1
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Kanso H, Ben Jrad A, Inguimbert N, Rammal W, Philouze C, Thomas F, Noguer T, Calas-Blanchard C. Synthesis and Characterization of Bis-1,2,3-Triazole Ligand and its Corresponding Copper Complex for the Development of Electrochemical Affinity Biosensors. Chemistry 2021; 27:9580-9588. [PMID: 33822403 DOI: 10.1002/chem.202100250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Indexed: 12/11/2022]
Abstract
The bis-triazole ligand and its corresponding copper complexes were synthesized and characterized for the first time and proposed as new labels for the development of electrochemical aptasensors. The bis-triazole ligand was prepared from methyl 1,6-heptadiyne-4-carboxylate and 2-(azidomethyl)phenol using classical CuAAC in presence of different copper salts. The X-ray structure of bis-triazole showed a symmetry center (C1). UV-Vis and X-band EPR spectra showed that the coordination capacity of the bis-triazole ligand was improved in the presence of triethylamine due to deprotonation of the triazole and phenolate moieties. After complexation with copper, the obtained complex was successfully attached to an anti-estradiol aptamer through thiol-maleimide coupling, and the resulting labelled aptamer was immobilized on a carbon screen-printed electrode by carbodiimide coupling. The electrochemical response of the resulting sensor was shown to decrease in the presence of estradiol, demonstrating that the developed complexes can be applied for the development of aptasensors.
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Affiliation(s)
- Hussein Kanso
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, 66860, Perpignan, France.,Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France.,Faculté de Médecine Dentaire, Université Libanaise, Campus Rafic Hariri, Hadath, Liban
| | - Amani Ben Jrad
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, 66860, Perpignan, France.,Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Nicolas Inguimbert
- Centre de Recherche Insulaire et Observatoire de l'Environnement (CRIOBE), USR CNRS 3278, Université de Perpignan Via Domitia, Bâtiment T, 58 avenue P. Alduy, 66860, Perpignan, France
| | - Wassim Rammal
- Faculté des Sciences, Université Libanaise Section V, Nabatieh, Liban
| | - Christian Philouze
- Département de Chimie Moléculaire, UMR-5250 CNRS, Université de Grenoble Alpes, B.P. 53, 38041, Grenoble Cedex 9, France
| | - Fabrice Thomas
- Département de Chimie Moléculaire, UMR-5250 CNRS, Université de Grenoble Alpes, B.P. 53, 38041, Grenoble Cedex 9, France
| | - Thierry Noguer
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, 66860, Perpignan, France.,Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Carole Calas-Blanchard
- Biocapteurs-Analyses-Environnement, Université de Perpignan Via Domitia, 66860, Perpignan, France.,Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
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2
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Kodr D, Yenice CP, Simonova A, Saftić DP, Pohl R, Sýkorová V, Ortiz M, Havran L, Fojta M, Lesnikowski ZJ, O'Sullivan CK, Hocek M. Carborane- or Metallacarborane-Linked Nucleotides for Redox Labeling. Orthogonal Multipotential Coding of all Four DNA Bases for Electrochemical Analysis and Sequencing. J Am Chem Soc 2021; 143:7124-7134. [PMID: 33929195 DOI: 10.1021/jacs.1c02222] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report a series of 2'-deoxyribonucleoside triphosphates bearing dicarba-nido-undecaborate ([C2B9H11]1-), [3,3'-iron-bis(1,2-dicarbollide)]- (FESAN, [Fe(C2B9H11)2]2-) or [3,3'-cobalt-bis(1,2-dicarbollide)]- (COSAN, [Co(C2B9H11)2]2-) groups prepared either through the Sonogashira cross-coupling or the CuAAC click reaction. The modified dNXTPs were substrates for KOD XL DNA polymerase in enzymatic synthesis of modified DNA through primer extension (PEX). The nido-carborane- and FESAN-modified nucleotides gave analytically useful oxidation signals in square-wave voltammetry and were used for redox labeling of DNA. The redox-modified DNA probes were prepared by PEX using tailed primers and were hybridized to electrode (gold or glassy carbon) containing capture oligonucleotides. The combination of nido-carborane- and FESAN-linked nucleotides with 7-ferrocenylethynyl-7-deaza-dATP and 7-deaza-dGTP allowed polymerase synthesis of DNA fully modified at all four nucleobases, and each of the redox labels gave four differentiable and ratiometric signals in voltammetry. Thus, the combination of these four redox labels constitutes the first fully orthogonal redox coding of all four canonical nucleobases, which can be used for determination of nucleobase composition of short DNA stretches in one simple PEX experiment with electrochemical readout.
