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Goodchild SA, Gao R, Shenton DP, McIntosh AJS, Brown T, Bartlett PN. Direct Detection and Discrimination of Nucleotide Polymorphisms Using Anthraquinone Labeled DNA Probes. Front Chem 2020; 8:381. [PMID: 32478035 PMCID: PMC7235368 DOI: 10.3389/fchem.2020.00381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/14/2020] [Indexed: 02/04/2023] Open
Abstract
A novel electrochemical detection approach using DNA probes labeled with Anthraquinone (AQ) as a reporter moiety has been successfully exploited as a method for the direct detection of DNA targets. This assay uses simple voltammetry techniques (Differential Pulse Voltammetry) to exploit the unique responsiveness of AQ to its chemical environments within oxygenated aqueous buffers, providing a specific detection mechanism as a result of DNA hybridization. This measurement is based on a cathodic shift of the reduction potential of the AQ tag and the concurrent reduction in peak current upon DNA binding. The further utility of this approach for discrimination of closely related DNA targets is demonstrated using DNA strands specific to B. anthracis and closely related bacillus species. DNA targets were designed to the rpoB gene incorporating nucleotide polymorphisms associated with different bacillus species. This assay was used to demonstrate that the shift in reduction potential is directly related to the homology of the target DNA. The discriminatory mechanism is dependent on the presence of oxygen in the measurement buffer and is strongly linked to the position of the nucleotide polymorphisms; with homology at the terminus carrying the AQ functionalised nucleotide critical to achieving accurate discrimination. This understanding of assay design was used to demonstrate an optimized assay capable of discriminating between Yersinia pestis (the causative agent of plague) and closely related species based on the groEL gene. This method is attractive as it can not only detect DNA binding, but can also discriminate between multiple Single Nucleotide Polymorphisms (SNPs) within that DNA without the need for any additional reagents, reporters, or processes such as melting of DNA strands. This indicates that this approach may have great potential to be exploited within novel biosensors for detection and diagnosis of infectious disease in future Point of Care (PoC) devices.
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Affiliation(s)
- Sarah A Goodchild
- Defence Science and Technology Laboratory, Salisbury, United Kingdom.,University of Southampton, Southampton, United Kingdom
| | - Rachel Gao
- University of Southampton, Southampton, United Kingdom
| | - Daniel P Shenton
- Defence Science and Technology Laboratory, Salisbury, United Kingdom
| | | | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Philip N Bartlett
- Defence Science and Technology Laboratory, Salisbury, United Kingdom
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Electrochemical reduction, radical anions and solvation energies of 1,2,3,4-tetrafluoro-9,10-anthraquinone and its N -piperidyl derivatives in DMF and DMF–water mixtures. MENDELEEV COMMUNICATIONS 2018. [DOI: 10.1016/j.mencom.2018.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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3
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Ferrocene conjugated oligonucleotide for electrochemical detection of DNA base mismatch. Bioorg Med Chem Lett 2017; 27:3555-3557. [PMID: 28583799 DOI: 10.1016/j.bmcl.2017.05.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/01/2017] [Accepted: 05/16/2017] [Indexed: 01/25/2023]
Abstract
We describe the synthesis, binding, and electrochemical properties of ferrocene-conjugated oligonucleotides (Fc-oligos). The key step for the preparation of Fc-oligos contains the coupling of vinylferrocene to 5-iododeoxyuridine via Heck reaction. The Fc-conjugated deoxyuridine phosphoramidite was used in the Fc-oligonucleotide synthesis. We show that thiol-modified Fc-oligos deposited onto gold electrodes possess potential ability in electrochemical detection of DNA base mismatch.
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Duprey JLHA, Carr-Smith J, Horswell SL, Kowalski J, Tucker JHR. Macrocyclic Metal Complex-DNA Conjugates for Electrochemical Sensing of Single Nucleobase Changes in DNA. J Am Chem Soc 2016; 138:746-9. [PMID: 26694542 DOI: 10.1021/jacs.5b11319] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The direct incorporation of macrocyclic cyclidene complexes into DNA via automated synthesis results in a new family of metal-functionalized DNA derivatives that readily demonstrate their utility through the ability of one redox-active copper(II)-containing strand to distinguish electrochemically between all four canonical DNA nucleobases at a single site within a target sequence of DNA.
