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Luchian T, Mereuta L, Park Y, Asandei A, Schiopu I. Single-molecule, hybridization-based strategies for short nucleic acids detection and recognition with nanopores. Proteomics 2021; 22:e2100046. [PMID: 34275186 DOI: 10.1002/pmic.202100046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/21/2021] [Accepted: 07/13/2021] [Indexed: 12/23/2022]
Abstract
DNA nanotechnology has seen large developments over the last 30 years through the combination of detection and discovery of DNAs, and solid phase synthesis to increase the chemical functionalities on nucleic acids, leading to the emergence of novel and sophisticated in features, nucleic acids-based biopolymers. Arguably, nanopores developed for fast and direct detection of a large variety of molecules, are part of a revolutionary technological evolution which led to cheaper, smaller and considerably easier to use devices enabling DNA detection and sequencing at the single-molecule level. Through their versatility, the nanopore-based tools proved useful biomedicine, nanoscale chemistry, biology and physics, as well as other disciplines spanning materials science to ecology and anthropology. This mini-review discusses the progress of nanopore- and hybridization-based DNA detection, and explores a range of state-of-the-art applications afforded through the combination of certain synthetically-derived polymers mimicking nucleic acids and nanopores, for the single-molecule biophysics on short DNA structures.
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Affiliation(s)
- Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, Republic of Korea
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, "Alexandru I. Cuza" University, Iasi, Romania
| | - Irina Schiopu
- Interdisciplinary Research Institute, Sciences Department, "Alexandru I. Cuza" University, Iasi, Romania
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2
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Wu Y, Ali S, White RJ. Use of Electrocatalysis for Differentiating DNA Polymorphisms and Enhancing the Sensitivity of Electrochemical Nucleic Acid-Based Sensors with Covalent Redox Tags-Part II. ACS Sens 2020; 5:3842-3849. [PMID: 33305566 DOI: 10.1021/acssensors.0c02363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-nucleotide polymorphisms (SNPs), insertion/deletion (indel) polymorphisms, and DNA methylation are the most frequent types of genetic variations. As such, DNA polymorphisms play significant roles in genetic mapping and diagnostics. Thus, analytical methods enabling DNA polymorphism detection will provide an invaluable means for early disease diagnosis. However, no single electrochemical nucleic acid-based sensor has achieved the detection of the three major polymorphisms (SNPs, indel polymorphisms, and DNA methylation) with sufficient specificity and sensitivity. In response, we explore the utilization of a catalytic reaction between methylene blue (MB) covalently linked to surface-bound nucleic acid and freely diffusing ferricyanide (Fe(CN)63-) to improve specificity and sensitivity of DNA polymorphism detection. We find that the dynamics of the nucleic acid tether is an additional rate-limiting factor for the electrocatalytic reaction, in addition to the more traditional kinetic and excess factors. Our proof-of-concept experiments demonstrate that the use of electrocatalysis enables differentiation of the three polymorphisms when target sequences are present at 10 nM. We hypothesize that this ability is a result of the distinct dynamics of the DNA probe with each respective polymorphism. In addition to the specificity the sensor displays, the sensor achieves a 20 pM limit of detection. We believe that the electrocatalysis between nucleic acid-tethered MB and Fe(CN)63- is highly promising for electrochemical nucleic acid-based sensors to achieve better specificity and sensitivity.
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Affiliation(s)
| | - Sufyaan Ali
- Walnut Hills High School, Cincinnati, Ohio 45207, United States
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3
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Abstract
Pancreatic cancer is the fourth leading cause of cancer death in the United States. Pancreatic cancer presents dismal clinical outcomes in patients, and the incidence of pancreatic cancer has continuously increased to likely become the second most common cause of cancer-related deaths by as early as 2030. One of main reasons for the high mortality rate of pancreatic cancer is the lack of tools for early-stage detection. Current practice in detecting and monitoring therapeutic response in pancreatic cancer relies on imaging analysis and invasive endoscopic examination. Liquid biopsy-based analysis of genetic alterations in biofluids has become a fundamental component in the diagnosis and management of cancers. There is an urgent need for scientific and technological advancement to detect pancreatic cancer early and to develop effective therapies. The development of a highly sensitive and specific liquid biopsy tool will require extensive understanding on the characteristics of circulating tumor DNA in biofluids. Here, we have reviewed the current status of liquid biopsy in detecting and monitoring pancreatic cancers and our understanding of circulating tumor DNA that should be considered for the development of a liquid biopsy tool, which will greatly aid in the diagnosis and healthcare of people at risk.