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Affiliation(s)
- David Kodr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Cansu Pinar Yenice
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007 Tarragona, Spain
| | - Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
| | - Dijana Pavlović Saftić
- Laboratory of Medicinal Chemistry, Institute of Medical Biology PAS, Lodowa 106, 92-232 Łódź, Poland
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Mayreli Ortiz
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007 Tarragona, Spain
| | - Ludĕk Havran
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Zbigniew J Lesnikowski
- Laboratory of Medicinal Chemistry, Institute of Medical Biology PAS, Lodowa 106, 92-232 Łódź, Poland
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007 Tarragona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010, Barcelona, Spain
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
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3
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Shundrin LA, Os’kina IA, Irtegova IG, Poveshchenko AF. 9H-Thioxanthen-9-one S,S-dioxide based redox active labels for electrochemical detection of DNA duplexes immobilized on Au electrodes. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Simonova A, Magriñá I, Sýkorová V, Pohl R, Ortiz M, Havran L, Fojta M, O'Sullivan CK, Hocek M. Tuning of Oxidation Potential of Ferrocene for Ratiometric Redox Labeling and Coding of Nucleotides and DNA. Chemistry 2020; 26:1286-1291. [PMID: 31725178 PMCID: PMC7384099 DOI: 10.1002/chem.201904700] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Indexed: 12/21/2022]
Abstract
Three sets of 7‐deazaadenine and cytosine nucleosides and nucleoside triphosphates bearing either unsubstituted ferrocene, octamethylferrocene and ferrocenecarboxamide linked through an alkyne tether to position 7 or 5, respectively, were designed and synthesized. The modified dNFcXTPs were good substrates for KOD XL DNA polymerase in primer extension and were used for enzymatic synthesis of redox‐labelled DNA probes. Square‐wave voltammetry showed that the octamethylferrocene oxidation potential was shifted to lower values, whilst the ferrocenecarboxamide was shifted to higher potentials, as compared to ferrocene. Tailed PEX products containing different ratios of Fc‐labelled A (dAFc) and FcPa‐labelled C (dCFcPa) were synthesized and hybridized with capture oligonucleotides immobilized on gold electrodes to study the electrochemistry of the redox‐labelled DNA. Clearly distinguishable, fully orthogonal and ratiometric peaks were observed for the dAFc and dCFcPa bases in DNA, demonstrating their potential for use in redox coding of nucleobases and for the direct electrochemical measurement of the relative ratio of nucleobases in an unknown sequence of DNA.
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Affiliation(s)
- Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2, 12843, Czech Republic
| | - Ivan Magriñá
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 16610, Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 16610, Prague 6, Czech Republic
| | - Mayreli Ortiz
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Luděk Havran
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010, Barcelona, Spain
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2, 12843, Czech Republic
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5
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Silva SM, Hoque S, Gonçales VR, Gooding JJ. The Impact of the Position of the Redox Label on Charge Transfer and Hybridization Efficiency at DNA Interfaces. ELECTROANAL 2018. [DOI: 10.1002/elan.201800197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Saimon Moraes Silva
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology; The University of New South Wales; Sydney 2052 Australia
| | - Sharmin Hoque
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology; The University of New South Wales; Sydney 2052 Australia
| | - Vinicius R. Gonçales
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology; The University of New South Wales; Sydney 2052 Australia
| | - J. Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology; The University of New South Wales; Sydney 2052 Australia
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6
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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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7
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Simonova A, Havran L, Pohl R, Fojta M, Hocek M. Phenothiazine-linked nucleosides and nucleotides for redox labelling of DNA. Org Biomol Chem 2018; 15:6984-6996. [PMID: 28792547 DOI: 10.1039/c7ob01439b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nucleosides and 2'-deoxyribonucleoside triphosphates (dNTPs) bearing phenothiazine (PT) attached to a nucleobase (cytosine or 7-deazaadenine) either directly or through an acetylene linker were prepared through Suzuki or Sonogashira cross-coupling and triphosphorylation, and were studied as building blocks for polymerase construction of modified DNA. The directly PT-substituted dNTPs were better substrates for polymerases than the alkyne-linked dNTPs but all of them were used in enzymatic synthesis of DNA using primer extension, nicking enzyme amplification, PCR or 3'-tail labelling by terminal deoxynucleotidyl transferase. The phenothiazine served as an oxidizable redox label (giving two analytically useful signals of oxidation on electrode) for nucleosides and DNA and was also used in orthogonal combination with previously developed benzofurazane or nitrophenyl labels for redox coding of DNA bases. Therefore, the title PT-linked dNTPs are useful additions to the portfolio of nucleotides for enzymatic synthesis of redox-labelled DNA for electrochemical analysis.
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Affiliation(s)
- Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
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8
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Silva SM, Tavallaie R, Gonçales VR, Utama RH, Kashi MB, Hibbert DB, Tilley RD, Gooding JJ. Dual Signaling DNA Electrochemistry: An Approach To Understand DNA Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1249-1255. [PMID: 29345941 DOI: 10.1021/acs.langmuir.7b02787] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Electrochemical DNA biosensors composed of a redox marker modified nucleic acid probe tethered to a solid electrode is a common experimental construct for detecting DNA and RNA targets, proteins, inorganic ions, and even small molecules. This class of biosensors generally relies on the binding-induced conformational changes in the distance of the redox marker relative to the electrode surface such that the charge transfer is altered. The conventional design is to attach the redox species to the distal end of a surface-bound nucleic acid strand. Here we show the impact of the position of the redox marker, whether on the distal or proximal end of the DNA monolayer, on the DNA interface electrochemistry. Somewhat unexpectedly, greater currents were obtained when the redox molecules were located on the distal end of the surface-bound DNA monolayer, notionally furthest away from the electrode, compared with currents when the redox species were located on the proximal end, close to the electrode. Our results suggest that a limitation in ion accessibility is the reason why smaller currents were obtained for the redox markers located at the bottom of the DNA monolayer. This understanding shows that to allow the quantification of the amount of redox labeled target DNA strand that hybridizes to probe DNA immobilized on the electrode surface, the redox species must be on the distal end of the surface-bound duplex.
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Affiliation(s)
- Saimon Moraes Silva
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales , Sydney 2052, Australia
| | - Roya Tavallaie
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales , Sydney 2052, Australia
| | - Vinicius R Gonçales
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales , Sydney 2052, Australia
| | - Robert H Utama
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales , Sydney 2052, Australia
| | - Mehran B Kashi
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales , Sydney 2052, Australia
| | - D Brynn Hibbert
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales , Sydney 2052, Australia
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales , Sydney 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales , Sydney 2052, Australia
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9
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Debela AM, Thorimbert S, Hasenknopf B, O'Sullivan CK, Ortiz M. Electrochemical primer extension for the detection of single nucleotide polymorphisms in the cardiomyopathy associated MYH7 gene. Chem Commun (Camb) 2016; 52:757-9. [PMID: 26567828 DOI: 10.1039/c5cc07762a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We report the labelling of dideoxy nucleotides (ddNTPs) for use in electrochemical array based primer extension for the detection of single nucleotide polymorphisms (SNPs). The results confirm the extension of the immobilised primers for each of the four ddNTPs, representing a significant advance in achieving a cost-effective platform for screening of disease-specific SNPs.
