1
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Chen WT, Chiu PY, Chen CF. A flash signal amplification approach for ultrasensitive and rapid detection of single nucleotide polymorphisms in tuberculosis. Biosens Bioelectron 2023; 237:115514. [PMID: 37423064 DOI: 10.1016/j.bios.2023.115514] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
In recent years, the demand for rapid, sensitive, and simple methods for diagnosing deoxyribonucleic acid (DNA) has grown due to the increase in the variation of infectious diseases. This work aimed to develop a flash signal amplification method coupled with electrochemical detection for polymerase chain reaction (PCR)-free tuberculosis (TB) molecular diagnosis. We exploited the slightly miscible properties of butanol and water to instantly concentrate a capture probe DNA, a single-stranded mismatch DNA, and gold nanoparticles (AuNPs) to a small volume to reduce the diffusion and reaction time in the solution. In addition, the electrochemical signal was enhanced once two strands of DNA were hybridized and bound to the surface of the gold nanoparticle at an ultra-high density. To eliminate non-specific adsorption and identify mismatched DNA, the self-assembled monolayers (SAMs) and Muts proteins were sequentially modified on the working electrode. This sensitive and specific approach can detect as low as attomolar levels of DNA targets (18 aM) and is successfully applied to detecting tuberculosis-associated single nucleotide polymorphisms (SNPs) in synovial fluid. More importantly, as this biosensing strategy can amplify the signal in only a few seconds, it possesses a great potential for point-of-care and molecular diagnosis applications.
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Affiliation(s)
- Wei-Ting Chen
- Institute of Applied Mechanics, National Taiwan University, Taipei, 106, Taiwan
| | - Ping-Yeh Chiu
- Institute of Applied Mechanics, National Taiwan University, Taipei, 106, Taiwan; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, 333, Taiwan
| | - Chien-Fu Chen
- Institute of Applied Mechanics, National Taiwan University, Taipei, 106, Taiwan; Graduate School of Advanced Technology, National Taiwan University, Taipei, 106, Taiwan.
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2
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Lee S, You J, Baek I, Park H, Jang K, Park C, Na S. Synergistic enhanced rolling circle amplification based on mutS and radical polymerization for single-point mutation DNA detection. Biosens Bioelectron 2022; 210:114295. [PMID: 35477153 DOI: 10.1016/j.bios.2022.114295] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/12/2022] [Accepted: 04/18/2022] [Indexed: 12/29/2022]
Abstract
The detection of nucleic acids in biofluids is essential for changing the paradigm of disease diagnosis. As there are very few nucleic acids present in human biofluids, a high sensitivity method is required to detect nucleic acids for disease diagnosis. The Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation is associated with non-small cell lung cancer. It is a point mutation and requires a highly selective detection technique. In this study, high sensitivity and selectivity were achieved for the detection of KRAS mutation using rolling circle amplification (RCA), atomic transfer radical polymerization (ATRP), mutS enzyme, and electrochemical sensors. Although RCA can isothermally amplify DNA, it has low selectivity for detecting single-base mismatch DNA, and its sensitivity is not suitable for circulating tumor DNA detection. The selectivity of RCA was improved by using mutS, which can bind specifically to point mutations. In addition, as a method of isothermal radical polymerization, ATRP was used to amplify the weak signal of RCA. Since RCA and ATRP reactions occur simultaneously, detection time was reduced, and the calculated detection limit was 3.09 aM. Computational and experimental analyses were conducted to verify each detection step and the combination of mutS, ATRP, and RCA. The experiment was performed using normal human serum samples for biological application, and the proposed detection method was confirmed to have excellent potential for diagnosing cancer patients.
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Affiliation(s)
- Seonwoo Lee
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Juneseok You
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Inchul Baek
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Hyunjun Park
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Kuewhan Jang
- School of Mechanical Engineering, Hoseo University, Asan, 31499, Republic of Korea
| | - Chanho Park
- Division of Foundry, Samsung Electronics, Hwaseong-si, 18448, Republic of Korea.
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea.
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3
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Jiang H, Xi H, Juhas M, Zhang Y. Biosensors for Point Mutation Detection. Front Bioeng Biotechnol 2021; 9:797831. [PMID: 34976987 PMCID: PMC8714947 DOI: 10.3389/fbioe.2021.797831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/17/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Hanlin Jiang
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Hui Xi
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Mario Juhas
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Yang Zhang
- College of Science, Harbin Institute of Technology, Shenzhen, China
- *Correspondence: Yang Zhang,
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4
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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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5
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Highly sensitive and selective detection of single-nucleotide polymorphisms using gold nanoparticle MutS enzymes and a micro cantilever resonator. Talanta 2019; 205:120154. [DOI: 10.1016/j.talanta.2019.120154] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 12/21/2022]
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6
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Park JH, Jang H, Jung YK, Jung YL, Shin I, Cho DY, Park HG. A mass spectrometry-based multiplex SNP genotyping by utilizing allele-specific ligation and strand displacement amplification. Biosens Bioelectron 2017; 91:122-127. [DOI: 10.1016/j.bios.2016.10.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 01/21/2023]
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7
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Hamidi-Asl E, Raoof JB, Naghizadeh N, Akhavan-Niaki H, Ojani R, Banihashemi A. A bimetallic nanocomposite modified genosensor for recognition and determination of thalassemia gene. Int J Biol Macromol 2016; 91:400-8. [PMID: 27235732 DOI: 10.1016/j.ijbiomac.2016.05.087] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 05/22/2016] [Accepted: 05/25/2016] [Indexed: 01/16/2023]
Abstract
The main roles of DNA in the cells are to maintain and properly express genetic information. It is important to have analytical methods capable of fast and sensitive detection of DNA damage. DNA hybridization sensors are well suited for diagnostics and other purposes, including determination of bacteria and viruses. Beta thalassemias (βth) are due to mutations in the β-globin gene. In this study, an electrochemical biosensor which detects the sequences related to the β-globin gene issued from real samples amplified by polymerase chain reaction (PCR) is described for the first time. The biosensor relies on the immobilization of 20-mer single stranded oligonucleotide (probe) related to βth sequence on the carbon paste electrode (CPE) modified by 15% silver (Ag) and platinum (Pt) nanoparticles to prepare the bimetallic nanocomposite electrode and hybridization of this oligonucleotide with its complementary sequence (target). The extent of hybridization between the probe and target sequences was shown by using linear sweep voltammetry (LSV) with methylene blue (MB) as hybridization indicator. The selectivity of sensor was investigated using PCR samples containing non-complementary oligonucleotides. The detection limit of biosensor was calculated about 470.0pg/μL.