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Affiliation(s)
- Jean-Louis H A Duprey
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
| | - James Carr-Smith
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
| | - Sarah L Horswell
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
| | - Jarosław Kowalski
- Insitute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - James H R Tucker
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
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Kongpeth J, Jampasa S, Chaumpluk P, Chailapakul O, Vilaivan T. Immobilization-free electrochemical DNA detection with anthraquinone-labeled pyrrolidinyl peptide nucleic acid probe. Talanta 2015; 146:318-25. [PMID: 26695270 DOI: 10.1016/j.talanta.2015.08.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/25/2015] [Accepted: 08/26/2015] [Indexed: 01/04/2023]
Abstract
Electrochemical detection provides a simple, rapid, sensitive and inexpensive method for DNA detection. In traditional electrochemical DNA biosensors, the probe is immobilized onto the electrode. Hybridization with the DNA target causes a change in electrochemical signal, either from the intrinsic signal of the probe/target or through a label or a redox indicator. The major drawback of this approach is the requirement for probe immobilization in a controlled fashion. In this research, we take the advantage of different electrostatic properties between PNA and DNA to develop an immobilization-free approach for highly sequence-specific electrochemical DNA sensing on a screen-printed carbon electrode (SPCE) using a square-wave voltammetric (SWV) technique. Anthraquinone-labeled pyrrolidinyl peptide nucleic acid (AQ-PNA) was employed as a probe together with an SPCE that was modified with a positively-charged polymer (poly quaternized-(dimethylamino-ethyl)methacrylate, PQDMAEMA). The electrostatic attraction between the negatively-charged PNA-DNA duplex and the positively-charged modified SPCE attributes to the higher signal of PNA-DNA duplex than that of the electrostatically neutral PNA probe, resulting in a signal change. The calibration curve of this proposed method exhibited a linear range between 0.35 and 50 nM of DNA target with a limit of detection of 0.13 nM (3SD(blank)/Slope). The sub-nanomolar detection limit together with a small sample volume required (20 μL) allowed detection of <10 fmol (<1 ng) of DNA. With the high specificity of the pyrrolidinyl PNA probe used, excellent discrimination between complementary and various single-mismatched DNA targets was obtained. An application of this new platform for a sensitive and specific detection of isothermally-amplified shrimp's white spot syndrome virus (WSSV) DNA was successfully demonstrated.
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Affiliation(s)
- Jutatip Kongpeth
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Sakda Jampasa
- Program in Petrochemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Piyasak Chaumpluk
- Laboratory of Plant Transgenic Technology and Biosensor, Department of Botany, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Orawon Chailapakul
- Electrochemistry and Optical Spectroscopy Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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Ahmad K, Shah AH, Adhikari B, Rana UA, uddin SN, Vijayaratnam C, Muhammad N, Shujah S, Rauf A, Hussain H, Badshah A, Qureshi R, Kraatz HB, Shah A. pH-dependent redox mechanism and evaluation of kinetic and thermodynamic parameters of a novel anthraquinone. RSC Adv 2014. [DOI: 10.1039/c4ra04462b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The pH-dependent oxidation of a novel anthraquinone was investigated and several important kinetic and thermodynamic parameters were determined.