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Affiliation(s)
- A M Debela
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain. and Sorbonne Universités, UPMC Univ Paris 06 Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, 4 place Jussieu, 75005 Paris, France
| | - S Thorimbert
- Sorbonne Universités, UPMC Univ Paris 06 Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, 4 place Jussieu, 75005 Paris, France
| | - B Hasenknopf
- Sorbonne Universités, UPMC Univ Paris 06 Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, 4 place Jussieu, 75005 Paris, France
| | - C K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain. and ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - M Ortiz
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain.
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10
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Shundrin LA, Irtegova IG, Vasilieva NV, Khalfina IA. Benzoquinone and naphthoquinone based redox-active labels for electrochemical detection of modified oligonucleotides on Au electrodes. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2015.12.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Lee AC, Du D, Chen B, Heng CK, Lim TM, Lin Y. Electrochemical detection of leukemia oncogenes using enzyme-loaded carbon nanotube labels. Analyst 2015; 139:4223-30. [PMID: 24961450 DOI: 10.1039/c3an01156a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe an ultrasensitive electrochemical nucleic acid assay amplified by carbon nanotubes (CNTs)-based labels for the detection of human acute lymphocytic leukemia (ALL)-related p185 BCR-ABL fusion transcript. The carboxylated CNTs were functionalized with horseradish peroxidase (HRP) molecules and target-specific detection probes (DP) via diimide-activated amidation and used to label and amplify the target hybridization signal. The activity of captured HRP was monitored by square-wave voltammetry measuring the electroactive enzymatic product in the presence of 2-aminophenol and hydrogen peroxide substrate solution. The signal-amplified assay achieved a detection limit of 83 fM (5 × 10(-18) mol in 60 μL) targets oligonucleotides and has a 4-order-wide dynamic range of target concentration. The resulting assay allowed robust discrimination between the perfect match and a three-base mismatch sequence. When exposed to the full-length (491 bp) DNA oncogene, the approach demonstrated a detection limit of 1 × 10(-16) mol in 60 μL, corresponding to approximately 33 pg of the target gene. The high sensitivity and specificity of the assay enabled a PCR-free detection of target transcripts in as little as 65 ng of mRNA extracted from positive ALL cell lines SUP-B15 in comparison to those obtained from negative cell line HL-60. The approach enables a simple, low-cost and ultrasensitive electrochemical nucleic acid detection in portable devices, point-of-care and early disease diagnostic applications.
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Affiliation(s)
- Ai-Cheng Lee
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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12
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Takada T, Takemura M, Kawano Y, Nakamura M, Yamana K. Photoresponsive DNA monolayer prepared by primer extension reaction on the electrode. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3993-3998. [PMID: 25807074 DOI: 10.1021/la505013u] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe a simple and convenient method for the preparation of photoresponsive DNA-modified electrodes using primer extension (PEX) reactions. A naphthalimide derivative was used as the photosensitizer that was attached to the C5-position of 2'-deoxyuridine-5'-triphosphate (dUTP(NI)). It has been found that dUTP(NI) is a good substrate for the PEX reactions using KOD Dash and Vent (exo-) enzymes in solutions to incorporate naphthalimide (NI) moieties into the DNA sequences. On the electrode surface immobilized with the primer/template DNA, the PEX reactions to incorporate dUTP(NI) molecules into the DNA sequence were found to efficiently proceed. With this solid-phase method, the DNA monolayers capable of generating photocurrent due to the photoresponsive NI molecule can be constructed. It was shown that the photocurrent generation was significantly suppressed by a single-nucleotide mismatch included in the primer/template DNA, which is applicable for the design of photoelectrochemical sensors to discriminate single-nucleotide sequences.
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Affiliation(s)
- Tadao Takada
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Mai Takemura
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Yuta Kawano
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Mitsunobu Nakamura
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Kazushige Yamana
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
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13
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Hocek M. Synthesis of base-modified 2'-deoxyribonucleoside triphosphates and their use in enzymatic synthesis of modified DNA for applications in bioanalysis and chemical biology. J Org Chem 2014; 79:9914-21. [PMID: 25321948 DOI: 10.1021/jo5020799] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The synthesis of 2'-deoxyribonucleoside triphosphates (dNTPs) either by classical triphosphorylation of nucleosides or by aqueous cross-coupling reactions of halogenated dNTPs is discussed. Different enzymatic methods for synthesis of modified oligonucleotides and DNA by polymerase incorporation of modified nucleotides are summarized, and the applications in redox or fluorescent labeling, as well as in bioconjugations and modulation of interactions of DNA with proteins, are outlined.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center , Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
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14
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Duprey JLHA, Tucker JHR. Metal–Carbon Bonds in Biopolymer Conjugates: Bioorganometallic Nucleic Acid Chemistry. CHEM LETT 2014. [DOI: 10.1246/cl.131019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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15
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Ménová P, Cahová H, Plucnara M, Havran L, Fojta M, Hocek M. Polymerase synthesis of oligonucleotides containing a single chemically modified nucleobase for site-specific redox labelling. Chem Commun (Camb) 2013; 49:4652-4. [PMID: 23579777 DOI: 10.1039/c3cc41438h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzymatic construction of single-nucleobase redox-labelled oligonucleotides was developed either based on polymerase incorporation of a single modified nucleoside triphosphate (dNTP) followed by primer extension (PEX) with natural dNTPs or based on PEX with a biotinylated one-nucleotide overhang template, magnetoseparation and the second PEX with a full-length template.