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4
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Erdem A, Eksin E. Impedimetric Sensing of Factor V Leiden Mutation by Zip Nucleic Acid Probe and Electrochemical Array. BIOSENSORS-BASEL 2020; 10:bios10090116. [PMID: 32906640 PMCID: PMC7559847 DOI: 10.3390/bios10090116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 12/02/2022]
Abstract
A carbon nanofiber enriched 8-channel screen-printed electrochemical array was used for the impedimetric detection of SNP related to Factor V Leiden (FV Leiden) mutation, which is the most common inherited form of thrombophilia. FV Leiden mutation sensing was carried out in three steps: solution-phase nucleic acid hybridization between zip nucleic acid probe (Z-probe) and mutant type DNA target, followed by the immobilization of the hybrid on the working electrode area of array, and measurement by electrochemical impedance spectroscopy (EIS). The selectivity of the assay was tested against mutation-free DNA sequences and synthetic polymerase chain reaction (PCR) samples. The developed biosensor was a trustful assay for FV Leiden mutation diagnosis, which can effectively discriminate wild type and mutant type even in PCR samples.
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Chahin N, Uribe LA, Debela AM, Thorimbert S, Hasenknopf B, Ortiz M, Katakis I, O'Sullivan CK. Electrochemical primer extension based on polyoxometalate electroactive labels for multiplexed detection of single nucleotide polymorphisms. Biosens Bioelectron 2018; 117:201-206. [PMID: 29906767 DOI: 10.1016/j.bios.2018.06.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 12/14/2022]
Abstract
Polyoxymetalates (POMs) ([SiW11O39{Sn(CH2)2CO)}]4- and [P2W17O61{Sn(CH2)2CO)}]6-) were used to modify dideoxynucleotides (ddNTPs) through amide bond formation, and applied to the multiplexed detection of single nucleotide polymorphisms (SNPs) in an electrochemical primer extension reaction. Each gold electrode of an array was functionalised with a short single stranded thiolated DNA probe, specifically designed to extend with the POM-ddNTP at the SNP site to be interrogated. The system was applied to the simultaneous detection of 4 SNPs within a single stranded 103-mer model target generated using asymmetric PCR, highlighting the potential of POM-ddNTPs for targeted, multiplexed SNP detection. The four DNA bases were successfully labelled with both ([SiW11O39{Sn(CH2)2CO)}]4- and [P2W17O61{Sn(CH2)2CO)}]6-), and [SiW11O39{Sn(CH2)2CO)}]4- demonstrated to be the more suitable due to its single oxidation peak, which provides an unequivocal signal. The POM-ddNTP enzymatically incorporated to the DNA anchored to the surface was visualised by AFM using gold coated mica. The developed assay has been demonstrated to be highly reproducible, simple to carry out and with very low non-specific background signals. Future work will focus on applying the developed platform to the detection of SNPs associated with rifampicin resistance in real samples from patients suffering from tuberculosis.
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Affiliation(s)
- Nassif Chahin
- Departament d'Enginyeria Quıímica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Laura A Uribe
- Departament d'Enginyeria Quıímica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Ahmed M Debela
- Sorbonne Université, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, 4 place Jussieu, 75005 Paris, France
| | - Serge Thorimbert
- Sorbonne Université, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, 4 place Jussieu, 75005 Paris, France
| | - Bernold Hasenknopf
- Sorbonne Université, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, 4 place Jussieu, 75005 Paris, France
| | - Mayreli Ortiz
- Departament d'Enginyeria Quıímica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain.
| | - Ioannis Katakis
- Departament d'Enginyeria Quıímica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Quıímica, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain.