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Affiliation(s)
- Khurshid Ahmad
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad, Pakistan
| | | | - Bimalendu Adhikari
- Department of Physical and Environmental Sciences
- University of Toronto Scarborough
- Toronto, Canada
| | - Usman Ali Rana
- Deanship of Scientific Research
- College of Engineering
- King Saud University
- Riyadh 11421, Saudi Arabia
| | - Syed Noman uddin
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad, Pakistan
| | - Chandrika Vijayaratnam
- Department of Physical and Environmental Sciences
- University of Toronto Scarborough
- Toronto, Canada
| | - Niaz Muhammad
- Department of Chemistry
- Abdul Wali Khan University Mardan
- Pakistan
| | - Shaukat Shujah
- Department of Chemistry
- Kohat University of Science & Technology
- Kohat, Pakistan
| | - Abdur Rauf
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad, Pakistan
| | - Hidayat Hussain
- UoN Chair of Oman’s Medicinal Plants and Marine Natural Products
- University of Nizwa
- Nizwa 616, Sultanate of Oman
| | - Amin Badshah
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad, Pakistan
| | - Rumana Qureshi
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad, Pakistan
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences
- University of Toronto Scarborough
- Toronto, Canada
| | - Afzal Shah
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad, Pakistan
- Department of Physical and Environmental Sciences
- University of Toronto Scarborough
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Abi A, Ferapontova EE. Unmediated by DNA Electron Transfer in Redox-Labeled DNA Duplexes End-Tethered to Gold Electrodes. J Am Chem Soc 2012; 134:14499-507. [DOI: 10.1021/ja304864w] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Alireza Abi
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds Vej 1590-14, DK-8000
Aarhus C, Denmark
| | - Elena E. Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Aarhus University, Gustav Wieds Vej 1590-14, DK-8000
Aarhus C, Denmark
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9
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Sun T, Zhang H, Yan H, Li J, Cheng G, Hao A, Qiao H, Xin F. Sensitive fluorescent vesicles based on the supramolecular inclusion of β-cyclodextrins withN-alkylamino-l-anthraquinone. Supramol Chem 2011. [DOI: 10.1080/10610278.2010.514614] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Tao Sun
- a Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , 250100 , P.R. China
| | - Huacheng Zhang
- a Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , 250100 , P.R. China
| | - Hui Yan
- a Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , 250100 , P.R. China
| | - Jianye Li
- a Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , 250100 , P.R. China
| | - Guanghui Cheng
- b Department of Medical Genetics and Key Laboratory for Experimental Teratology, Ministry of Education , Shandong University , Jinan , 250012 , P.R. China
| | - Aiyou Hao
- a Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , 250100 , P.R. China
| | - Hongwei Qiao
- c Shandong Shengquan Chemical Co., Ltd , Jinan , 250204 , P.R. China
| | - Feifei Xin
- a Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , 250100 , P.R. China
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Sun T, Li Y, Zhang H, Li J, Xin F, Kong L, Hao A. pH-reversible vesicles based on the “supramolecular amphiphilies” formed by cyclodextrin and anthraquinone derivate. Colloids Surf A Physicochem Eng Asp 2011. [DOI: 10.1016/j.colsurfa.2010.11.067] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Nasirizadeh N, Zare HR, Pournaghi-Azar MH, Hejazi MS. Introduction of hematoxylin as an electroactive label for DNA biosensors and its employment in detection of target DNA sequence and single-base mismatch in human papilloma virus corresponding to oligonucleotide. Biosens Bioelectron 2010; 26:2638-44. [PMID: 21146975 DOI: 10.1016/j.bios.2010.11.026] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Accepted: 11/17/2010] [Indexed: 01/21/2023]
Abstract
For the detection of DNA hybridization, a new electrochemical biosensor was developed on the basis of the interaction of hematoxylin with 20-mer deoxyoligonucleotides (from human papilloma virus, HPV). The study was performed based on the interaction of hematoxylin with an alkanethiol DNA probe self-assembled gold electrode (ss-DNA/AuE) and its hybridization form (ds-DNA/AuE). The optimum conditions were found for the immobilization of HPV probe on the gold electrode (AuE) surface and its hybridization with the target DNA. Electrochemical detection of the self-assembled DNA and the hybridization process were performed by cyclic voltammetry (CV) and differential pulse voltammetry (DPV) over the potential range where the accumulated hematoxylin at the modified electrode was electroactive. Observing a remarkable difference between the voltammetric signals of the hematoxylin obtained from different hybridization samples (non-complementary, mismatch and complementary DNAs), we confirmed the potential of the developed biosensor in detecting and discriminating the target complementary DNA from non-complementary and mismatch oligonucleotides. Under optimum conditions, the electrochemical signal had a linear relationship with the concentration of the target DNA ranging from 12.5 nM to 350.0 nM, and the detection limit was 3.8 nM.
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Affiliation(s)
- Navid Nasirizadeh
- Department of Chemistry, Yazd University, P.O. Box 89195-741, Yazd, Iran
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Affiliation(s)
- Joseph C. Genereux
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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Kaczmarek O, Scheidt HA, Bunge A, Föse D, Karsten S, Arbuzova A, Huster D, Liebscher J. 2′-Linking of Lipids and Other Functions to Uridine through 1,2,3-Triazoles and Membrane Anchoring of the Amphiphilic Products. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Maie K, Miyagi K, Takada T, Nakamura M, Yamana K. RNA-mediated electron transfer: double exponential distance dependence. J Am Chem Soc 2010; 131:13188-9. [PMID: 19754178 DOI: 10.1021/ja902647j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the long-range excess electron transfer through RNA duplexes consisting of a pyrene electron donor and a nitrobenzene electron acceptor that shows double exponential distance dependence.