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Affiliation(s)
- Petra Ménová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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16
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Lee JK, Kim MR, Choi IS, Kim YG, Jung YH. Surface-initiated, reversible polymerization from surface-tethered oligonucleotides by enzymatic processes. Chem Asian J 2013; 8:908-11. [PMID: 23281246 DOI: 10.1002/asia.201201092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Indexed: 11/07/2022]
Abstract
Back and forth: Enzymatic, reversible polymerization on gold surfaces was efficiently carried out from surface-tethered self-priming oligodeoxynucleotides in a sequence-specific fashion by using two kinds of enzymes. Taq DNA polymerase, acting as a catalyst, facilitated DNA polymerization, and DNA restriction enzymes cut DNA polymers from the surface.
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Affiliation(s)
- Jungkyu K Lee
- Department of Chemistry, Kyungpook National University, Daegu, Korea
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17
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Electrochemical detection of DNA hybridization using metallacarborane unit. Bioelectrochemistry 2012; 87:78-83. [DOI: 10.1016/j.bioelechem.2011.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 08/26/2011] [Accepted: 10/28/2011] [Indexed: 11/17/2022]
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18
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Ahangar LE, Mehrgardi MA. Nanoporous gold electrode as a platform for the construction of an electrochemical DNA hybridization biosensor. Biosens Bioelectron 2012; 38:252-7. [PMID: 22727625 DOI: 10.1016/j.bios.2012.05.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 11/30/2022]
Abstract
The application of a nanoporous gold electrode (NPGE) in the fabrication of an electrochemical sensing system for the detection of single base mismatches (SBMs) using ferrocene-modified DNA probe has been investigated in the present manuscript. Ferrocene carboxylic acid is covalently attached to the amino-modified probe using EDC/NHS chemistry. By covalent attachment of the redox reporter molecules on the top of DNA, the direct oxidation of the ferrocene on the electrode surface is avoided. On the other hand, the electrochemical signals are amplified by anodizing the electrode surface and converting it to nanoporous form. By improving the sensitivity of the biosensor, the different SBMs including the thermodynamically stable G-A and G-T mismatches, can be easily distinguished. In this research, NPGE was prepared by anodization and chemical reduction of Au surface and used for signal amplification. Nanoporous electrode enhances the sensitivity of DNA biosensor and makes it capable to detect complementary target DNA in sub-nanomole scales.
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Affiliation(s)
- Laleh Enayati Ahangar
- Department of Chemistry, Faculty of Science, University of Isfahan, Isfahan 81746-73441, Iran
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19
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Pheeney CG, Barton JK. DNA electrochemistry with tethered methylene blue. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:7063-70. [PMID: 22512327 PMCID: PMC3398613 DOI: 10.1021/la300566x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Methylene blue (MB'), covalently attached to DNA through a flexible C(12) alkyl linker, provides a sensitive redox reporter in DNA electrochemistry measurements. Tethered, intercalated MB' is reduced through DNA-mediated charge transport; the incorporation of a single base mismatch at position 3, 10, or 14 of a 17-mer causes an attenuation of the signal to 62 ± 3% of the well-matched DNA, irrespective of position in the duplex. The redox signal intensity for MB'-DNA is found to be least 3-fold larger than that of Nile blue (NB)-DNA, indicating that MB' is even more strongly coupled to the π-stack. The signal attenuation due to an intervening mismatch does, however, depend on DNA film density and the backfilling agent used to passivate the surface. These results highlight two mechanisms for reduction of MB' on the DNA-modified electrode: reduction mediated by the DNA base pair stack and direct surface reduction of MB' at the electrode. These two mechanisms are distinguished by their rates of electron transfer that differ by 20-fold. The extent of direct reduction at the surface can be controlled by assembly and buffer conditions.
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Affiliation(s)
- Catrina G Pheeney
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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20
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Electrochemical reduction and radical anions of benzo[b]thioxanthene-6,11,12-trione and thioxanthene-1,4,9-trione. MENDELEEV COMMUNICATIONS 2012. [DOI: 10.1016/j.mencom.2012.03.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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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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22
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Gooding JJ, Darwish N. The rise of self-assembled monolayers for fabricating electrochemical biosensors-an interfacial perspective. CHEM REC 2011; 12:92-105. [DOI: 10.1002/tcr.201100013] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Indexed: 11/08/2022]
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23
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Balintová J, Pohl R, Horáková P, Vidláková P, Havran L, Fojta M, Hocek M. Anthraquinone as a redox label for DNA: synthesis, enzymatic incorporation, and electrochemistry of anthraquinone-modified nucleosides, nucleotides, and DNA. Chemistry 2011; 17:14063-73. [PMID: 22095665 DOI: 10.1002/chem.201101883] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Indexed: 11/11/2022]
Abstract
Modified 2'-deoxynucleosides and deoxynucleoside triphosphates (dNTPs) bearing anthraquinone (AQ) attached through an acetylene or propargylcarbamoyl linker at the 5-position of pyrimidine (C) or at the 7-position of 7-deazaadenine were prepared by Sonogashira cross-coupling of halogenated dNTPs with 2-ethynylanthraquinone or 2-(2-propynylcarbamoyl)anthraquinone. Polymerase incorporations of the AQ-labeled dNTPs into DNA by primer extension with KOD XL polymerase have been successfully developed. The electrochemical properties of the AQ-labeled nucleosides, nucleotides, and DNA were studied by cyclic and square-wave voltammetry, which show a distinct reversible couple of peaks around -0.4 V that make the AQ a suitable redox label for DNA.
