No (298)
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298
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Electrochemical Analysis of Sybr Green I and its Interaction with DNA
Dudová, Zdenka; Pivoňková, Hana; Havran, Luděk; Fojta, Miroslav
2015 - English
There are used many methods such real-time PCR and electrophoresis in molecular biology and biochemistry which are based on utilization of a fluorescent dye Sybr Green I (SG) for selective detection of double stranded (ds) DNA and its quantification. SG is a planar molecule (see Fig. 1) that intercalates into the DNA double helix and simultaneously can bind into minor groove of dsDNA. In our work we focused on electrochemical behavior of SG on a pyrolytic graphite electrode (PGE) using square-wave voltammetry (SWV). The voltammetric method was used in measurements of SG interactions with DNA at the PGE.
Keywords:
gels; Sybr Green I; Pyrolytic graphite electrode; Square wave voltammetry
Available at various institutes of the ASCR
Electrochemical Analysis of Sybr Green I and its Interaction with DNA
There are used many methods such real-time PCR and electrophoresis in molecular biology and biochemistry which are based on utilization of a fluorescent dye Sybr Green I (SG) for selective detection ...
Electrochemical Reduction and Oxidation of Nucleic Acids Bases and their Analogues: a Brief Overview
Fojta, Miroslav; Špaček, Jan; Dudová, Zdenka; Pivoňková, Hana; Daňhel, Aleš; Fojt, Lukáš; Havran, Luděk
2015 - English
Nucleic acids are known as electroactive biomacromolecules containing electrochemically reducible or oxidizable constituents. Nucleobases cytosine, 5-methylcytosine, adenine and guanine can be reduced in aqueous media on mercury or silver amalgam electrodes. Oxidation of all natural nucleic acids bases (in addition to the above mentioned ones, also uracil and thymine) was demonstrated using various types of carbon electrodes. Some of synthetic nucleobases or nucleotide analogues (e g., 7-deazapurines, cytidine analogues used as epigenetic modulators, etc.) exhibit specific electrochemical properties that differ from those of the parent bases and can be utilized to determine the given substance in the presence of natural nucleic acids or their components.
Keywords:
elimination voltammetry; dna; oligonucleotides; structure
Available at various institutes of the ASCR
Electrochemical Reduction and Oxidation of Nucleic Acids Bases and their Analogues: a Brief Overview
Nucleic acids are known as electroactive biomacromolecules containing electrochemically reducible or oxidizable constituents. Nucleobases cytosine, 5-methylcytosine, adenine and guanine can be reduced ...
Possibility of Using Purine Oxidation Signals for DNA Sequence Analysis
Špaček, Jan; Cahová, Kateřina; Havran, Luděk; Fojta, Miroslav
2015 - English
Signals provided by electrochemical oxidation of single stranding DNA on the surface of pyrolytic graphite electrode, which correspond to the oxidation of adenine and guanine (A and G) are known for over forty years. The mechanism of oxidation of free A and G as well as nucleoside mono-, and triphosphates of these bases is know but the mechanism of oxidation of purines in the DNA still remains unexplained. Ratiometry of A and G signals could be a new tool for DNA sequence analysis, if signals of A and G oxidation obtained from single-stranded DNA adsorbed at the electrode surface are proportional to the number of oxidized As and Gs in studied samples. Our preliminary results suggest that there is a correlation, yet we encountered problems, which yet has to be addressed and explained before this method could be applied for DNA analysis.
Keywords:
DNA oxidation; DNA sequence analysis; Electrochemistry
Available at various institutes of the ASCR
Possibility of Using Purine Oxidation Signals for DNA Sequence Analysis
Signals provided by electrochemical oxidation of single stranding DNA on the surface of pyrolytic graphite electrode, which correspond to the oxidation of adenine and guanine (A and G) are known for ...