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6
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Analysis of the evolution of the detection limits of electrochemical nucleic acid biosensors II. Anal Bioanal Chem 2017; 409:4335-4352. [DOI: 10.1007/s00216-017-0377-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/11/2017] [Accepted: 04/21/2017] [Indexed: 01/07/2023]
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7
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Haque MH, Islam MN, Islam F, Gopalan V, Nguyen NT, Lam AK, Shiddiky MJA. Electrochemical Detection of FAM134B Mutations in Oesophageal Cancer Based on DNA-Gold Affinity Interactions. ELECTROANAL 2017. [DOI: 10.1002/elan.201700039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Md. Hakimul Haque
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland; Griffith University; Gold Coast Campus Australia
- School of Natural Sciences; Griffith University; Nathan Campus QLD 4111 Australia
- Queensland Micro and Nanotechnology Centre; Griffith University; Nathan Campus QLD 4111 Australia
| | - Md. Nazmul Islam
- School of Natural Sciences; Griffith University; Nathan Campus QLD 4111 Australia
- Queensland Micro and Nanotechnology Centre; Griffith University; Nathan Campus QLD 4111 Australia
| | - Farhadul Islam
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland; Griffith University; Gold Coast Campus Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland; Griffith University; Gold Coast Campus Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre; Griffith University; Nathan Campus QLD 4111 Australia
| | - Alfred K. Lam
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland; Griffith University; Gold Coast Campus Australia
| | - Muhammad J. A. Shiddiky
- School of Natural Sciences; Griffith University; Nathan Campus QLD 4111 Australia
- Queensland Micro and Nanotechnology Centre; Griffith University; Nathan Campus QLD 4111 Australia
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8
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Tram DTN, Wang H, Sugiarto S, Li T, Ang WH, Lee C, Pastorin G. Advances in nanomaterials and their applications in point of care (POC) devices for the diagnosis of infectious diseases. Biotechnol Adv 2016; 34:1275-1288. [PMID: 27686397 PMCID: PMC7127209 DOI: 10.1016/j.biotechadv.2016.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 07/13/2016] [Accepted: 09/23/2016] [Indexed: 01/17/2023]
Abstract
Nanotechnology has gained much attention over the last decades, as it offers unique opportunities for the advancement of the next generation of sensing tools. Point-of-care (POC) devices for the selective detection of biomolecules using engineered nanoparticles have become a main research thrust in the diagnostic field. This review presents an overview on how the POC-associated nanotechnology, currently applied for the identification of nucleic acids, proteins and antibodies, might be further exploited for the detection of infectious pathogens: although still premature, future integrations of nanoparticles with biological markers that target specific microorganisms will enable timely therapeutic intervention against life-threatening infectious diseases.
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Affiliation(s)
- Dai Thien Nhan Tram
- Pharmacy Department National University of Singapore, Singapore 117543, Singapore.
| | - Hao Wang
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering, Drive 3, Singapore 117576, Singapore.
| | - Sigit Sugiarto
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Tao Li
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Wee Han Ang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Chengkuo Lee
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering, Drive 3, Singapore 117576, Singapore.
| | - Giorgia Pastorin
- Pharmacy Department National University of Singapore, Singapore 117543, Singapore; NanoCore, Faculty of Engineering, National University of Singapore, Singapore 117576, Singapore; NUS Graduate School for Integrative Sciences and Engineering, Centre for Life Sciences (CeLS), Singapore 117456, Singapore.