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Affiliation(s)
- Jana Balintová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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24
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Ahangar LE, Mehrgardi MA. 3,4-Diaminobenzoic acid (DABA) as a redox label for electrochemical detection of single base mismatches. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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25
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Detection of single-nucleotide polymorphism on uidA gene of Escherichia coli by a multiplexed electrochemical DNA biosensor with oligonucleotide-incorporated nonfouling surface. SENSORS 2011; 11:8018-27. [PMID: 22164059 PMCID: PMC3231733 DOI: 10.3390/s110808018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 07/16/2011] [Accepted: 07/21/2011] [Indexed: 11/16/2022]
Abstract
We report here a practical application of a multiplexed electrochemical DNA sensor for highly specific single-nucleotide polymorphism (SNP) detection. In this work, a 16-electrode array was applied with an oligonucleotide-incorporated nonfouling surfaces (ONS) on each electrode for the resistance of unspecific absorption. The fully matched target DNA templated the ligation between the capture probe assembled on gold electrodes and the tandem signal probe with a biotin moiety, which could be transduced to peroxidase-based catalyzed amperometric signals. A mutant site (T93G) in uidA gene of E. coli was analyzed in PCR amplicons. 10% percentage of single mismatched mutant gene was detected, which clearly proved the selectivity of the multiplexed electrochemical DNA biosensor when practically applied.
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Hocek M, Fojta M. Nucleobase modification as redox DNA labelling for electrochemical detection. Chem Soc Rev 2011; 40:5802-14. [PMID: 21625726 DOI: 10.1039/c1cs15049a] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Basic aspects of DNA electrochemistry with a strong focus on the use of modified nucleobases as redox probes for electrochemical bioanalysis are reviewed. Intrinsic electrochemical properties of nucleobases in combination with artificial redox-active nucleobase modifications are frequently applied in this field. Synthetic approaches (both chemical and enzymatic) to base-modified nucleic acids are briefly summarized and their applications in redox labelling are discussed. Finally, analytical applications including DNA hybridization, primer extension, PCR, SNP typing, DNA damage and DNA-protein interaction analysis are presented (critical review, 91 references).
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Prague, Czech Republic.
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28
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Macíčková-Cahová H, Pohl R, Horáková P, Havran L, Špaček J, Fojta M, Hocek M. Alkylsulfanylphenyl derivatives of cytosine and 7-deazaadenine nucleosides, nucleotides and nucleoside triphosphates: synthesis, polymerase incorporation to DNA and electrochemical study. Chemistry 2011; 17:5833-41. [PMID: 21472803 DOI: 10.1002/chem.201003496] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Indexed: 01/19/2023]
Abstract
Aqueous Suzuki-Miyaura cross-coupling reactions of halogenated nucleosides, nucleotides and nucleoside triphosphates derived from 5-iodocytosine and 7-iodo-7-deazaadenine with methyl-, benzyl- and tritylsufanylphenylboronic acids gave the corresponding alkylsulfanylphenyl derivatives of nucleosides and nucleotides. The modified nucleoside triphosphates were incorporated into DNA by primer extension by using Vent(exo-) polymerase. The electrochemical behaviour of the alkylsulfanylphenyl nucleosides indicated formation of compact layers on the electrode. Modified nucleotides and DNA with incorporated benzyl- or tritylsulfanylphenyl moieties produced signals in [Co(NH(3))(6)](3+) ammonium buffer, attributed to the Brdička catalytic response, depending on the negative potential applied. Repeated constant current chronopotentiometric scans in this medium showed increased Brdička catalytic response, which suggests the deprotection of the alkylsulfanyl derivatives to free thiols under the conditions.
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Affiliation(s)
- Hana Macíčková-Cahová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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29
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He Y, Zeng K, Gurung AS, Baloda M, Xu H, Zhang X, Liu G. Visual detection of single-nucleotide polymorphism with hairpin oligonucleotide-functionalized gold nanoparticles. Anal Chem 2011; 82:7169-77. [PMID: 20681563 DOI: 10.1021/ac101275s] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report a simple, fast, and sensitive approach for visual detection of single-nucleotide polymorphism (SNP) based on hairpin oligonucleotide-functionalized gold nanoparticle (HO-Au-NP) and lateral flow strip biosensor (LFSB). The results presented here expand on prior work ( Mao , X. , Xu , H. , Zeng , Q. , Zeng , L. , and Liu , G. Chem. Commun. 2009 , 3065-3067 .) by providing new approach to prepare HO-Au-NP conjugates with a deoxyadenosine triphosphate (dATP) blocker, which shortens the preparation time of the conjugates from 50 to 8 h and lowers the detection limit 500 times. A hairpin oligonucleotide modified with a thiol at the 5'-end and a biotin at the 3'-end was conjugated with Au-NP through a self-assembling process. Following a blocking step with dATP, the hairpin structure of HO and dATP embed the biotin groups, and make the biotin groups in close proximity to the Au-NP surface, leading to the biotins being "inactive". The strategy of detecting SNP depends on the unique molecular recognition properties of HO to the perfect-matched DNA and single-base-mismatched DNA to generate different quantities of "active" biotin groups on the Au-NP surface. After hybridization reactions, the Au-NPs associated with the activated biotins are captured on the test zone of LFSB via the specific reaction between the activated biotin and preimmobilized streptavidin. Accumulation of Au-NPs produces the characteristic red bands, enabling visual detection of SNP. The preparations of HO-Au-NP conjugates with dATP and the parameters of assay were optimized systematically, and the abilities of detecting SNP were examined in details. The current approach is capable of discriminating as low as 10 pM of perfect-matched DNA and single-base-mismatched DNA within 25 min without instrumentation. Moreover, the approach provides a lower background and higher selectivity compared to the current molecular beacon-based SNP detection. The protocol should facilitate the simple, fast, and cost-effective screening of important SNPs and could readily find wide applications in molecular diagnosis laboratories and in point-of-care testing (field testing).
