranded DNA containing an A and C mismatched base pair in a sample can be captured by the MutS protein, causing increased absorption of green light launching into the fiber and hence a decrease in transmitted light intensity through the fiber. As the signal change is enhanced through consecutive total internal reflections along the fiber, the limit of detection for an AC mismatch heteroduplex DNA can be as low as 0.49 nM. Because a microfluidic chip is used to contain the optical fiber, the narrow channel width allows an analysis time as short as 15 min. Furthermore, the label-free and real-time nature of the FOPPR sensing system enables determination of binding affinity and kinetics between MutS and single-base mismatched DNA. The method has been validated using a heterozygous PCR sample from a patient to determine the allelic fraction. The obtained allelic fraction of 0.474 reasonably agrees with the expected allelic fraction of 0.5. Therefore, the MutS-functionalized FOPPR sensor may potentially provide a convenient quantitative tool to detect single nucleotide polymorphisms in biological samples with a short analysis time at the point-of-care sites.
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Affiliation(s)
- Loan Thi Ngo
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi, 62102, Taiwan
| | - Wei-Kai Wang
- Department of Dentistry, Institute of Oral Medicine, Department of Stomatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yen-Ta Tseng
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi, 62102, Taiwan
| | - Ting-Chou Chang
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi, 62102, Taiwan
| | - Pao-Lin Kuo
- Department of Obstetrics Gynecology, National Cheng Kung University Hospital, College of Medicine and Hospital, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi, 62102, Taiwan.
| | - Tze-Ta Huang
- Department of Dentistry, Institute of Oral Medicine, Department of Stomatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan.
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An electrochemical lipopolysaccharide sensor based on an immobilized Toll-Like Receptor-4. Biosens Bioelectron 2017; 87:794-801. [DOI: 10.1016/j.bios.2016.09.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/20/2016] [Accepted: 09/01/2016] [Indexed: 11/20/2022]
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3
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Chang K, Deng S, Chen M. Novel biosensing methodologies for improving the detection of single nucleotide polymorphism. Biosens Bioelectron 2015; 66:297-307. [DOI: 10.1016/j.bios.2014.11.041] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/28/2014] [Accepted: 11/20/2014] [Indexed: 12/11/2022]
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4
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Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
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5
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A protein-based electrochemical method for label-free characterization of sequence-specific protein–DNA interactions. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.04.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Chiba J, Akaishi A, Ikeda R, Inouye M. Electrochemical detection of insertion/deletion mutations based on enhanced flexibility of bulge-containing duplexes on electrodes. Chem Commun (Camb) 2010; 46:7563-5. [PMID: 20852766 DOI: 10.1039/c0cc02371j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ferrocene-modified DNA probes formed fully matched duplexes and bulge-containing ones with wild-type and insertion/deletion-type complements of clinical importance, respectively. Cyclic voltammetry measurements revealed that the bulge-containing duplexes showed an increased flexibility compared to the fully matched duplexes. The difference in the bending elasticity could be read out electrochemically by square wave voltammetry.
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Affiliation(s)
- Junya Chiba
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan.
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Breaking the barrier to fast electron transfer. Bioelectrochemistry 2009; 76:19-27. [PMID: 19351583 DOI: 10.1016/j.bioelechem.2009.03.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Revised: 02/25/2009] [Accepted: 03/12/2009] [Indexed: 11/21/2022]
Abstract
A study of the electron transfer for a non-glycosylated redox variant of GOx is reported, immobilised onto an electrode via a polyhistidine tag. The non-glycosylated variant allows the enzyme to be brought closer to the electrode, and within charge transfer distances predicted by Marcus' theory. The enzyme-electrode-hybrid shows direct very fast reversible electrochemical electron transfer, with a rate constant of approximately 350 s(-1) under anaerobic conditions. This is 2 orders of magnitude faster than the enzyme-free flavin adenine dinucleotide (FAD). These results are discussed in the context of the conformation of FAD in the active site of GOx. Further data, presented in the presence of oxygen, show a reduced electron transfer rate (approximately 160 s(-1)) that may be associated with the oxygen interaction with the histidines in the active site. These residues are implicated in the proton transfer mechanism and thus suggest that the presence of oxygen may have a profound effect in attenuating the direct electron transfer rate and thus moderating 'short-circuit' incidental electron transfer between proteins.
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Electrochemical scanning of DNA point mutations via MutS protein-mediated mismatch recognition. Biosens Bioelectron 2009; 24:1955-61. [DOI: 10.1016/j.bios.2008.09.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/11/2008] [Accepted: 09/30/2008] [Indexed: 11/21/2022]
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Peled D, Daube SS, Naaman R. Selective enzymatic labeling to detect packing-induced denaturation of double-stranded DNA at interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:11842-11846. [PMID: 18800816 DOI: 10.1021/la801437n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The adsorption of DNA on surfaces is a widespread procedure and is a common way for fabrication of biosensors, DNA chips, and nanoelectronic devices. Although the biologically relevant and prevailing in vivo structure of DNA is its double-stranded (dsDNA) conformation, the characterization of DNA on surfaces has mainly focused on single-stranded DNA (ssDNA). Studying the structure of dsDNA on surfaces is of invaluable importance to microarray performance since their effectiveness relies on the ability of two DNA molecules to hybridize and remain stable. In addition, many of the enzymatic transactions performed on DNA require dsDNA, rather than ssDNA, as a substrate. However, it is not established that adsorbed dsDNA remains in its structure and does not denature. Here, two methodologies have been developed for distinguishing between surface-adsorbed single- and double-stranded DNA. We demonstrate that, upon formation of a dense monolayer, the nonthiolated strand comprising the dsDNA is released and the monolayer consists of mostly ssDNA. The fraction of dsDNA within the ssDNA monolayer depends on the length of the oligomers. A likely mechanism leading to this rearrangement is discussed.