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9
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Iurlo M, Mengozzi L, Rapino S, Marcaccio M, Perone RC, Masiero S, Cozzi P, Paolucci F. New Approaches toward Ferrocene–Guanine Conjugates: Synthesis and Electrochemical Behavior. Organometallics 2014. [DOI: 10.1021/om5002809] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matteo Iurlo
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Luca Mengozzi
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Stefania Rapino
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Massimo Marcaccio
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Rosaria C. Perone
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Stefano Masiero
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Piergiorgio Cozzi
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
| | - Francesco Paolucci
- Alma Mater Studiorum-Università
di Bologna and INSTM, Unit of Bologna, Dipartimento di Chimica “Giacomo
Ciamician”, via Selmi, 2, 40126 Bologna, Italy
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10
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Huang Y, Zhu J, Li G, Chen Z, Jiang JH, Shen GL, Yu RQ. Electrochemical detection of point mutation based on surface hybridization assay conjugated allele-specific polymerase chainreaction. Biosens Bioelectron 2013; 42:526-31. [DOI: 10.1016/j.bios.2012.10.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/23/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022]
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11
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Analysis of the evolution of the detection limits of electrochemical DNA biosensors. Anal Bioanal Chem 2013; 405:3705-14. [DOI: 10.1007/s00216-012-6672-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 12/04/2012] [Accepted: 12/18/2012] [Indexed: 11/26/2022]
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12
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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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13
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Sato S, Tsueda M, Kanezaki Y, Takenaka S. Detection of an aberrant methylation of CDH4 gene in PCR product by ferrocenylnaphthalene diimide-based electrochemical hybridization assay. Anal Chim Acta 2012; 715:42-8. [DOI: 10.1016/j.aca.2011.12.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/28/2011] [Accepted: 12/07/2011] [Indexed: 12/16/2022]
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14
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Ishige Y, Goto Y, Yanagi I, Ishida T, Itabashi N, Kamahori M. Feasibility Study on Direct Counting of Viruses and Bacteria by Using Microelectrode Array. ELECTROANAL 2011. [DOI: 10.1002/elan.201100482] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Shi C, Ge Y, Gu H, Ma C. Highly sensitive chemiluminescent point mutation detection by circular strand-displacement amplification reaction. Biosens Bioelectron 2011; 26:4697-701. [DOI: 10.1016/j.bios.2011.05.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 05/14/2011] [Indexed: 11/30/2022]
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16
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Yang L, Xu Y, Wang X, Zhu J, Zhang R, He P, Fang Y. The application of β-cyclodextrin derivative functionalized aligned carbon nanotubes for electrochemically DNA sensing via host–guest recognition. Anal Chim Acta 2011; 689:39-46. [DOI: 10.1016/j.aca.2011.01.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 12/25/2010] [Accepted: 01/12/2011] [Indexed: 02/03/2023]
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17
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Kashida H, Kondo N, Sekiguchi K, Asanuma H. Detection of three-base deletion by exciplex formation with perylene derivatives. Chem Commun (Camb) 2011; 47:6404-6. [DOI: 10.1039/c1cc11041a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Fan H, Xu Y, Chang Z, Xing R, Wang Q, He P, Fang Y. A non-immobilizing electrochemical DNA sensing strategy with homogenous hybridization based on the host–guest recognition technique. Biosens Bioelectron 2011; 26:2655-9. [DOI: 10.1016/j.bios.2010.02.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 02/17/2010] [Accepted: 02/19/2010] [Indexed: 12/28/2022]
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19
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Kim JS, Cho JB, Park BG, Lee W, Lee KB, Oh MK. Size-controllable quartz nanostructure for signal enhancement of DNA chip. Biosens Bioelectron 2011; 26:2085-9. [DOI: 10.1016/j.bios.2010.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 09/05/2010] [Accepted: 09/06/2010] [Indexed: 11/27/2022]
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20
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Wei MY, Guo LH, Famouri P. DNA biosensors based on metallo-intercalator probes and electrocatalytic amplification. Mikrochim Acta 2010. [DOI: 10.1007/s00604-010-0519-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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21
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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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22
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Abstract
The detection of mismatched base pairs in DNA plays a crucial role in the diagnosis of genetic-related diseases and conditions, especially for early stage treatment. Among the various biosensors that have been used for DNA detection, EC sensors show great promise because they are capable of precise DNA recognition and efficient signal transduction. Advancements in micro- and nanotechnologies, specifically fabrication techniques and new nanomaterials, have enabled for the development of highly sensitive, highly specific sensors making them attractive for the detection of small sequence variations. Furthermore, the integration of sensors with sample preparation and fluidic processes enables for rapid, multiplexed DNA detection essential for POC clinical diagnostics.