Electrodeposited Coatings at ITO/FTO Enhancing their Applicability in Electroanalysis
Daňhel, Aleš; Fojta, Miroslav
2015 - English
Recent possibilities of modification of transparent electrodes based on indium-tin oxide and/or fluorine doped tin oxide by electrodeposited coatings enhancing their electrochemical applicability in electroanalysis are discussed in this work. Ordered mesoporous silica and/or chemically functionalized mesoporous silica thin films may serve, among the common utilization in solid phase extraction, as protective layer of the electrode surface against its fouling and/or as molecular sieve permeable for small molecules and blocking large ones (DNA, proteins, etc.). Furthermore an electrodeposition of organic modifiers and/or metal (nano) particles inside of the ordered silica nanochanels together with direct electrodeposition of selected metal (nano) particles onto selected conductive transparent supports are presented here as well.
Keywords:
nucleic-acids; dna; guanine; films
Available at various institutes of the ASCR
Electrodeposited Coatings at ITO/FTO Enhancing their Applicability in Electroanalysis
Recent possibilities of modification of transparent electrodes based on indium-tin oxide and/or fluorine doped tin oxide by electrodeposited coatings enhancing their electrochemical applicability in ...
Examples of Using of Electrochemical Detection at Pencil Graphite Electrode with Enzymatic Labeling for Analysis of Nucleotide Sequence
Plucnara, Medard; Haroniková, Lucia; Špaček, Jan; Havran, Luděk; Horáková, Petra; Pivoňková, Hana; Ecsin, E.; Erdem, A.; Fojta, Miroslav
2015 - English
Many examples of utilization of enzymatic labeling for DNA sequence analysis has been described in literature so far. Some of them involve hybridization with complementary biotinylated probe, while others use incorporation of biotinylated nucleotides into DNA strand by DNA polymerases. Common approach is then binding of streptavidine-enzyme conjugates to biotin tags and incubation with substrate, which is converted to detectable product. Here, two recent applications using this principle are described for the detection of PCR amplicons and for SNP typing. Both techniques are combined with detection at pencil graphite electrodes.
Keywords:
dna hybridization; Enzymatic labeling; Alkaline phosphatase
Available at various institutes of the ASCR
Examples of Using of Electrochemical Detection at Pencil Graphite Electrode with Enzymatic Labeling for Analysis of Nucleotide Sequence
Many examples of utilization of enzymatic labeling for DNA sequence analysis has been described in literature so far. Some of them involve hybridization with complementary biotinylated probe, while ...
ANALYSIS OF SEQUENCE SPECIFIC INTERACTIONS BETWEEN DNA AND P53 FAMILY PROTEINS BY ELISA, SLOT-BLOT AND EMSA
Adámik, Matěj; Holanová, L.; Navrátilová, Lucie; Nygrinova, J.; Pokorova, J.; Petr, Marek; Tichý, Vlastimil; Brázdová, Marie
2014 - English
DNA-protein interactions of core domains of p53, p63 and p73, members of tumor suppressor p53 family, were investigated by multiple methods with regard to verifying the sequence specificity with which short target oligonucleotides/long DNA fragments can be recognized. The sequence specificity of core domains and wtp53 full protein binding to specific sequence in both types of DNA substrates was confirmed in solution, on surface and in gels by ELISA, slot-blot and EMSA.
Keywords:
binding; p63
Available at various institutes of the ASCR
ANALYSIS OF SEQUENCE SPECIFIC INTERACTIONS BETWEEN DNA AND P53 FAMILY PROTEINS BY ELISA, SLOT-BLOT AND EMSA
DNA-protein interactions of core domains of p53, p63 and p73, members of tumor suppressor p53 family, were investigated by multiple methods with regard to verifying the sequence specificity with which ...