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Affiliation(s)
- Dana Peled
- Department of Chemical Physics and Chemical Research Support, Weizmann Institute, Rehovot 76100, Israel
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Olijnyk VV, Filinchuk YE, Lenkivs'ka TP. Polymorphism of Copper(I) Halide π-Complexes: Synthesis and Structure of a New Modification of [Cu2Cl2(CH2=CH–CH2)2O]. Z Anorg Allg Chem 2008. [DOI: 10.1002/zaac.200800042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Skeika T, Marcovicz C, Nakagaki S, Fujiwara S, Wohnrath K, Nagata N, Pessoa C. Electrochemical Studies of an Iron Porphyrin Immobilized on Nb2O5/SiO2 and Its Application for Simultaneous Determination of Dopamine and Ascorbic Acid Using Multivariate Calibration Methodology. ELECTROANAL 2007. [DOI: 10.1002/elan.200703994] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Masarík M, Cahová K, Kizek R, Palecek E, Fojta M. Label-free voltammetric detection of single-nucleotide mismatches recognized by the protein MutS. Anal Bioanal Chem 2007; 388:259-70. [PMID: 17333147 DOI: 10.1007/s00216-007-1181-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Accepted: 02/02/2007] [Indexed: 11/26/2022]
Abstract
MutS, a protein involved in DNA mismatch repair, recognizes mispaired and unpaired bases in duplex DNA. We have previously used MutS in an electrochemical double-surface technique (DST) for in-vitro detection of point mutations in DNA. The DST involved binding of unlabeled MutS to DNA heteroduplexes at the surface of magnetic beads followed by a highly sensitive electrochemical determination of the protein by measurement of a catalytic protein signal (peak H) at mercury electrodes. Detection of MutS using a peak resulting from oxidation of tyrosine and tryptophan residues of the protein at a carbon-paste electrode (CPE) was also possible but was approximately three orders of magnitude less sensitive. In this work we present an optimized technique for ex-situ voltammetric determination of MutS at a CPE. Choice of optimum experimental conditions (pH of supporting electrolyte, square-wave voltammetry settings, etc.) resulted in substantial improvement of the sensitivity of the assay, enabling detection of approximately 140 pg (1.6 fmol protein monomer) MutS in a 5-microL sample. The sensitivity was increased further by acid hydrolysis of the protein before measurement. The hydrolyzed protein was detectable down to 5 pg (approx. 56 amol) MutS in 5 microL solution. By using the DST combined with determination of the bound unlabeled MutS at the CPE we demonstrated selective interactions of the protein with single-base mismatches and discrimination among different base mispairs in 30-mer or 95-mer DNA duplexes. In agreement with previous studies, binding of the protein to the 30-mer substrates followed the trend G:T>>C:A>A:A>C:T>homoduplex. The electrochemical data were confirmed by use of an independent technique-a quartz-crystal microbalance for real-time monitoring of MutS interactions with DNA duplexes containing different base mispairs. By using the electrochemical DST a G:T mismatch was detectable in up to 1000-fold excess of homoduplex DNA.
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Affiliation(s)
- Michal Masarík
- Institute of Biophysics v.v.i., Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65, Brno, Czech Republic
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Aoki H, Umezawa Y, Vertova A, Rondinini S. Ion-channel Sensors Based on ETH 1001 Ionophore Embedded in Charged-alkanethiol Self-assembled Monolayers on Gold Electrode Surfaces. ANAL SCI 2006; 22:1581-4. [PMID: 17159319 DOI: 10.2116/analsci.22.1581] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An ion-channel sensor was demonstrated by immobilizing ETH 1001, an ionophore for ion-selective electrodes, on a gold electrode surface. The approach for preparing the sensor was to incorporate the ionophore into a mixed self-assembled monolayer of 10-mercaptodecanesulfonate and 11-hydroxy-1-undecanethiol formed on the surface. The voltammetric responses for the thus prepared sensor to the primary cation Ca(2+) were observed by using [Fe(CN)(6)](3-/4-) as an electroactive marker. The ionophore was stably immobilized on the electrode surface with the hydrophobic interaction between its alkyl chains and those of the alkanethiol. The introduction of a proper charge density to the electrode surface improved the sensor sensitivity with retaining the selective response to Ca(2+) against Mg(2+) with concentrations above 10(-4) M.
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Affiliation(s)
- Hiroshi Aoki
- Department of Chemistry, School of Science, The University of Tokyo, Japan.
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