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Affiliation(s)
- Fang Wei
- Mechanical and Aerospace Engineering Department, School of Engineering and Applied Science, University of California, Los Angeles, California 90095, USA
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23
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Xiao Y, Lou X, Uzawa T, Plakos KJI, Plaxco KW, Soh HT. An electrochemical sensor for single nucleotide polymorphism detection in serum based on a triple-stem DNA probe. J Am Chem Soc 2010; 131:15311-6. [PMID: 19807078 DOI: 10.1021/ja905068s] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report here an electrochemical approach that offers, for the first time, single-step, room-temperature single nucleotide polymorphism (SNP) detection directly in complex samples (such as blood serum) without the need for target modification, postwashing, or the addition of exogenous reagents. This sensor, which is sensitive, stable, and reusable, is comprised of a single, self-complementary, methylene blue-labeled DNA probe possessing a triple-stem structure. This probe takes advantage of the large thermodynamic changes in enthalpy and entropy that result from major conformational rearrangements that occur upon binding a perfectly matched target, resulting in a large-scale change in the faradaic current. As a result, the discrimination capabilities of this sensor greatly exceed those of earlier single- and double-stem electrochemical sensors and support rapid (minutes), single-step, reagentless, room-temperature detection of single nucleotide substitutions. To elucidate the theoretical basis of the sensor's selectivity, we present a comparative thermodynamic analysis among single-, double-, and triple-stem probes.
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Affiliation(s)
- Yi Xiao
- Materials Department, University of California, Santa Barbara, California 93106, USA.
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24
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A label-free strategy for SNP detection with high fidelity and sensitivity based on ligation-rolling circle amplification and intercalating of methylene blue. Biosens Bioelectron 2009; 24:3201-7. [DOI: 10.1016/j.bios.2009.03.012] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 03/05/2009] [Accepted: 03/09/2009] [Indexed: 11/17/2022]
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25
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Huang Y, Zhang YL, Xu X, Jiang JH, Shen GL, Yu RQ. Highly Specific and Sensitive Electrochemical Genotyping via Gap Ligation Reaction and Surface Hybridization Detection. J Am Chem Soc 2009; 131:2478-80. [DOI: 10.1021/ja808700d] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yong Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Yan-Li Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Xiangmin Xu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Guo-Li Shen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
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Ultra-sensitive detection of mutated papillary thyroid carcinoma DNA using square wave stripping voltammetry method and amplified gold nanoparticle biomarkers. Biosens Bioelectron 2008; 24:1899-904. [PMID: 19010660 DOI: 10.1016/j.bios.2008.09.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 09/06/2008] [Accepted: 09/23/2008] [Indexed: 11/20/2022]
Abstract
This study presents an ultra-sensitive technique for the electrochemical detection of the mutated BRAF gene associated with papillary thyroid carcinomas (PTC). In the proposed approach, a biotinylated 30-nucleotides probe DNA was immobilized in a streptavidin-modified 96-well microtiter plate and the free active sites of the streptavidin were blocked using biotinylated bovine serum albumin (BSA). The biotinylated target DNA was then added and allowed to hybridize with the immobilized probe DNA for 30min. Subsequently, streptavidin-labeled gold nanoparticles were added, and a nanoparticle enlargement process was performed using gold ion solution and formaldehyde reductant. The gold particles were then dissolved in bromide and DNA hybridization detection process was performed using a square wave stripping voltammetry (SWSV) technique. The results indicated a stable SWSV response in differential detection between blank solution and target DNA solution with a concentration of 130aM. Moreover, the coefficient of determination (R(2)) of the semi-log plot of the SWSV response current against the target DNA concentration (0.52-1300aM) was found to be 0.9982. The detection limit was estimated to be 0.35aM (based on a signal-to-noise ratio of 3:1). This value was approximately three orders of magnitude lower than that obtained using the same method but without gold amplification process. Finally, the proposed approach is successful in differentiating between the mutant and wildtype BRAF sequences that are present in genuine 224-nucleotides DNA.