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Affiliation(s)
- Ezat Hamidi-Asl
- Eletroanalytical Chemistry Research Laboratory, Department of Analytical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran
| | - Jahan Bakhsh Raoof
- Eletroanalytical Chemistry Research Laboratory, Department of Analytical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran.
| | - Nahid Naghizadeh
- Eletroanalytical Chemistry Research Laboratory, Department of Analytical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran
| | - Haleh Akhavan-Niaki
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran; Genetic Laboratory of Amirkola Children Hospital, Babol University of Medical Sciences, Babol, Iran
| | - Reza Ojani
- Eletroanalytical Chemistry Research Laboratory, Department of Analytical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran
| | - Ali Banihashemi
- Genetic Laboratory of Amirkola Children Hospital, Babol University of Medical Sciences, Babol, Iran
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8
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Huang J, Wang Z, Kim JK, Su X, Li Z. Detecting Arbitrary DNA Mutations Using Graphene Oxide and Ethidium Bromide. Anal Chem 2015; 87:12254-61. [DOI: 10.1021/acs.analchem.5b03369] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jiahao Huang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Zhenyu Wang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jang-Kyo Kim
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuefen Su
- School of Public
Health and Primary Care, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong
| | - Zhigang Li
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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9
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Multispot array combined with S1 nuclease-mediated elimination of unpaired nucleotides. BIOCHIP JOURNAL 2015. [DOI: 10.1007/s13206-015-9301-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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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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11
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Simple and label-free electrochemical impedance Amelogenin gene hybridization biosensing based on reduced graphene oxide. Biosens Bioelectron 2014; 58:145-52. [DOI: 10.1016/j.bios.2014.01.053] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/22/2014] [Accepted: 01/28/2014] [Indexed: 11/19/2022]
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12
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An electronic sensor array for label-free detection of single-nucleotide polymorphisms. Biosens Bioelectron 2013; 43:165-72. [DOI: 10.1016/j.bios.2012.12.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 12/03/2012] [Accepted: 12/10/2012] [Indexed: 11/22/2022]
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13
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Gao Z, Shen W, Deng H, Ren Y. Detection of single-nucleotide polymorphisms based on the formation of an electron-transfer impeding layer on an electrode surface. Chem Commun (Camb) 2013. [DOI: 10.1039/c2cc37450a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Highly sensitive and selective colorimetric genotyping of single-nucleotide polymorphisms based on enzyme-amplified ligation on magnetic beads. Biosens Bioelectron 2012; 36:89-94. [DOI: 10.1016/j.bios.2012.03.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 03/26/2012] [Accepted: 03/29/2012] [Indexed: 11/22/2022]
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15
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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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16
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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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17
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Wang X, Dong P, He P, Fang Y. A solid-state electrochemiluminescence sensing platform for detection of adenosine based on ferrocene-labeled structure-switching signaling aptamer. Anal Chim Acta 2009; 658:128-32. [PMID: 20103085 DOI: 10.1016/j.aca.2009.11.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 10/27/2009] [Accepted: 11/03/2009] [Indexed: 11/29/2022]
Abstract
A solid-state electrochemiluminescence sensing platform based on ferrocene-labeled structure-switching signaling aptamer (Fc-aptamer) for highly sensitive detection of small molecules is developed successfully using adenosine as a model analyte. Such special sensing platform included two main parts, an electrochemiluminescence (ECL) substrate and an ECL intensity switch. The ECL substrate was made by modifying the complex of Au nanoparticle and Ruthenium (II) tris-(bipyridine) (Ru(bpy)(3)(2+)-AuNPs) onto Au electrode. An anti-adenosine aptamer labeled by ferrocene acted as the ECL intensity switch. A short complementary ssDNA for the aptamer was applied to hybridizing with the aptamer, yielding a double-stranded complex of the aptamer and the ssDNA on the electrode surface. The introduction of adenosine triggered structure switching of the aptamer. As a result, the ssDNA was forced to dissociate from the sensing platform. Such structural change of the aptamer resulted in an obvious ECL intensity decrease due to the increased quenching effect of Fc to the ECL substrate. The analytic results were sensitive and specific.
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Affiliation(s)
- Xiaoying Wang
- School of Public Health, Southeast University, Nanjing 210009, China
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