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Affiliation(s)
- Yuqing He
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou 510095, China
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30
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Electrochemical detection of aberrant methylated gene using naphthalene diimide derivative carrying four ferrocene moieties. J Organomet Chem 2010. [DOI: 10.1016/j.jorganchem.2010.04.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Khalfina IA, Vasil’eva NV, Irtegova IG, Shundrin LA, Reznikov VA. Synthesis and electrochemical Reduction of 2,2′-diaryl-5,5,5′,5′-tetramethyl-3,3′-bi(pyrrol-3-ylidene)-4,4′(5H,5′H)-dione 1,1′-dioxides. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2010. [DOI: 10.1134/s1070428010030176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Gong H, Zhong T, Gao L, Li X, Bi L, Kraatz HB. Unlabeled hairpin DNA probe for electrochemical detection of single-nucleotide mismatches based on MutS-DNA interactions. Anal Chem 2010; 81:8639-43. [PMID: 19769379 DOI: 10.1021/ac901371n] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The paper described a label-free assay for the detection of single-nucleotide mismatches in which an unlabeled hairpin DNA probe and a MutS protein conjugate (His6-MutS-linker peptide-streptavidin binding peptide (HMLS)) are exploited for the detection of mismatches by electrochemical impedance spectroscopy (EIS). We demonstrate this method for eight single-nucleotide mismatches. Upon hybridization of the target strand with the hairpin DNA probe, the stem-loop structure is opened forming a duplex DNA. In duplexes containing a single nucleotide mismatch, the mismatch is present at the solvent exposed side, enabling more effective HMLS recognition and binding. The binding event is evaluated by EIS and analyzed with the help of Randles' equivalent circuits. The differences in the charge transfer resistance DeltaR(CT) before and after protein binding to the duplex DNA allows the unequivocal detection of all eight single-nucleotide mismatches. DeltaR(CT) allows the discrimination of a C-A mismatch with the concentration of the target strand as low as 100 pM.
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Affiliation(s)
- He Gong
- Department of Chemistry, Beijing Normal University, Beijing, China 100875
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33
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Abstract
Binding target strands with single base selectivity at a terminal position is difficult with natural DNA or RNA hybridization probes. Nature uses a degenerate genetic code that is based on RNA:RNA codon:anticodon duplexes tolerating wobble base pairs at the terminus. The importance of short RNA strands in regulatory processes in the cell make it desirable to develop receptor-like approaches for high fidelity binding, even at the very 3'-terminus of a probe. Here, we report the three-dimensional structure of a DNA duplex with a 3'-terminal 2'-anthraquinoylamido-2'-deoxyuridine (Uaq) residue that was solved by NMR and restrained molecular dynamics. The Uaq residue binds the 5'-terminus of the target strand through a combination of pi-stacking, hydrogen bonding, and interactions in the minor groove. The acylated aminonucleoside is the best molecular cap for 3'-termini reported to date. The Uaq motif assists binding of DNA strands, but is particularly effective in enhancing the affinity for RNA target strands, with a DeltaT(m) in the UV melting point of up to +18.2 degrees C per residue. Increased base pairing selectivity is induced for all sequence motifs tested, even in cases where unmodified duplexes show no preference for the canonical base pair at all. A single mismatched nucleobase facing the 3'-terminus gives DeltaDeltaT(m) values as large as -23.9 degrees C (RNA) or -29.5 degrees C (DNA). The 5'-phosphoramidite of the Uaq cap reported here allows for routine incorporation during automated syntheses.
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Affiliation(s)
- Amritraj Patra
- Institute for Organic Chemistry, University of Karlsruhe (TH), 76131 Karlsruhe, Germany
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34
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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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35
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Ami T, Fujimoto K. Click chemistry as an efficient method for preparing a sensitive DNA probe for photochemical ligation. Chembiochem 2009; 9:2071-4. [PMID: 18666308 DOI: 10.1002/cbic.200800316] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Takehiro Ami
- School of Materials Science, Japan Advanced Institute of Science and Technology, Asahidai, Nomi, Ishikawa 923-1292, Japan
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36
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Olejniczak A, Grűner B, Šicha V, Broniarek S, Lesnikowski Z. Metallacarboranes as Labels for Multipotential Electrochemical Coding of DNA. [3-Chromium bis(dicarbollide)](-1)ate and Its Nucleoside Conjugates. ELECTROANAL 2009. [DOI: 10.1002/elan.200804434] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Abstract
The base pair stack of DNA has been demonstrated as a medium for long-range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here, we discuss the characteristic features, applications, and advantages of DNA-mediated electrochemistry.