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Zhang P, Chu X, Xu X, Shen G, Yu R. Electrochemical detection of point mutation based on surface ligation reaction and biometallization. Biosens Bioelectron 2007; 23:1435-41. [PMID: 18242973 DOI: 10.1016/j.bios.2007.12.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 12/10/2007] [Accepted: 12/13/2007] [Indexed: 12/20/2022]
Abstract
A highly sensitive electrochemical method for point mutation detection based on surface enzymatic ligation reaction and biometallization is demonstrated. In this method the surface-immobilized allele-specific probe, complementary to the mutant target, undergoes allele-specific ligation with the 5'-phosphorylated ligation probe in the presence of the mutant oligonucleotide target and E. coli DNA ligase. If there is an allele mismatch, no ligation takes place. After thermal treatment at 90 degrees C, the formed duplex melts apart, which merely allows the ligation product to remain on the electrode surface. Then, biotinylated detection probes hybridize with the ligation product. With the binding of streptavidin-alkaline phosphatase (SA-ALP) to the biotinylated probes, a non-reductive substrate of alkaline phosphatase, ascorbic acid 2-phosphate (AA-P), can be converted into ascorbic acid (AA) at the electrode surface. Silver ions in solution are then reduced by AA, resulting in the deposition of silver metal onto the electrode surface. Linear sweep voltammetry (LSV) is used to detect the amount of deposited silver. The proposed approach has been successfully implemented for the identification of single base mutation in codon 12 of K-ras oncogene target with a detection limit of 80fM, demonstrating that this method provides a highly specific, sensitive and cost-efficient approach for point mutation detection.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Chemo/Bio-sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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Kumamoto S, Watanabe M, Kawakami N, Nakamura M, Yamana K. 2'-anthraquinone-conjugated oligonucleotide as an electrochemical probe for DNA mismatch. Bioconjug Chem 2007; 19:65-9. [PMID: 17988077 DOI: 10.1021/bc070097f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We previously prepared the oligonucleotides (ODNs) conjugated to an anthraquinone (AQ) group via one carbon linker at the 2'-sugar position. When these modified ODNs bind to cDNA sequences, the AQ moiety can be intercalated into the predetermined base-pair pocket of a duplex DNA. In this paper, 2'-AQ-modified ODNs are shown to be an excellent electrochemical probe to clarify the effect of a mismatch base on the charge transfer (CT) though DNA. Two types of DNA-modified electrodes were constructed by assembly of disulfide-terminated 2'-AQ-ODN duplexes onto gold electrodes. One type of electrodes (system I) contains fully matched base pairs or a single-base mismatch in duplex DNA between the redox center and the electrode. The other (system II) consists of the mismatch but at the outside of the redox center. The modified electrodes were analyzed by cyclic voltammetry to estimate the CT rate through duplex DNA. In system I, the CT rate was found to be approximately 50 s (-1) for the fully matched AQ-ODN duplexes, while the CT rates of the mismatched DNA were considerably slower than that of the fully matched DNA. In system II, the AQ-ODN duplexes showed almost similar CT rates ( approximately 50 s (-1)) for the fully matched DNA and for the mismatched DNAs. The detection of a single-base mismatch was then performed by chronocoulometry (CC). All the DNA duplexes containing a mismatch base in system I gave the reduced electrochemical responses when compared to the fully matched DNA. In particular, the mismatched DNAs including G--A mismatch can be differentiated from fully matched DNA without using any electrochemical catalyst. We further tested the usefulness of single-stranded (ss) AQ-ODN immobilized on a gold electrode in the electrochemical detection of a single-base mismatch through hybridization assay. The ss-AQ-ODN electrodes were immersed in target-containing buffer at room temperature, and the CC measurements were carried out to see the changes in the integrated charge. Within 60 min, the mismatched DNA was clearly distinguishable by the CC differences from the fully matched target. Thus, the electrochemical hybridization assay provides an easy and convenient detection for DNA mutation that does not require any extra reagents, catalyst, target labeling, and washing steps.