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Affiliation(s)
- Kenji Maie
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji 671-2201, Japan
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15
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Jin X, Fei Y, Zhang L, Liu X, Shen G, Yu R. An electrochemical molecular switch for one-step, reusable detection of a single-base mutation of DNA. Analyst 2009; 135:121-6. [PMID: 20024191 DOI: 10.1039/b911672a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new strategy for one-step, reusable and sensitive detection of a single-base mutation based on an electrochemical molecular switch is developed in the present work. When the hybridization reaction takes place in the presence of target DNA, the Fc-labeled terminal of the open switch molecule can be captured by the probe through the predesigned complementary bases of both sequences. By this method, a signal-on sensor featuring both generalizability and simplicity towards reagentless detection of DNA with sensitivity and selectivity electrochemical system is built on. The approach had been demonstrated with the identification of a single-base mutation of alpha-thalassemia point mutation in Hb Constant Spring codon 142 (TAA --> CAA). The wild-type and mutant-type of the synthetic 16 mer DNA sequences as the model targets were successfully discriminated. The results showed that the response signal was linear to the logarithm of the target concentration in the range from 0.01 to 100 pM with a detection limit of 0.01 pM. The regeneration experiment demonstrated that the sensor interface can be easily and successfully regenerated. All these revealed that the present system is a promising candidate for single-base mutation discrimination.
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Affiliation(s)
- Xiaoyong Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Chemistry and Chemical Engineering College, Hunan University, Changsha 410082, PR China.
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Mahajan S, Richardson J, Gaied N, Zhao Z, Brown T, Bartlett P. The Use of an Electroactive Marker as a SERS Label in anE-melting Mutation Discrimination Assay. ELECTROANAL 2009. [DOI: 10.1002/elan.200904681] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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17
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Abou-Elkhair RAI, Dixon DW, Netzel TL. Synthesis and Electrochemical Evaluation of Conjugates between 2′-Deoxyadenosine and Modified Anthraquinone: Probes for Hole-Transfer Studies in DNA. J Org Chem 2009; 74:4712-9. [DOI: 10.1021/jo900306g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Dabney W. Dixon
- Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302-4098
| | - Thomas L. Netzel
- Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302-4098
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Watanabe M, Kumamoto S, Nakamaura M, Yamana K. Electronic detection of DNA mutation based on strand exchange reaction. Bioorg Med Chem 2009; 17:1494-7. [DOI: 10.1016/j.bmc.2009.01.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 01/07/2009] [Accepted: 01/08/2009] [Indexed: 12/25/2022]
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Jacobsen MF, Ferapontova EE, Gothelf KV. Synthesis and electrochemical studies of an anthraquinone-conjugated nucleoside and derived oligonucleotides. Org Biomol Chem 2009; 7:905-8. [PMID: 19225673 DOI: 10.1039/b816820b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The synthesis of a 2'-deoxyuridine nucleoside linked to an anthraquinone moiety, and its incorporation into oligonucleotides are described, including a facile oxidative demethylation with phenyliodine(iii) bis(trifluoroacetate) to reveal the anthraquinone motif. Furthermore, some useful physical and electrochemical properties of the obtained oligonucleotide are also reported, which allow its principal use in electrochemical DNA assays.
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Affiliation(s)
- Mikkel F Jacobsen
- Danish National Research Foundation: Centre for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the Department of Chemistry, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark
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Won BY, Shin SC, Chung WY, Shin S, Cho DY, Park HG. Mismatch DNA-specific enzymatic cleavage employed in a new method for the electrochemical detection of genetic mutations. Chem Commun (Camb) 2009:4230-2. [DOI: 10.1039/b907268c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Boussicault F, Robert M. Electron Transfer in DNA and in DNA-Related Biological Processes. Electrochemical Insights. Chem Rev 2008; 108:2622-45. [DOI: 10.1021/cr0680787] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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