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Affiliation(s)
- Alon A Gorodetsky
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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38
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Gorodetsky AA, Hammond WJ, Hill MG, Slowinski K, Barton JK. Scanning electrochemical microscopy of DNA monolayers modified with Nile Blue. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:14282-14288. [PMID: 19053641 PMCID: PMC2668266 DOI: 10.1021/la8029243] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Scanning electrochemical microscopy (SECM) is used to probe long-range charge transport (CT) through DNA monolayers containing the redox-active Nile Blue (NB) intercalator covalently affixed at a specific location in the DNA film. At substrate potentials negative of the formal potential of covalently attached NB, the electrocatalytic reduction of Fe(CN)6(3-) generated at the SECM tip is observed only when NB is located at the DNA/solution interface; for DNA films containing NB in close proximity to the DNA/electrode interface, the electrocatalytic effect is absent. This behavior is consistent with both rapid DNA-mediated CT between the NB intercalator and the gold electrode as well as a rate-limiting electron transfer between NB and the solution phase Fe(CN)6(3-). The DNA-mediated nature of the catalytic cycle is confirmed through sequence-specific and localized detection of attomoles of TATA-binding protein, a transcription factor that severely distorts DNA upon binding. Importantly, the strategy outlined here is general and allows for the local investigation of the surface characteristics of DNA monolayers both in the absence and in the presence of DNA binding proteins. These experiments highlight the utility of DNA-modified electrodes as versatile platforms for SECM detection schemes that take advantage of CT mediated by the DNA base pair stack.
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39
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Carrillo I, Quintana M, Esteva A, Hernández L, Hernández P. Influence of the Chain Length of Alkanethiols in Self-Assembled Submonolayers on the Electrochemical Response of Aromatic Amine Mixtures. ELECTROANAL 2008. [DOI: 10.1002/elan.200804365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Cahová H, Havran L, Brázdilová P, Pivonková H, Pohl R, Fojta M, Hocek M. Aminophenyl- and nitrophenyl-labeled nucleoside triphosphates: synthesis, enzymatic incorporation, and electrochemical detection. Angew Chem Int Ed Engl 2008; 47:2059-62. [PMID: 18260080 DOI: 10.1002/anie.200705088] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hana Cahová
- Institute of Organic Chemistry and Biochemistry, v.v.i. Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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42
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Hocek M, Fojta M. Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 2008; 6:2233-41. [PMID: 18563253 DOI: 10.1039/b803664k] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
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43
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Cahová H, Havran L, Brázdilová P, Pivoňková H, Pohl R, Fojta M, Hocek M. Aminophenyl- and Nitrophenyl-Labeled Nucleoside Triphosphates: Synthesis, Enzymatic Incorporation, and Electrochemical Detection. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705088] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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44
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Brázdilová P, Vrábel M, Pohl R, Pivonková H, Havran L, Hocek M, Fojta M. Ferrocenylethynyl derivatives of nucleoside triphosphates: synthesis, incorporation, electrochemistry, and bioanalytical applications. Chemistry 2008; 13:9527-33. [PMID: 17896337 DOI: 10.1002/chem.200701249] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Modified dATP (2'-deoxyadenosine-5'-triphosphate) and dUTP (2'-deoxyuridine-5'-triphosphate) bearing ferrocene (Fc) labels linked via a conjugate acetylene spacer were prepared by single-step aqueous-phase cross-coupling reactions of 7-iodo-7-deaza-dATP or 5-iodo-dUTP with ethynylferrocene. The Fc-labeled dNTPs were good substrates for DNA polymerases and were efficiently incorporated to DNA by primer extension (PEX). Electrochemical analysis of the 2'-deoxyribonucleoside triphosphates (dNTPs) and PEX products revealed significant differences in redox potentials of the Fc label bound either to U or to 7-deazaA and between isolated dNTPs and conjugates incorporated to DNA. Prospective bioanalytical applications are outlined.
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Affiliation(s)
- Petra Brázdilová
- Institute of Biophysics, v.v.i. Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic
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Wang Y, Li C, Li X, Li Y, Kraatz HB. Unlabeled hairpin-DNA probe for the detection of single-nucleotide mismatches by electrochemical impedance spectroscopy. Anal Chem 2008; 80:2255-60. [PMID: 18290674 DOI: 10.1021/ac7024688] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An unlabeled hairpin-DNA probe was used for the detection of eight single-nucleotide mismatches by electrochemical impedance spectroscopy (EIS). Upon hybridization of the target strand with the hairpin DNA probe, the stem-loop structure is opened and forms a duplex DNA. Accordingly, the film thickness is increased, which causes differences in the electrical properties of the film before and after hybridization. Randles equivalent circuits were employed to evaluate the EIS result. The differences in the charge-transfer resistance DeltaR(CT) between hairpin DNA (before hybridization) and duplex DNA (after hybridization) shows the consequence of a large structural rearrangement from hairpin to duplex. If a single-nucleotide mismatch is present in the center of the duplex, the difference in charge-transfer resistance DeltaR(CT) between B-DNA in the absence and presence of Zn(2+) allows the unequivocal detection of all eight single-nucleotide mismatches. The detection limit was measured, and DeltaR(CT) allows the discrimination of a single-nucleotide mismatch with the concentration of the target strand as low as 10 pM.
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Affiliation(s)
- Ying Wang
- Department of Chemistry, Beijing Normal University, Beijing, China, 100875
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Enzyme-Linked Electrochemical Detection of PCR-Amplified Nucleotide Sequences Using Disposable Screen-Printed Sensors. Applications in Gene Expression Monitoring. SENSORS 2008; 8:193-210. [PMID: 27879703 PMCID: PMC3681127 DOI: 10.3390/s8010193] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Accepted: 01/07/2008] [Indexed: 11/17/2022]
Abstract
Electrochemical enzyme-linked techniques for sequence-specific DNA sensing are presented. These techniques are based on attachment of streptavidin-alkaline phosphatase conjugate to biotin tags tethered to DNA immobilized at the surface of disposable screen-printed carbon electrodes (SPCE), followed by production and electrochemical determination of an electroactive indicator, 1-naphthol. Via hybridization of SPCE surface-confined target DNAs with end-biotinylated probes, highly specific discrimination between complementary and non-complementary nucleotide sequences was achieved. The enzyme-linked DNA hybridization assay has been successfully applied in analysis of PCR-amplified real genomic DNA sequences, as well as in monitoring of plant tissue-specific gene expression. In addition, we present an alternative approach involving sequence-specific incorporation of biotin-labeled nucleotides into DNA by primer extension. Introduction of multiple biotin tags per probe primer resulted in considerable enhancement of the signal intensity and improvement of the specificity of detection.