DNA POLYMERASE STOP ASSAY FOR DETECTION OF G-QUADRUPLEXES
Petr, Marek; Bažantová, Pavla; Adámik, Matěj; Kejnovská, Iva; Dvořáková, Zuzana; Vorlíčková, Michaela; Pečinka, Petr; Brázdová, Marie
2014 - English
In this work we performed DNA polymerase stop assays while using template DNA derived from promoter regions of VEGF and c-Myc proto-oncogenes under variety of experimental conditions. Partial stopping of DNA synthesis along the template strand was observed in the presence of K+ ions due to formation of stable G-quadruplex structures. In contrast, Na+ ions alone were unable to stabilize G-quadruplexes to stop the reaction at their site. These data suggest that K+ and Na+ ions, which are both known to stabilize G-quadruplexes, do this in different manner or extent.
Keywords:
DNA
Available at various institutes of the ASCR
DNA POLYMERASE STOP ASSAY FOR DETECTION OF G-QUADRUPLEXES
In this work we performed DNA polymerase stop assays while using template DNA derived from promoter regions of VEGF and c-Myc proto-oncogenes under variety of experimental conditions. Partial stopping ...
Use of Monovalent Copper for Sensitive Detection of Methyl Derivatives of Xanthine
Navrátil, R.; Motlova, D.; Jelen, F.; Trnková, L.
2014 - Czech
This work is concerned with the electroanalysis of xanthine (Xan) and its methylated derivatives (1-, 3-, 7-, and 9-mXan) on a pencil graphite electrode in the presence of copper ions. The main idea of using copper consists in the in situ formation of the complex Cu(I)-mXan on the electrode surface and improvement of oxidative signals of the corresponding mXan during the detection. Linear sweep voltammetry (LSV) in connection with adsorption stripping techniques was used for the determination of mXan. To enhance the oxidation signals the elimination voltammetric procedure (EVP) was applied.
Keywords:
elimination voltammetry; oxidation; Oxidation of methylxanthines; Copper complexes
Available at various institutes of the ASCR
Use of Monovalent Copper for Sensitive Detection of Methyl Derivatives of Xanthine
This work is concerned with the electroanalysis of xanthine (Xan) and its methylated derivatives (1-, 3-, 7-, and 9-mXan) on a pencil graphite electrode in the presence of copper ions. The main idea ...
THE WAYS OF ACTIVATING TP53
Polášková, Alena; Helma, Robert; Adámik, Matěj; Hronešová, L.; Holacka, K.; Ballová, L.; Brázdová, Marie
2014 - English
P53, AGENTS, CELLS,P53, AGENTS, CELLS,P53, AGENTS, CELLS,P53, AGENTS, CELLS
Keywords:
p53; agents; cells
Available at various institutes of the ASCR
THE WAYS OF ACTIVATING TP53
P53, AGENTS, CELLS,P53, AGENTS, CELLS,P53, AGENTS, CELLS,P53, AGENTS, CELLS
Electrochemical Detection of p53 Protein Interactions with Plasmid DNAs Modified with Cisplatin Using Immunoprecipitation at Magnetic Microbeads
Pivoňková, Hana; Tichý, Vlastimil; Orság, Petr; Šebest, Peter; Fojta, Miroslav
2014 - English
Antineoplastic drug [cis-diamminedichloroplatinum(II)] (cisplatin) forms covalent adducts with DNA. Cisplatin-modified DNA can be determined sensitively using square-wave voltammetry at mercury electrodes. Tumor suppressor protein p53 binds to DNA in different modes, including sequence-and structure-specific ones and these interactions are influenced by modification of the DNA with cisplatin. In this contribution we present a simple immunoprecipitation technique with magnetic beads, followed by voltammetric determination of recovered cisplatinated DNA, for the evaluation of p53 protein binding to DNAs containing various target sites differing in their proneness to being internally modified with the platinum complex.
Keywords:
recognition; platinum; binding
Available at various institutes of the ASCR
Electrochemical Detection of p53 Protein Interactions with Plasmid DNAs Modified with Cisplatin Using Immunoprecipitation at Magnetic Microbeads
Antineoplastic drug [cis-diamminedichloroplatinum(II)] (cisplatin) forms covalent adducts with DNA. Cisplatin-modified DNA can be determined sensitively using square-wave voltammetry at mercury ...
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