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Affiliation(s)
- Satoshi Kumamoto
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2201, Japan
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González-García MB, Fernández-Abedul MT, Costa-García A. Chapter 26 Thick- and thin-film DNA sensors. ELECTROCHEMICAL SENSOR ANALYSIS 2007. [PMCID: PMC7148874 DOI: 10.1016/s0166-526x(06)49026-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The use of thick- and thin film electrodes as supports for genosensor devices offers enormous opportunities for their application in molecular diagnosis. The technologies used in the fabrication of both thick- and thin-film electrodes allow the mass production of reproducible, inexpensive and mechanically robust strip solid electrodes. Other important advantages of these electrodes are the possibility of miniaturization as well as their ease of manipulation in a disposable manner and therefore the use of small volumes. To detect transcriptional profiling and single nucleotide polymorphism thin-film arrays of 14, 20, 25, 48, and 64 electrodes have been fabricated, using lithographic techniques. Readout systems for these arrays based on electrical detection have also been developed. Moreover, a thick-film sensor array suitable for automation combined to readout based on intermittent pulse amperometry (IPA) has been commercialized. These genosensors and the readout instruments provide a simple, accurate and inexpensive platform for patient diagnosis. It is more than probable that arrays for 50–100 DNA sequences will be needed for some clinical applications. Although it is not difficult to design electrode pads with reproducible dimensions of a micron or less, the electrochemical readout requires mechanical connections to each individual electrode.
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Urata T, Takahashi N, Hakamata Y, Iijima Y, Kuwahara N, Ozaki N, Ono Y, Amano M, Inada T. Gene-gene interaction analysis of personality traits in a Japanese population using an electrochemical DNA array chip analysis. Neurosci Lett 2006; 414:209-12. [PMID: 17208375 DOI: 10.1016/j.neulet.2006.12.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 12/01/2006] [Accepted: 12/14/2006] [Indexed: 11/24/2022]
Abstract
It has been suggested that genes involved in the central dopaminergic pathway may contribute to personality traits. However, the results of association studies for these genes have not been consistent. The present study investigated the relationship between the specific polymorphisms of MAO-A, COMT, DRD2, DRD3 and personality traits in Japanese women using a novel genotyping method involving electrochemical DNA array (ECA) chip analysis. Single marker association analysis for each mutation revealed no significant association between scores for Neuroticism Extraversion Openness-Five Factor Inventory (NEO-FFI) items. Gene-gene interaction analysis showed that a MAO-A 30-bp repeatxCOMT (Val158Met)xDRD3 (Ser9Gly) had a marginally significant association with Agreeableness (P=0.0547). The present results suggest that a combination of polymorphisms of MAO-A, COMT, and DRD3 might affect personality traits in Japanese women.