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Capek P, Cahová H, Pohl R, Hocek M, Gloeckner C, Marx A. An efficient method for the construction of functionalized DNA bearing amino acid groups through cross-coupling reactions of nucleoside triphosphates followed by primer extension or PCR. Chemistry 2007; 13:6196-203. [PMID: 17487908 DOI: 10.1002/chem.200700220] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Single-step aqueous cross-coupling reactions of nucleobase-halogenated 2'-deoxynucleosides (8-bromo-2'-deoxyadenosine, 7-iodo-7-deaza-2'-deoxyadenosine, or 5-iodo-2'-deoxy-uridine) or their 5'-triphosphates with 4-boronophenylalanine or 4-ethynylphenylalanine have been developed and used for efficient synthesis of modified 2'-deoxynucleoside triphosphates (dNTPs) bearing amino acid groups. These dNTPs were then tested as substrates for DNA polymerases for construction of functionalized DNA through primer extension and PCR. While 8-substituted adenosine triphosphates were poor substrates for DNA polymerases, the corresponding 7-substituted 7-deazaadenine and 5-substituted uracil nucleotides were efficiently incorporated in place of dATP or dTTP, respectively, by Pwo (Pyrococcus woesei) DNA polymerase. Nucleotides bearing the amino acid connected through the less bulky acetylene linker were incorporated more efficiently than those directly linked through a more bulky phenylene group. In addition, combinations of modified dATPs and dTTPs were incorporated by Pwo polymerase. Novel functionalized DNA duplexes bearing amino acid moieties were prepared by this two-step approach. PCR can be used for amplification of duplexes bearing large number of modifications, while primer extension is suitable for introduction of just one or several modifications in a single DNA strand.
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Affiliation(s)
- Petr Capek
- Gilead Sciences & IOCB Research Center, Institute of Organic Chemistry and Biochemistry, v. v. i. Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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Gorodetsky AA, Green O, Yavin E, Barton JK. Coupling into the Base Pair Stack Is Necessary for DNA-Mediated Electrochemistry. Bioconjug Chem 2007; 18:1434-41. [PMID: 17580927 DOI: 10.1021/bc0700483] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The electrochemistry of DNA films modified with different redox probes linked to DNA through saturated and conjugated tethers was investigated. Experiments feature two redox probes bound to DNA on two surfaces: anthraquinone (AQ)-modified uridines incorporated into thiolated DNA on gold (Au) and 2,2,6,6-tetramethylpiperidine 1-oxyl (TEMPO)-modified uridines in pyrene-labeled DNA on highly oriented pyrolytic graphite (HOPG). The electrochemistry of these labels when incorporated into DNA has been examined in DNA films containing both well matched and mismatched DNA. DNA-mediated electrochemistry is found to be effective for the TEMPO probe linked with an acetylene linker but not for a saturated TEMPO connected through an ethylenediamine linker. For the AQ probe, DNA-mediated electrochemistry is found with an acetylene linker to uridine but not with an alkyl chain to the 5' terminus of the oligonucleotide. Large electrochemical signals and effective discrimination of intervening base mismatches are achieved for the probes connected through the acetylene linkages, while probes connected through saturated linkages exhibit small electrochemical signals associated only with direct surface to probe charge transfer and poor mismatch discrimination. Thus DNA electrochemistry with these probes is dramatically influenced by the chemical nature of their linkage to DNA. These results highlight the importance of effective coupling into the pi-stack for long-range DNA-mediated electrochemistry.
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Affiliation(s)
- Alon A Gorodetsky
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Nowicka AM, Zabost E, Donten M, Mazerska Z, Stojek Z. Electrooxidation of dissolved dsDNA backed by in situ UV–Vis spectroscopy. Bioelectrochemistry 2007; 70:440-5. [PMID: 16904386 DOI: 10.1016/j.bioelechem.2006.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Revised: 05/19/2006] [Accepted: 07/05/2006] [Indexed: 11/26/2022]
Abstract
The electrooxidation of double-stranded DNA (dsDNA) from calf thymus was carried by using cyclic voltammetry. A glassy carbon disk-, a platinum disk-, a platinum mesh- and a carbon vapor-deposited platinum mesh electrodes were used. It is shown that the appropriate chemical and biological (steam treatment) purification of the complete cell allows, for the graphite electrode, formation of a wide anodic dsDNA signal with two visible anodic peaks. There was no necessity of preaccumulation of dsDNA on the electrode surface and of use of mediators to get well defined voltammetric signals. These peaks apparently reflect electrooxidation of the DNA's guanine and adenine. The spectrophotometric data obtained during the electrooxidation indicate that the absorbance increases with an increase in potential and electrooxidation current of dsDNA. However, the absorption band maximum either does or does not change its position depending on the mesh material. This different spectroscopic behavior may mean that the changes in the dsDNA structure upon electrooxidation are different in the case of Pt and C electrodes.
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Affiliation(s)
- Anna M Nowicka
- Department of Chemistry, Warsaw University, ul. Pasteura 1, 02-093 Warsaw, Poland
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Abstract
Electrochemical DNA biosensors exploit the affinity of single-stranded DNA for complementary strands of DNA and are used in the detection of specific sequences of DNA with a view towards developing portable analytical devices. Great progress has been made in this field but there are still numerous challenges to overcome. This review for researchers new to the field describes the components of electrochemical DNA biosensors and the important issues in their design. Methods of transducing DNA binding events are discussed along with future directions for DNA biosensors.
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