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Akagi Y, Makimura M, Yokoyama Y, Fukazawa M, Fujiki S, Kadosaki M, Tanino K. Development of a ligation-based impedimetric DNA sensor for single-nucleotide polymorphism associated with metabolic syndrome. Electrochim Acta 2006. [DOI: 10.1016/j.electacta.2006.04.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Sato S, Hokazono K, Irie T, Ueki T, Waki M, Nojima T, Kondo H, Takenaka S. Ferrocenylnaphthalene diimide-based electrochemical detection of methylated gene. Anal Chim Acta 2006; 578:82-7. [PMID: 17723697 DOI: 10.1016/j.aca.2006.04.056] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 04/13/2006] [Accepted: 04/20/2006] [Indexed: 11/21/2022]
Abstract
Ferrocenylnaphthalene diimide (FND)-based electrochemical hybridization assay was applied to the detection of methylated cytosine of DNA using the products obtained after treatment with bisulfite followed by polymerase chain reaction (PCR), where unmethylated cytosine is converted to thymine and methylated one to cytosine. Twenty-meric DNA probes for the methylated (cytosine) and unmethylated (thymine) types of the part of the promoter region of cyclin D-dependent protein kinase inhibitor, p16, gene (p16(Ink4a)) were used to be immobilized on the electrochemical array (ECA) chip. Using 1 microL of 10 ng/microL of methylated sample obtained from the methylation-specific PCR of methylated genome containing 10-times excess of unmethylated one, the methylated PCR sample could be detected by the identical electrochemical signals from the two DNA probes under the settled optimum hybridization conditions.
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Affiliation(s)
- Shinobu Sato
- Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka 820-8502, Japan
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Abad-Valle P, Fernández-Abedul MT, Costa-García A. DNA single-base mismatch study with an electrochemical enzymatic genosensor. Biosens Bioelectron 2006; 22:1642-50. [PMID: 16950611 PMCID: PMC7127251 DOI: 10.1016/j.bios.2006.07.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Revised: 07/11/2006] [Accepted: 07/13/2006] [Indexed: 11/28/2022]
Abstract
A thorough selectivity study of DNA hybridization employing an electrochemical enzymatic genosensor is discussed here. After immobilizing on a gold film a 30-mer 3′-thiolated DNA strand, hybridization with a biotinylated complementary one takes place. Then, alkaline phosphatase is incorporated to the duplex through the interaction streptavidin–biotin. Enzymatic generation of indigo blue from 3-indoxyl phosphate and subsequent electrochemical detection was made. The influence of hybridization conditions was studied in order to better discern between fully complementary and mismatched strands. Detection of 3, 2 and 1 mismatch was possible. The type and location of the single-base mismatch, as well as the influence of the length of the strands was studied too. Mutations that suppose displacement of the reading frame were also considered. The effect of the concentration on the selectivity was tested, resulting a highly selective genosensor with an adequate sensitivity and stability.
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Affiliation(s)
- Patricia Abad-Valle
- Departamento de Química Física y Analítica, Universidad de Oviedo, Asturias, Spain
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Okamoto A, Kamei T, Saito I. DNA hole transport on an electrode: application to effective photoelectrochemical SNP typing. J Am Chem Soc 2006; 128:658-62. [PMID: 16402854 DOI: 10.1021/ja057040t] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A useful feature of DNA is that long-range hole transport through DNA is readily achieved. Photostimulated long-range hole transport through DNA has prospective use in the development of a conceptually new electrochemical single-nucleotide polymorphism (SNP) typing method for use as a versatile platform for gene diagnostics and pharmacogenetics. We have applied artificial DNAs designed for photostimulated long-range hole transport through DNA to SNP typing. By hybridizing photosensitizer-equipped DNA probes, immobilized on gold working electrodes, with a target DNA strand containing an SNP site, we observed a cathodic photocurrent, which markedly changed depending on the nature of the base at the specific site. The use of a combination of hole-transporting bases constitutes a very powerful method for a single-step electrochemical assay applicable to SNP typing of all types of sequences.
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Affiliation(s)
- Akimitsu Okamoto
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Japan.
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Mukumoto K, Nojima T, Takenaka S. Synthesis of ferrocenylcarbodiimide as a convenient electrochemically active labeling reagent for nucleic acids. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.09.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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36
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Altshuler IM, Zhulidov PA, Bogdanova EA, Mudrik NN, Shagin DA. Application of the Duplex-Specific Nuclease Preference Method to the Analysis of Single Nucleotide Polymorphisms in Human Genes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2005. [DOI: 10.1007/s11171-005-0078-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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